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ORCIDJournal of Chemical Information and Modeling, Volume 54
Volume 54, Number 1, January 2014
- Alexander Golbraikh, Eugene N. Muratov, Denis Fourches
, Alexander Tropsha:
Data Set Modelability by QSAR. 1-4
- Steven M. Kearnes, Imran S. Haque, Vijay S. Pande:
SCISSORS: Practical Considerations. 5-15 - Aliuska Duardo-Sánchez, Cristian R. Munteanu, Pablo Riera-Fernández, Antonio López-Díaz, Alejandro Pazos, Humberto González Díaz:
Modeling Complex Metabolic Reactions, Ecological Systems, and Financial and Legal Networks with MIANN Models Based on Markov-Wiener Node Descriptors. 16-29 - Ammar Abdo, Valérie Leclère, Philippe Jacques, Naomie Salim, Maude Pupin:
Prediction of New Bioactive Molecules using a Bayesian Belief Network. 30-36 - Matthew K. Matlock, S. Joshua Swamidass:
Sharing Chemical Relationships Does Not Reveal Structures. 37-48 - Kentaro Kawai, Naoya Nagata, Yoshimasa Takahashi:
De Novo Design of Drug-Like Molecules by a Fragment-Based Molecular Evolutionary Approach. 49-56 - Tina M. Kouri, Mahendra Awale, James K. Slyby, Jean-Louis Reymond, Dinesh P. Mehta:
"Social" Network of Isomers Based on Bond Count Distance: Algorithms. 57-68 - Zhijian Xu, Zhuo Yang, Yingtao Liu, Yunxiang Lu, Kaixian Chen, Weiliang Zhu:
Halogen Bond: Its Role beyond Drug-Target Binding Affinity for Drug Discovery and Development. 69-78 - N. Yi Mok, Ruth Brenk, Nathan Brown:
Increasing the Coverage of Medicinal Chemistry-Relevant Space in Commercial Fragments Screening. 79-85
- Jaroslaw J. Panek, Aneta Jezierska-Mazzarello, Pawel Lipkowski, Agata Martyniak, Aleksander Filarowski:
Comparison of Resonance Assisted and Charge Assisted Effects in Strengthening of Hydrogen Bonds in Dipyrrins. 86-95 - Yocheved Gilad, Hanoch Senderowitz:
Docking Studies on DNA Intercalators. 96-107 - Clara D. Christ, Thomas Fox:
Accuracy Assessment and Automation of Free Energy Calculations for Drug Design. 108-120 - Lukas Wirz, Ralf Tonner, James Avery, Peter Schwerdtfeger:
Structure and Properties of the Nonface-Spiral Fullerenes T-C380, D3-C384, D3-C440, and D3-C672 and Their Halma and Leapfrog Transforms. 121-130 - Konrad Hinsen:
MOSAIC: A Data Model and File Formats for Molecular Simulations. 131-137 - Inna Slynko, Michael Scharfe, Tobias Rumpf, Julia Eib, Eric Metzger, Roland Schüle, Manfred Jung, Wolfgang Sippl:
Virtual Screening of PRK1 Inhibitors: Ensemble Docking, Rescoring Using Binding Free Energy Calculation and QSAR Model Development. 138-150 - Balder Lai, Gábor Nagy, José Antonio Garate, Chris Oostenbrink:
Entropic and Enthalpic Contributions to Stereospecific Ligand Binding from Enhanced Sampling Methods. 151-158
- Setareh Tasdighian, Luisa Di Paola, Micol De Ruvo, Paola Paci, Daniele Santoni, Pasquale Palumbo, Giampiero Mei, Almerinda Di Venere, Alessandro Giuliani:
Modules Identification in Protein Structures: The Topological and Geometrical Solutions. 159-168 - Davide Sabbadin, Antonella Ciancetta, Stefano Moro:
Bridging Molecular Docking to Membrane Molecular Dynamics To Investigate GPCR-Ligand Recognition: The Human A2A Adenosine Receptor as a Key Study. 169-183 - Anat Levit, Thijs Beuming, Goran Krilov, Woody Sherman, Masha Y. Niv:
Predicting GPCR Promiscuity Using Binding Site Features. 184-194 - Elisabetta Moroni, Huiping Zhao, Brian S. J. Blagg, Giorgio Colombo:
Exploiting Conformational Dynamics in Drug Discovery: Design of C-Terminal Inhibitors of Hsp90 with Improved Activities. 195-208 - Panagiotis I. Koukos, Nicholas M. Glykos:
On the Application of Good-Turing Statistics to Quantify Convergence of Biomolecular Simulations. 209-217
- Freya Klepsch, Poongavanam Vasanthanathan, Gerhard F. Ecker:
Ligand and Structure-Based Classification Models for Prediction of P-Glycoprotein Inhibitors. 218-229 - Alexios Koutsoukas, Shardul Paricharak, Warren R. J. D. Galloway, David R. Spring, Adriaan P. IJzerman, Robert C. Glen, David Marcus, Andreas Bender:
How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space. 230-242 - Trayder Thomas, Kimberley C. McLean, Fiona M. McRobb, David T. Manallack, David K. Chalmers, Elizabeth Yuriev:
Homology Modeling of Human Muscarinic Acetylcholine Receptors. 243-253 - Joshua Pottel, Eric Therrien, James L. Gleason, Nicolas Moitessier:
Docking Ligands into Flexible and Solvated Macromolecules. 6. Development and Application to the Docking of HDACs and other Zinc Metalloenzymes Inhibitors. 254-265
- Gábor Nagy, Chris Oostenbrink:
Dihedral-Based Segment Identification and Classification of Biopolymers I: Proteins. 266-277 - Gábor Nagy, Chris Oostenbrink:
Dihedral-Based Segment Identification and Classification of Biopolymers II: Polynucleotides. 278-288 - Guillaume Bouvier, Nathalie Duclert-Savatier, Nathan Desdouits, Djalal Meziane-Cherif, Arnaud Blondel, Patrice Courvalin, Michael Nilges, Thérèse E. Malliavin:
Functional Motions Modulating VanA Ligand Binding Unraveled by Self-Organizing Maps. 289-301 - María Larriva, Antonio Rey:
Design of a Rotamer Library for Coarse-Grained Models in Protein-Folding Simulations. 302-313
- Javier Klett, Álvaro Cortés Cabrera, Rubén Gil-Redondo, Federico Gago, Antonio Morreale:
ALFA: Automatic Ligand Flexibility Assignment. 314-323 - Xiaohua Zhang, Sergio Ernesto Wong, Felice C. Lightstone:
Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment. 324-337 - Ning-Ning Wei, Adel Hamza:
SABRE: Ligand/Structure-Based Virtual Screening Approach Using Consensus Molecular-Shape Pattern Recognition. 338-346 - Maciej Wójcikowski, Piotr Zielenkiewicz, Pawel Siedlecki:
DiSCuS: An Open Platform for (Not Only) Virtual Screening Results Management. 347-354
Volume 54, Number 2, February 2014
- Prakash Chandra Rathi, Hans Wolfgang Höffken, Holger Gohlke:
Quality Matters: Extension of Clusters of Residues with Good Hydrophobic Contacts Stabilize (Hyper)Thermophilic Proteins. 355-361 - Paola Bisignano, Stefan Doerr, Matt J. Harvey, Angelo D. Favia, Andrea Cavalli, Gianni De Fabritiis:
Kinetic Characterization of Fragment Binding in AmpC β-Lactamase by High-Throughput Molecular Simulations. 362-366 - Veronika Temml, Constance V. Voss, Verena M. Dirsch, Daniela Schuster:
Discovery of New Liver X Receptor Agonists by Pharmacophore Modeling and Shape-Based Virtual Screening. 367-371 - Davide Sabbadin, Stefano Moro:
Supervised Molecular Dynamics (SuMD) as a Helpful Tool To Depict GPCR-Ligand Recognition Pathway in a Nanosecond Time Scale. 372-376
- Valery R. Polyakov, Neil D. Moorcroft, Amar Drawid:
Enrichment Analysis for Discovering Biological Associations in Phenotypic Screens. 377-386 - Peter Lind:
Construction and Use of Fragment-Augmented Molecular Hasse Diagrams. 387-395 - Alberto Massarotti, Angelo Brunco, Giovanni Sorba, Gian Cesare Tron:
ZINClick: A Database of 16 Million Novel, Patentable, and Readily Synthesizable 1, 4-Disubstituted Triazoles. 396-406 - Yongmei Pan, Tiejun Cheng, Yanli Wang, Stephen H. Bryant:
Pathway Analysis for Drug Repositioning Based on Public Database Mining. 407-418 - Reino Laatikainen, Tommi Hassinen, Juuso Lehtivarjo, Mika Tiainen, Juha Jungman, Tuulia Tynkkynen, Samuli-Petrus Korhonen, Matthias Niemitz, Pekka Poutiainen, Olli Jääskeläinen, Topi Väisänen, Janne Weisell, Pasi Soininen, Pekka Laatikainen, Henri Martonen, Kari Tuppurainen:
Comprehensive Strategy for Proton Chemical Shift Prediction: Linear Prediction with Nonlinear Corrections. 419-430 - Marko Toplak, Rok Mocnik, Matija Polajnar, Zoran Bosnic, Lars Carlsson, Catrin Hasselgren Arnby, Janez Demsar, Scott Boyer, Blaz Zupan, Jonna C. Stålring:
Assessment of Machine Learning Reliability Methods for Quantifying the Applicability Domain of QSAR Regression Models. 431-441 - Shilva Kayastha, Dilyana Dimova, Preeti Iyer, Martin Vogt, Jürgen Bajorath:
Large-Scale Assessment of Activity Landscape Feature Probabilities of Bioactive Compounds. 442-450 - Dagmar Stumpfe, Dilyana Dimova, Jürgen Bajorath:
Composition and Topology of Activity Cliff Clusters Formed by Bioactive Compounds. 451-461
- Yong-Liang Zhu, Paul Beroza, Dean R. Artis:
Including Explicit Water Molecules as Part of the Protein Structure in MM/PBSA Calculations. 462-469 - Jagdish Suresh Patel, Anna Berteotti, Simone Ronsisvalle, Walter Rocchia, Andrea Cavalli:
Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5. 470-480 - Maria Letizia Barreca, Nunzio Iraci, Giuseppe Manfroni, Rosy Gaetani, Chiara Guercini, Stefano Sabatini, Oriana Tabarrini, Violetta Cecchetti:
Accounting for Target Flexibility and Water Molecules by Docking to Ensembles of Target Structures: The HCV NS5B Palm Site I Inhibitors Case Study. 481-497 - Anastasia V. Rudik, Alexander V. Dmitriev, Alexey Lagunin, Dmitry Filimonov, Vladimir Poroikov:
Metabolism Site Prediction Based on Xenobiotic Structural Formulas and PASS Prediction Algorithm. 498-507 - Adrien B. Larsen, Jeffrey R. Wagner, Abhinandan Jain, Nagarajan Vaidehi:
Protein Structure Refinement of CASP Target Proteins Using GNEIMO Torsional Dynamics Method. 508-517 - William J. Allen, Robert C. Rizzo:
Implementation of the Hungarian Algorithm to Account for Ligand Symmetry and Similarity in Structure-Based Design. 518-529 - Harrison J. Hocker, Nandini Rambahal, Alemayehu A. Gorfe:
LIBSA - A Method for the Determination of Ligand-Binding Preference to Allosteric Sites on Receptor Ensembles. 530-538 - Patrisha Joseph Therese, Dinesh Manvar, Sridevi Kondepudi, Madhu Babu Battu, Dharmaranjan Sriram, Amartya Basu, Perumal Yogeeswari, Neerja Kaushik-Basu:
Multiple e-Pharmacophore Modeling, 3D-QSAR, and High-Throughput Virtual Screening of Hepatitis C Virus NS5B Polymerase Inhibitors. 539-552 - Anthony J. Green, Paul L. A. Popelier:
Theoretical Prediction of Hydrogen-Bond Basicity pKBHX Using Quantum Chemical Topology Descriptors. 553-561 - Michael R. Jones, Cong Liu, Angela K. Wilson:
Molecular Dynamics Studies of the Protein-Protein Interactions in Inhibitor of κB Kinase-β. 562-572
- Hui Wen Ng, Charles A. Laughton, Stephen W. Doughty:
Molecular Dynamics Simulations of the Adenosine A2a Receptor in POPC and POPE Lipid Bilayers: Effects of Membrane on Protein Behavior. 573-581 - Sergey A. Samsonov, Jan-Philip Gehrcke, M. Teresa Pisabarro:
Flexibility and Explicit Solvent in Molecular-Dynamics-Based Docking of Protein-Glycosaminoglycan Systems. 582-592 - Yufei Yue, Hong Guo:
Quantum Mechanical/Molecular Mechanical Study of Catalytic Mechanism and Role of Key Residues in Methylation Reactions Catalyzed by Dimethylxanthine Methyltransferase in Caffeine Biosynthesis. 593-600 - Christopher E. Dempsey, Dominic Wright, Charlotte K. Colenso, Richard B. Sessions, Jules C. Hancox:
Assessing hERG Pore Models As Templates for Drug Docking Using Published Experimental Constraints: The Inactivated State in the Context of Drug Block. 601-612 - Alexandra T. P. Carvalho, Marcel Swart:
Electronic Structure Investigation and Parametrization of Biologically Relevant Iron-Sulfur Clusters. 613-620
- Weiwei Xue, Yihe Ban, Huanxiang Liu, Xiaojun Yao:
Computational Study on the Drug Resistance Mechanism against HCV NS3/4A Protease Inhibitors Vaniprevir and MK-5172 by the Combination Use of Molecular Dynamics Simulation, Residue Interaction Network, and Substrate Envelope Analysis. 621-633 - Man Luo, Xiang Simon Wang, Bryan L. Roth, Alexander Golbraikh, Alexander Tropsha:
Application of Quantitative Structure-Activity Relationship Models of 5-HT1A Receptor Binding to Virtual Screening Identifies Novel and Potent 5-HT1A Ligands. 634-647 - Nagakumar Bharatham, Kavitha Bharatham, Anang A. Shelat, Donald Bashford:
Ligand Binding Mode Prediction by Docking: Mdm2/Mdmx Inhibitors as a Case Study. 648-659 - Richard D. Cramer, Bernd Wendt:
Template CoMFA: The 3D-QSAR Grail? 660-671
- Satoshi Yamasaki, Takatsugu Hirokawa, Kiyoshi Asai, Kazuhiko Fukui:
Tertiary Structure Prediction of RNA-RNA Complexes Using a Secondary Structure and Fragment-Based Method. 672-682 - Oleg A. Raevsky, Veniamin Yu. Grigor'ev, Daniel E. Polianczyk, Olga E. Raevskaja, John C. Dearden:
Calculation of Aqueous Solubility of Crystalline Un-Ionized Organic Chemicals and Drugs Based on Structural Similarity and Physicochemical Descriptors. 683-691
Volume 54, Number 3, March 2014
- Diane Joseph-McCarthy, Arthur J. Campbell, Gunther Kern, Demetri Moustakas:
Fragment-Based Lead Discovery and Design. 693-704
- Alexey V. Zakharov, Megan L. Peach, Markus Sitzmann, Marc C. Nicklaus:
QSAR Modeling of Imbalanced High-Throughput Screening Data in PubChem. 705-712 - Alexey V. Zakharov, Megan L. Peach, Markus Sitzmann, Marc C. Nicklaus:
A New Approach to Radial Basis Function Approximation and Its Application to QSAR. 713-719 - Violeta I. Pérez-Nueno, Arnaud Sinan Karaboga, Michel Souchet, David W. Ritchie:
GES Polypharmacology Fingerprints: A Novel Approach for Drug Repositioning. 720-734 - Jing Tang, Agnieszka Szwajda, Sushil Kumar Shakyawar, Tao Xu, Petteri Hintsanen, Krister Wennerberg, Tero Aittokallio:
Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis. 735-743 - Humberto González Díaz, Diana María Herrera-Ibatá, Aliuska Duardo-Sánchez, Cristian R. Munteanu, Ricardo Alfredo Orbegozo-Medina, Alejandro Pazos:
ANN Multiscale Model of Anti-HIV Drugs Activity vs AIDS Prevalence in the US at County Level Based on Information Indices of Molecular Graphs and Social Networks. 744-755 - Sascha Urbaczek, Adrian Kolodzik, Matthias Rarey:
The Valence State Combination Model: A Generic Framework for Handling Tautomers and Protonation States. 756-766 - Marco Foscato, Giovanni Occhipinti, Vishwesh Venkatraman, Bjørn K. Alsberg, Vidar R. Jensen:
Automated Design of Realistic Organometallic Molecules from Fragments. 767-780 - Shagun Krishna, Deependra Kumar Singh, Sanjeev Meena, Dipak Datta, Mohammad Imran Siddiqi, Dibyendu Banerjee:
Pharmacophore-Based Screening and Identification of Novel Human Ligase I Inhibitors with Potential Anticancer Activity. 781-792 - Ruifeng Liu, Anders Wallqvist:
Merging Applicability Domains for in Silico Assessment of Chemical Mutagenicity. 793-800 - Disha Gupta-Ostermann, Veerabahu Shanmugasundaram, Jürgen Bajorath:
Neighborhood-Based Prediction of Novel Active Compounds from SAR Matrices. 801-809 - Juuso Lehtivarjo, Matthias Niemitz, Samuli-Petrus Korhonen:
Universal J-Coupling Prediction. 810-817
- Katarina Roos, Jenny Viklund, Johan Meuller, Karin Kaspersson, Mats Svensson:
Potency Prediction of β-Secretase (BACE-1) Inhibitors Using Density Functional Methods. 818-825 - Panagiotis L. Kastritis, João P. G. L. M. Rodrigues, Alexandre M. J. J. Bonvin:
HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein-Protein Interaction Inhibitors. 826-836 - Martin Eklund, Ulf Norinder, Scott Boyer, Lars Carlsson:
Choosing Feature Selection and Learning Algorithms in QSAR. 837-843 - James L. McDonagh, Neetika Nath, Luna De Ferrari, Tanja Van Mourik, John B. O. Mitchell:
Uniting Cheminformatics and Chemical Theory To Predict the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules. 844-856 - Christina Hayes, Daniel Ansbro, Maria Kontoyianni:
Elucidating Substrate Promiscuity in the Human Cytochrome 3A4. 857-869 - Ashutosh Kumar, Akihiro Ito, Misao Takemoto, Minoru Yoshida, Kam Y. J. Zhang:
Identification of 1, 2, 5-Oxadiazoles as a New Class of SENP2 Inhibitors Using Structure Based Virtual Screening. 870-880 - Kanin Wichapong, Alexander Rohe, Charlott Platzer, Inna Slynko, Frank Erdmann, Matthias Schmidt, Wolfgang Sippl:
Application of Docking and QM/MM-GBSA Rescoring to Screen for Novel Myt1 Kinase Inhibitors. 881-893 - Yao Sun, Rui Zhang, Ding Li, Lingling Feng, Di Wu, Lina Feng, Peipei Huang, Yanliang Ren, Jiangtao Feng, San Xiao, Jian Wan:
Pharmacophore-Based Virtual Screening and Experimental Validation of Novel Inhibitors against Cyanobacterial Fructose-1, 6-/Sedoheptulose-1, 7-bisphosphatase. 894-901 - Koteswara Rao Valasani, Jhansi Rani Vangavaragu, Victor Day, Shirley ShiDu Yan:
Structure Based Design, Synthesis, Pharmacophore Modeling, Virtual Screening, and Molecular Docking Studies for Identification of Novel Cyclophilin D Inhibitors. 902-912
- Ashini Bolia, Z. Nevin Gerek, S. Banu Ozkan:
BP-Dock: A Flexible Docking Scheme for Exploring Protein-Ligand Interactions Based on Unbound Structures. 913-925 - Gonzalo A. Jaña, Eduardo J. Delgado, Fabiola E. Medina:
How Important Is the Synclinal Conformation of Sulfonylureas To Explain the Inhibition of AHAS: A Theoretical Study. 926-932 - Mari Gabrielsen, Rafal Kurczab, Agata Siwek, Malgorzata Wolak, Aina Westrheim Ravna, Kurt Kristiansen, Irina Kufareva, Ruben Abagyan, Gabriel Nowak, Zdzislaw Chilmonczyk, Ingebrigt Sylte, Andrzej J. Bojarski:
Identification of Novel Serotonin Transporter Compounds by Virtual Screening. 933-943 - Pedro J. Ballester, Adrian Schreyer, Tom L. Blundell:
Does a More Precise Chemical Description of Protein-Ligand Complexes Lead to More Accurate Prediction of Binding Affinity? 944-955
- Flavio Ballante, Antonia Caroli, Richard B. Wickersham III, Rino Ragno:
Hsp90 Inhibitors, Part 1: Definition of 3-D QSAutogrid/R Models as a Tool for Virtual Screening. 956-969 - Antonia Caroli, Flavio Ballante, Richard B. Wickersham III, Federico Corelli, Rino Ragno:
Hsp90 Inhibitors, Part 2: Combining Ligand-Based and Structure-Based Approaches for Virtual Screening Application. 970-977 - Thomas Scior, Moritz Verhoff, Itzel Gutierrez-Aztatzi, Hermann P. T. Ammon, Stefan Laufer, Oliver Werz:
Interference of Boswellic Acids with the Ligand Binding Domain of the Glucocorticoid Receptor. 978-986 - Jens Kunze, Nickolay Todoroff, Petra Schneider, Tiago Rodrigues, Tim Geppert, Felix Reisen, Herman Schreuder, Joachim Saas, Gerhard Hessler, Karl-Heinz Baringhaus, Gisbert Schneider:
Targeting Dynamic Pockets of HIV-1 Protease by Structure-Based Computational Screening for Allosteric Inhibitors. 987-991
- Ashraf Yaseen, Yaohang Li:
Context-Based Features Enhance Protein Secondary Structure Prediction Accuracy. 992-1002
- Yifei Qi, Xi Cheng, Wei Han, Sunhwan Jo, Klaus Schulten, Wonpil Im:
CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations. 1003-1009
- Setareh Tasdighian, Luisa Di Paola, Micol De Ruvo, Paola Paci, Daniele Santoni, Pasquale Palumbo, Giampiero Mei, Almerinda Di Venere, Alessandro Giuliani:
Correction to Modules Identification in Protein Structures: The Topological and Geometrical Solutions. 1010
Volume 54, Number 4, April 2014
- Leo Ghemtio, Anne Soikkeli, Marjo Yliperttula, Jouni Hirvonen, Moshe Finel, Henri Xhaard:
SVM Classification and CoMSIA Modeling of UGT1A6 Interacting Molecules. 1011-1026 - Shungo Koichi, Masaki Arisaka, Hiroyuki Koshino, Atsushi Aoki, Satoru Iwata, Takeaki Uno, Hiroko Satoh:
Chemical Structure Elucidation from 13C NMR Chemical Shifts: Efficient Data Processing Using Bipartite Matching and Maximal Clique Algorithms. 1027-1035 - Adrián Kalászi, Dániel Szisz, Gábor Imre, Tímea Polgár:
Screen3D: A Novel Fully Flexible High-Throughput Shape-Similarity Search Method. 1036-1049 - Haibin Liu, Lirong Wang, Mingliang Lv, Rongrong Pei, Peibo Li, Zhong Pei, Yonggang Wang, Weiwei Su, Xiang-Qun Xie:
AlzPlatform: An Alzheimer's Disease Domain-Specific Chemogenomics Knowledgebase for Polypharmacology and Target Identification Research. 1050-1060 - Xiao Li, Lei Chen, Feixiong Cheng, Zengrui Wu, Hanping Bian, Congying Xu, Weihua Li, Guixia Liu, Xu Shen, Yun Tang:
In Silico Prediction of Chemical Acute Oral Toxicity Using Multi-Classification Methods. 1061-1069 - Sean Ekins, Richard Pottorf, Robert C. Reynolds, Antony J. Williams, Alex M. Clark, Joel S. Freundlich:
Looking Back to the Future: Predicting in Vivo Efficacy of Small Molecules versus Mycobacterium tuberculosis. 1070-1082 - Robert P. Sheridan:
Global Quantitative Structure-Activity Relationship Models vs Selected Local Models as Predictors of Off-Target Activities for Project Compounds. 1083-1092
- Tim Geppert, Bernd Beck:
Fuzzy Matched Pairs: A Means To Determine the Pharmacophore Impact on Molecular Interaction. 1093-1102 - Polina V. Oliferenko, Alexander A. Oliferenko, Adel S. Girgis, Dalia O. Saleh, Aladdin M. Srour, Riham F. George, Girinath G. Pillai, Chandramukhi S. Panda, C. Dennis Hall, Alan R. Katritzky:
Synthesis, Bioassay, and Molecular Field Topology Analysis of Diverse Vasodilatory Heterocycles. 1103-1116 - Mats Eriksson, Hongming Chen, Lars Carlsson, J. Willem M. Nissink, John G. Cumming, Ingemar Nilsson:
Beyond the Scope of Free-Wilson Analysis. 2 Can Distance Encoded R-Group Fingerprints Provide Interpretable Nonlinear Models? 1117-1128
- Indrajit Deb, Joanna Sarzynska, Lennart Nilsson, Ansuman Lahiri:
Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields. 1129-1142 - Garima Tiwari, Debasisa Mohanty:
Structure-Based Multiscale Approach for Identification of Interaction Partners of PDZ Domains. 1143-1156 - Darrick Pope, Jeffry D. Madura, Michael Cascio:
β-Amyloid and Neprilysin Computational Studies Identify Critical Residues Implicated in Binding Specificity. 1157-1165 - Adel Hamza, Jonathan M. Wagner, Timothy J. Evans, Mykhaylo S. Frasinyuk, Stefan Kwiatkowski, Chang-Guo Zhan, David S. Watt, Konstantin V. Korotkov:
Novel Mycosin Protease MycP1 Inhibitors Identified by Virtual Screening and 4D Fingerprints. 1166-1173 - Phanourios Tamamis, Christodoulos A. Floudas:
Elucidating a Key Component of Cancer Metastasis: CXCL12 (SDF-1α) Binding to CXCR4. 1174-1188 - Anna D. Koromyslova, Anton O. Chugunov, Roman G. Efremov:
Deciphering Fine Molecular Details of Proteins' Structure and Function with a Protein Surface Topography (PST) Method. 1189-1199
- Livia Basile, Matteo Pappalardo, Salvatore Guccione, Danilo Milardi, Rona R. Ramsay:
Computational Comparison of Imidazoline Association with the I2 Binding Site in Human Monoamine Oxidases. 1200-1207 - Arthitaya Meeprasert, Supot Hannongbua, Thanyada Rungrotmongkol:
Key Binding and Susceptibility of NS3/4A Serine Protease Inhibitors against Hepatitis C Virus. 1208-1217 - Mian Wang, Marc Baaden, Jianyi Wang, Zhiqun Liang:
A Cooperative Mechanism of Clotrimazoles in P450 Revealed by the Dissociation Picture of Clotrimazole from P450. 1218-1225 - Jeremy M. Beck, Clayton Springer:
Quantitative Structure-Activity Relationship Models of Chemical Transformations from Matched Pairs Analyses. 1226-1234 - Erchang Shang, Yaxia Yuan, Xinyi Chen, Ying Liu, Jianfeng Pei, Luhua Lai:
De Novo Design of Multitarget Ligands with an Iterative Fragment-Growing Strategy. 1235-1241
- Maiko Kobayashi, Tomohiro Kinjo, Yuji Koseki, Christina R. Bourne, William W. Barrow, Shunsuke Aoki:
Identification of Novel Potential Antibiotics against Staphylococcus Using Structure-Based Drug Screening Targeting Dihydrofolate Reductase. 1242-1253
- Katra Kolsek, Janez Mavri, Marija Sollner Dolenc, Stanislav Gobec, Samo Turk:
Endocrine Disruptome - An Open Source Prediction Tool for Assessing Endocrine Disruption Potential through Nuclear Receptor Binding. 1254-1267
Volume 54, Number 5, May 2014
- Osman F. Güner, J. Phillip Bowen:
Setting the Record Straight: The Origin of the Pharmacophore Concept. 1269-1283
- Patrick McCabe, Oliver Korb, Jason C. Cole:
Kernel Density Estimation Applied to Bond Length, Bond Angle, and Torsion Angle Distributions. 1284-1288
- Hiroshi Yamashita, Tomoyuki Higuchi, Ryo Yoshida:
Atom Environment Kernels on Molecules. 1289-1300 - Vigneshwaran Namasivayam, Disha Gupta-Ostermann, Jenny Balfer, Kathrin Heikamp, Jürgen Bajorath:
Prediction of Compounds in Different Local Structure-Activity Relationship Environments Using Emerging Chemical Patterns. 1301-1310 - Kamil Paduszynski, Urszula Domanska:
Viscosity of Ionic Liquids: An Extensive Database and a New Group Contribution Model Based on a Feed-Forward Artificial Neural Network. 1311-1324
- Anna Lucia Fallacara, Cristina Tintori, Marco Radi, Silvia Schenone, Maurizio Botta:
Insight into the Allosteric Inhibition of Abl Kinase. 1325-1338 - Paul C. D. Hawkins, Brian P. Kelley, Gregory L. Warren:
The Application of Statistical Methods to Cognate Docking: A Path Forward? 1339-1355 - Xue Qing Yang, Ji Yuan Liu, Xian Chun Li, Mao Hua Chen, Ya Lin Zhang:
Key Amino Acid Associated with Acephate Detoxification by Cydia pomonella Carboxylesterase Based on Molecular Dynamics with Alanine Scanning and Site-Directed Mutagenesis. 1356-1370 - Roland G. Huber, Michael A. Margreiter, Julian E. Fuchs, Susanne von Grafenstein, Christofer S. Tautermann, Klaus R. Liedl, Thomas Fox:
Heteroaromatic π-Stacking Energy Landscapes. 1371-1379
- Carlos H. B. da Cruz, Gustavo de M. Seabra:
Molecular Dynamics Simulations Reveal a Novel Mechanism for ATP Inhibition of Insulin Degrading Enzyme. 1380-1390 - Hubert Li, Vinod Kasam, Christofer S. Tautermann, Daniel Seeliger, Nagarajan Vaidehi:
Computational Method To Identify Druggable Binding Sites That Target Protein-Protein Interactions. 1391-1400 - Marcelino Arciniega, Oliver F. Lange:
Improvement of Virtual Screening Results by Docking Data Feature Analysis. 1401-1411 - Jacqueline C. Hargis, Justin K. White, Yu Chen, H. Lee Woodcock III:
Can Molecular Dynamics and QM/MM Solve the Penicillin Binding Protein Protonation Puzzle? 1412-1424 - Asghar M. Razavi, William M. Wuest, Vincent A. Voelz:
Computational Screening and Selection of Cyclic Peptide Hairpin Mimetics by Molecular Simulation and Kinetic Network Models. 1425-1432
- Jie Xia, Hongwei Jin, Zhenming Liu, Liang Ren Zhang, Xiang Simon Wang:
An Unbiased Method To Build Benchmarking Sets for Ligand-Based Virtual Screening and its Application To GPCRs. 1433-1450 - Andrej Perdih, Martina Hrast, Hélène Barreteau, Stanislav Gobec, Gerhard Wolber, Tomaz Solmajer:
Inhibitor Design Strategy Based on an Enzyme Structural Flexibility: A Case of Bacterial MurD Ligase. 1451-1466 - Qiantao Wang, Jihyun Park, Ashwini K. Devkota, Eun Jeong Cho, Kevin N. Dalby, Pengyu Y. Ren:
Identification and Validation of Novel PERK Inhibitors. 1467-1475 - James A. R. Dalton, Xavier Gómez-Santacana, Amadeu Llebaria, Jesús Giraldo:
Computational Analysis of Negative and Positive Allosteric Modulator Binding and Function in Metabotropic Glutamate Receptor 5 (In)Activation. 1476-1487 - Yasmin Shamsudin Khan, Hugo Gutiérrez-de-Terán, Lars Boukharta, Johan Åqvist:
Toward an Optimal Docking and Free Energy Calculation Scheme in Ligand Design with Application to COX-1 Inhibitors. 1488-1499 - Pau Carrió, Marta Pinto, Gerhard F. Ecker, Ferran Sanz, Manuel Pastor:
Applicability Domain Analysis (ADAN): A Robust Method for Assessing the Reliability of Drug Property Predictions. 1500-1511
- Boris Vishnepolsky, Malak Pirtskhalava:
Prediction of Linear Cationic Antimicrobial Peptides Based on Characteristics Responsible for Their Interaction with the Membranes. 1512-1523 - Filip Fratev, Elina Mihaylova, Ilza Pajeva:
Combination of Genetic Screening and Molecular Dynamics as a Useful Tool for Identification of Disease-Related Mutations: ZASP PDZ Domain G54S Mutation Case. 1524-1536
- Matteo Tiberti, Gaetano Invernizzi, Matteo Lambrughi, Yuval Inbar, Gideon Schreiber, Elena Papaleo:
PyInteraph: A Framework for the Analysis of Interaction Networks in Structural Ensembles of Proteins. 1537-1551
- E. Seifert:
OriginPro 9.1: Scientific Data Analysis and Graphing Software - Software Review. 1552
Volume 54, Number 6, June 2014
- Vignir Ísberg, Kirsten B. Andersen, Christoph Bisig, Gunnar P. H. Dietz, Hans Bräuner-Osborne, David E. Gloriam:
Computer-Aided Discovery of Aromatic l-α-Amino Acids as Agonists of the Orphan G Protein-Coupled Receptor GPR139. 1553-1557
- Kenichi Tanaka, Kiyoko F. Aoki-Kinoshita, Masaaki Kotera, Hiromichi Sawaki, Shinichiro Tsuchiya, Noriaki Fujita, Toshihide Shikanai, Masaki Kato, Shin Kawano, Issaku Yamada, Hisashi Narimatsu:
WURCS: The Web3 Unique Representation of Carbohydrate Structures. 1558-1566 - Abraham Yosipof, Hanoch Senderowitz:
Optimization of Molecular Representativeness. 1567-1577 - Sabrina Wollenhaupt, Knut Baumann:
inSARa: Intuitive and Interactive SAR Interpretation by Reduced Graphs and Hierarchical MCS-Based Network Navigation. 1578-1595 - Ulf Norinder, Lars Carlsson, Scott Boyer, Martin Eklund:
Introducing Conformal Prediction in Predictive Modeling. A Transparent and Flexible Alternative to Applicability Domain Determination. 1596-1603 - Robert P. Sheridan, Nicolas Zorn, Edward C. Sherer, Louis-Charles Campeau, Charlie (Zhenyu) Chang, Jared Cumming, Matthew L. Maddess, Philippe G. Nantermet, Christopher J. Sinz, Paul D. O'Shea:
Modeling a Crowdsourced Definition of Molecular Complexity. 1604-1616 - Peter Ertl:
Intuitive Ordering of Scaffolds and Scaffold Similarity Searching Using Scaffold Keys. 1617-1622
- Michael S. Bodnarchuk, Russell C. Viner, Julien Michel, Jonathan W. Essex:
Strategies to Calculate Water Binding Free Energies in Protein-Ligand Complexes. 1623-1633 - Fabio Broccatelli, Nathan Brown:
Best of Both Worlds: On the Complementarity of Ligand-Based and Structure-Based Virtual Screening. 1634-1641 - Romina Castañeda-Arriaga, J. Raúl Alvarez-Idaboy:
Lipoic Acid and Dihydrolipoic Acid. A Comprehensive Theoretical Study of Their Antioxidant Activity Supported by Available Experimental Kinetic Data. 1642-1652
- Kunihiro Kitamura, Yunoshin Tamura, Tomokazu Ueki, Koji Ogata, Shigeho Noda, Ryutaro Himeno, Hiroshi Chuman:
Binding Free-Energy Calculation Is a Powerful Tool for Drug Optimization: Calculation and Measurement of Binding Free Energy for 7-Azaindole Derivatives to Glycogen Synthase Kinase-3β. 1653-1660 - Krzysztof Rataj, Jagna Witek, Stefan Mordalski, Tomasz Kosciólek, Andrzej J. Bojarski:
Impact of Template Choice on Homology Model Efficiency in Virtual Screening. 1661-1668 - Manuel P. Luitz, Martin Zacharias:
Protein-Ligand Docking Using Hamiltonian Replica Exchange Simulations with Soft Core Potentials. 1669-1675 - Karen Schomburg, Stefan Bietz, Hans Briem, Angela M. Henzler, Sascha Urbaczek, Matthias Rarey:
Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening. 1676-1686 - Guang Qiang Dong, Sara Calhoun, Hao Fan, Chakrapani Kalyanaraman, Megan C. Branch, Susan T. Mashiyama, Nir London, Matthew P. Jacobson, Patricia C. Babbitt, Brian K. Shoichet, Richard N. Armstrong, Andrej Sali:
Prediction of Substrates for Glutathione Transferases by Covalent Docking. 1687-1699
- Yan Li, Zhihai Liu, Jie Li, Li Han, Jie Liu, Zhixiong Zhao, Renxiao Wang:
Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set. 1700-1716 - Yan Li, Li Han, Zhihai Liu, Renxiao Wang:
Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results. 1717-1736 - Eelke B. Lenselink, Thijs Beuming, Woody Sherman, Herman W. T. van Vlijmen, Adriaan P. IJzerman:
Selecting an Optimal Number of Binding Site Waters To Improve Virtual Screening Enrichments Against the Adenosine A2A Receptor. 1737-1746 - Yvonne Krautscheid, Carl Johann Åke Senning, Simone B. Sartori, Nicolas Singewald, Daniela Schuster, Hermann Stuppner:
Pharmacophore Modeling, Virtual Screening, and in Vitro Testing Reveal Haloperidol, Eprazinone, and Fenbutrazate as Neurokinin Receptors Ligands. 1747-1757 - Niel M. Henriksen, Hamed S. Hayatshahi, Darrell R. Davis, Thomas E. Cheatham III:
Structural and Energetic Analysis of 2-Aminobenzimidazole Inhibitors in Complex with the Hepatitis C Virus IRES RNA Using Molecular Dynamics Simulations. 1758-1772 - Alban Lepailleur, Thomas Freret, Stéphane Lemaître, Michel Boulouard, François Dauphin, Antoine Hinschberger, Fabienne Dulin, Aurélien Lesnard, Ronan Bureau, Sylvain Rault:
Dual Histamine H3R/Serotonin 5-HT4R Ligands with Antiamnesic Properties: Pharmacophore-Based Virtual Screening and Polypharmacology. 1773-1784 - Shengping Zhang, Jiani Tan, Zhonghui Lai, Ying Li, Junxia Pang, Jianhu Xiao, Zhangjian Huang, Yihua Zhang, Hui Ji, Yisheng Lai:
Effective Virtual Screening Strategy toward Covalent Ligands: Identification of Novel NEDD8-Activating Enzyme Inhibitors. 1785-1797
- Fei Guo, Shuai Cheng Li, Pufeng Du, Lusheng Wang:
Probabilistic Models for Capturing More Physicochemical Properties on Protein-Protein Interface. 1798-1809
- Julien C. Thibault, Thomas E. Cheatham III, Julio C. Facelli:
iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings. 1810-1819
Volume 54, Number 7, July 2014
- Yaw Sing Tan, David R. Spring, Chris Abell, Chandra Verma:
The Use of Chlorobenzene as a Probe Molecule in Molecular Dynamics Simulations. 1821-1827 - Francesco Ortuso, Rosario Amato, Anna Artese, Lucia D'antona, Giosuè Costa, Cristina Talarico, Francesco Gigliotti, Cataldo Bianco, Francesco Trapasso, Silvia Schenone, Francesca Musumeci, Lorenzo Botta, Nicola Perrotti, Stefano Alcaro:
In Silico Identification and Biological Evaluation of Novel Selective Serum/Glucocorticoid-Inducible Kinase 1 Inhibitors Based on the Pyrazolo-Pyrimidine Scaffold. 1828-1832
- Ana L. Teixeira, André O. Falcão:
Structural Similarity Based Kriging for Quantitative Structure Activity and Property Relationship Modeling. 1833-1849 - Takeshi Kawabata, Haruki Nakamura:
3D Flexible Alignment Using 2D Maximum Common Substructure: Dependence of Prediction Accuracy on Target-Reference Chemical Similarity. 1850-1863 - Richard Sherhod, Philip N. Judson, Thierry Hanser, Jonathan D. Vessey, Samuel J. Webb, Valerie J. Gillet:
Emerging Pattern Mining To Aid Toxicological Knowledge Discovery. 1864-1879 - Sereina Riniker, Yuan Wang, Jeremy L. Jenkins, Gregory A. Landrum:
Using Information from Historical High-Throughput Screens to Predict Active Compounds. 1880-1891 - Mahendra Awale, Jean-Louis Reymond:
Atom Pair 2D-Fingerprints Perceive 3D-Molecular Shape and Pharmacophores for Very Fast Virtual Screening of ZINC and GDB-17. 1892-1907 - Jérémy Desaphy, Didier Rognan:
sc-PDB-Frag: A Database of Protein-Ligand Interaction Patterns for Bioisosteric Replacements. 1908-1918 - Marco Foscato, Vishwesh Venkatraman, Giovanni Occhipinti, Bjørn K. Alsberg, Vidar R. Jensen:
Automated Building of Organometallic Complexes from 3D Fragments. 1919-1931
- Kai Zhu, Kenneth W. Borrelli, Jeremy R. Greenwood, Tyler Day, Robert Abel, Ramy Farid, Edward Harder:
Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring. 1932-1940 - Dora Toledo Warshaviak, Gali Golan, Kenneth W. Borrelli, Kai Zhu, Ori Kalid:
Structure-Based Virtual Screening Approach for Discovery of Covalently Bound Ligands. 1941-1950 - Rashmi Kumari, Rajendra Kumar, Andrew M. Lynn:
g_mmpbsa - A GROMACS Tool for High-Throughput MM-PBSA Calculations. 1951-1962 - Danuta Rusinska-Roszak, Grzegorz Sowinski:
Estimation of the Intramolecular O-H···O═C Hydrogen Bond Energy via the Molecular Tailoring Approach. Part I: Aliphatic Structures. 1963-1977 - Chad W. Hopkins, Adrian E. Roitberg:
Fitting of Dihedral Terms in Classical Force Fields as an Analytic Linear Least-Squares Problem. 1978-1986 - Ran Cao, Niu Huang, Yanli Wang:
Evaluation and Application of MD-PB/SA in Structure-Based Hierarchical Virtual Screening. 1987-1996 - Alexander N. Morozov, James P. Roach, Margarita Kotzer, David C. Chatfield:
A Possible Mechanism for Redox Control of Human Neuroglobin Activity. 1997-2003 - David Rodríguez, Anirudh Ranganathan, Jens Carlsson:
Strategies for Improved Modeling of GPCR-Drug Complexes: Blind Predictions of Serotonin Receptors Bound to Ergotamine. 2004-2021
- Hua Yu, Peng Zhou, Maolin Deng, Zhicai Shang:
Indirect Readout in Protein-Peptide Recognition: A Different Story from Classical Biomolecular Recognition. 2022-2032 - Yang Jiang, Lingli Li, Haiyang Zhang, Wei Feng, Tianwei Tan:
Lid Closure Mechanism of Yarrowia lipolytica Lipase in Methanol Investigated by Molecular Dynamics Simulation. 2033-2041 - Hanumanthappa Pradeep, G. Krishnamurthy Rajanikant:
Computational Prediction of a Putative Binding Site on Drp1: Implications for Antiparkinsonian Therapy. 2042-2050 - António César Pimenta, Daniel F. A. R. Dourado, João M. Martins, André Melo, M. N. Dias Soeiro Cordeiro, Ramiro D. Almeida, Giulia Morra, Irina S. Moreira:
Dynamic Structure of NGF and proNGF Complexed with p75NTR: Pro-Peptide Effect. 2051-2067 - Scott E. Mottarella, Dmitri Beglov, Natalia Beglova, Matthew A. Nugent, Dima Kozakov, Sandor Vajda:
Docking Server for the Identification of Heparin Binding Sites on Proteins. 2068-2078 - Hein J. Wijma, Siewert J. Marrink, Dick B. Janssen:
Computationally Efficient and Accurate Enantioselectivity Modeling by Clusters of Molecular Dynamics Simulations. 2079-2092 - Jan K. Marzinek, Peter J. Bond, Guoping Lian, Yanyan Zhao, Lujia Han, Massimo G. Noro, Efstratios N. Pistikopoulos, Athanasios Mantalaris:
Free Energy Predictions of Ligand Binding to an α-Helix Using Steered Molecular Dynamics and Umbrella Sampling Simulations. 2093-2104 - Bo Wang, Cameron D. Buchman, Liwei Li, Thomas D. Hurley, Samy O. Meroueh:
Enrichment of Chemical Libraries Docked to Protein Conformational Ensembles and Application to Aldehyde Dehydrogenase 2. 2105-2116 - Sathish Kumar Ramakrishnan, Marta Martin, Thierry Cloitre, Lucyna Firlej, Csilla Gergely:
Molecular Mechanism of Selective Binding of Peptides to Silicon Surface. 2117-2126
- Arthur J. Campbell, Michelle L. Lamb, Diane Joseph-McCarthy:
Ensemble-Based Docking Using Biased Molecular Dynamics. 2127-2138 - Hwangseo Park, Jae-Won Eom, Yang-Hee Kim:
Consensus Scoring Approach To Identify the Inhibitors of AMP-Activated Protein Kinase α2 with Virtual Screening. 2139-2146 - Richard D. Cramer:
Template CoMFA Applied to 116 Biological Targets. 2147-2156 - Sean Ekins, Joel S. Freundlich, Robert C. Reynolds:
Are Bigger Data Sets Better for Machine Learning? Fusing Single-Point and Dual-Event Dose Response Data for Mycobacterium tuberculosis. 2157-2165
- Jan Zacharias, Ernst-Walter Knapp:
Protein Secondary Structure Classification Revisited: Processing DSSP Information with PSSC. 2166-2179
- Alexios Koutsoukas, Robert Lowe, Yasaman KalantarMotamedi, Hamse Y. Mussa, Werner Klaffke, John B. O. Mitchell, Robert C. Glen, Andreas Bender:
Erratum for "In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naı̈ve Bayes and Parzen-Rosenblatt Window". 2180-2182 - Livia Basile, Matteo Pappalardo, Salvatore Guccione, Danilo Milardi, Rona R. Ramsay:
Correction to Computational Comparison of Imidazoline Association with the I2 Binding Site in Human Monoamine Oxidases. 2183
Volume 54, Number 8, August 2014
- Gianluigi Lauro, Noelia Ferruz, Simone Fulle, Matt J. Harvey, Paul W. Finn, Gianni De Fabritiis:
Reranking Docking Poses Using Molecular Simulations and Approximate Free Energy Methods. 2185-2189
- Katrina W. Lexa, Garrett B. Goh, Heather A. Carlson:
Parameter Choice Matters: Validating Probe Parameters for Use in Mixed-Solvent Simulations. 2190-2199 - Ilke Ugur, Antoine Marion, Stéphane Parant, Jan H. Jensen, Gerald Monard:
Rationalization of the pKa Values of Alcohols and Thiols Using Atomic Charge Descriptors and Its Application to the Prediction of Amino Acid pKa's. 2200-2213 - Craig Grimmer, Terry W. Moore, Aaron Padwa, Andrew Prussia, Gordon Wells, Shaoxiong Wu, Aiming Sun, James P. Snyder:
Antiviral Atropisomers: Conformational Energy Surfaces by NMR for Host-Directed Myxovirus Blockers. 2214-2223 - Katarzyna R. Przybylak, Abdullah Rzgallah Alzahrani, Mark T. D. Cronin:
How Does the Quality of Phospholipidosis Data Influence the Predictivity of Structural Alerts? 2224-2232 - Tengfei Liu, Xianchao Pan, Li Chao, Wen Tan, Sujun Qu, Li Yang, Bochu Wang, Hu Mei:
Subangstrom Accuracy in pHLA-I Modeling by Rosetta FlexPepDock Refinement Protocol. 2233-2242 - Antonella Ciancetta, Alberto Cuzzolin, Stefano Moro:
Alternative Quality Assessment Strategy to Compare Performances of GPCR-Ligand Docking Protocols: The Human Adenosine A2A Receptor as a Case Study. 2243-2254 - Mark A. Vincent, Ian H. Hillier:
Accurate Prediction of Adsorption Energies on Graphene, Using a Dispersion-Corrected Semiempirical Method Including Solvation. 2255-2260
- Karen Schomburg, Matthias Rarey:
Benchmark Data Sets for Structure-Based Computational Target Prediction. 2261-2274 - Hongchun Li, Shun Sakuraba, Aravind Chandrasekaran, Lee-Wei Yang:
Molecular Binding Sites Are Located Near the Interface of Intrinsic Dynamics Domains (IDDs). 2275-2285 - Kaan Yilancioglu, Zohar B. Weinstein, Cem Meydan, Azat Akhmetov, Isil Toprak, Arda Durmaz, Ivan Iossifov, Hilal Kazan, Frederick P. Roth, Murat Cokol:
Target-Independent Prediction of Drug Synergies Using Only Drug Lipophilicity. 2286-2293 - Georgios Leonis, Aggelos Avramopoulos, Ramin Ekhteiari Salmas, Serdar Durdagi, Mine Yurtsever, Manthos G. Papadopoulos:
Elucidation of Conformational States, Dynamics, and Mechanism of Binding in Human κ-Opioid Receptor Complexes. 2294-2308 - Ariane Nunes-Alves, Guilherme Menegon Arantes:
Ligand-Receptor Affinities Computed by an Adapted Linear Interaction Model for Continuum Electrostatics and by Protein Conformational Averaging. 2309-2319
- Peter Schmidtke, Marine Ciantar, Isabelle Theret, Pierre Ducrot:
Dynamics of hERG Closure Allow Novel Insights into hERG Blocking by Small Molecules. 2320-2333 - Sarah Sirin, Rajesh Kumar, Carlos Martínez, Michael J. Karmilowicz, Preeyantee Ghosh, Yuriy A. Abramov, Van Martin, Woody Sherman:
A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring. 2334-2346
- Muhammad Ammad-ud-din, Elisabeth Georgii, Mehmet Gönen, Tuomo Laitinen, Olli-P. Kallioniemi, Krister Wennerberg, Antti Poso, Samuel Kaski:
Integrative and Personalized QSAR Analysis in Cancer by Kernelized Bayesian Matrix Factorization. 2347-2359 - Sorin I. Avram, Liliana M. Pacureanu, Alina Bora, Luminita Crisan, Stefana Avram, Ludovic Kurunczi:
ColBioS-FlavRC: A Collection of Bioselective Flavonoids and Related Compounds Filtered from High-Throughput Screening Outcomes. 2360-2370
- Diogo Santos-Martins, Stefano Forli, Maria João Ramos, Arthur J. Olson:
AutoDock4Zn: An Improved AutoDock Force Field for Small-Molecule Docking to Zinc Metalloproteins. 2371-2379 - Paolo Frasconi, Francesco Gabbrielli, Marco Lippi, Simone Marinai:
Markov Logic Networks for Optical Chemical Structure Recognition. 2380-2390 - William L. Todsen:
ChemDoodle 6.0. 2391-2393
Volume 54, Number 9, September 2014
- Philipp Thiel, Lisa Sach-Peltason, Christian Ottmann, Oliver Kohlbacher:
Blocked Inverted Indices for Exact Clustering of Large Chemical Spaces. 2395-2401 - José Rogério A. Silva, Adrian E. Roitberg, Cláudio Nahum Alves:
Catalytic Mechanism of L, D-Transpeptidase 2 from Mycobacterium tuberculosis Described by a Computational Approach: Insights for the Design of New Antibiotics Drugs. 2402-2410 - Lennart T. Anger, Antje Wolf, Klaus-Jürgen Schleifer, Dieter Schrenk, Sebastian G. Rohrer:
Generalized Workflow for Generating Highly Predictive in Silico Off-Target Activity Models. 2411-2422 - Laura Guasch, Markus Sitzmann, Marc C. Nicklaus:
Enumeration of Ring-Chain Tautomers Based on SMIRKS Rules. 2423-2432 - Fidele Ntie-Kang, Justina Ngozi Nwodo, Akachukwu Ibezim, Conrad Veranso Simoben, Berin Karaman, Valery Fuh Ngwa, Wolfgang Sippl, Michael Umale Adikwu, Luc Meva'a Mbaze:
Molecular Modeling of Potential Anticancer Agents from African Medicinal Plants. 2433-2450 - Jenny Balfer, Jürgen Bajorath:
Introduction of a Methodology for Visualization and Graphical Interpretation of Bayesian Classification Models. 2451-2468
- Hiromasa Kaneko, Kimito Funatsu:
Applicability Domain Based on Ensemble Learning in Classification and Regression Analyses. 2469-2482 - Zhiwei Feng, Mohammed Hamed Alqarni, Peng Yang, Qin Tong, Ananda Chowdhury, Lirong Wang, Xiang-Qun Xie:
Modeling, Molecular Dynamics Simulation, and Mutation Validation for Structure of Cannabinoid Receptor 2 Based on Known Crystal Structures of GPCRs. 2483-2499 - Robin Taylor, Jason C. Cole, Oliver Korb, Patrick McCabe:
Knowledge-Based Libraries for Predicting the Geometric Preferences of Druglike Molecules. 2500-2514 - Qi Cao, K. M. Leung:
Prediction of Chemical Biodegradability Using Support Vector Classifier Optimized with Differential Evolution. 2515-2523 - Shilpi Mandal, Gunajyoti Das, Hassan Askari:
Experimental and Quantum Chemical Modeling Studies of the Interactions of l-Phenylalanine with Divalent Transition Metal Cations. 2524-2535
- A. Srinivas Reddy, Zhi Tan, Shuxing Zhang:
Curation and Analysis of Multitargeting Agents for Polypharmacological Modeling. 2536-2543 - Haoliang Yuan, Jin Zhuang, Shihe Hu, Huifang Li, Jinxing Xu, Yaning Hu, Xiao Xiong, Yadong Chen, Tao Lu:
Molecular Modeling of Exquisitely Selective c-Met Inhibitors through 3D-QSAR and Molecular Dynamics Simulations. 2544-2554 - C. Da, Dmitri B. Kireev:
Structural Protein-Ligand Interaction Fingerprints (SPLIF) for Structure-Based Virtual Screening: Method and Benchmark Study. 2555-2561 - Jihong Yang, Zheng Li, Xiaohui Fan, Yiyu Cheng:
Drug-Disease Association and Drug-Repositioning Predictions in Complex Diseases Using Causal Inference-Probabilistic Matrix Factorization. 2562-2569 - Jolanta Natalia Latosinska, Magdalena Latosinska, Grzegorz A. Olejniczak, Janez Seliger, Veselko Zagar:
Topology of the Interactions Pattern in Pharmaceutically Relevant Polymorphs of Methylxanthines (Caffeine, Theobromine, and Theophiline): Combined Experimental (1H-14N Nuclear Quadrupole Double Resonance) and Computational (DFT and Hirshfeld-Based) Study. 2570-2584
- Henry R. Wilman, Jean-Paul Ebejer, Jiye Shi, Charlotte M. Deane, Bernhard Knapp:
Crowdsourcing Yields a New Standard for Kinks in Protein Helices. 2585-2593
- Roman R. Kapaev, Ksenia S. Egorova, Philip V. Toukach:
Carbohydrate Structure Generalization Scheme for Database-Driven Simulation of Experimental Observables, Such as NMR Chemical Shifts. 2594-2611 - Yuri Pevzner, Emilie Frugier, Vinushka Schalk, Amedeo Caflisch, H. Lee Woodcock III:
Fragment-Based Docking: Development of the CHARMMing Web User Interface as a Platform for Computer-Aided Drug Design. 2612-2620
Volume 54, Number 10, October 2014
- Daniele Pala, Riccardo Castelli, Matteo Incerti, Simonetta Russo, Massimiliano Tognolini, Carmine Giorgio, Iftiin Hassan-Mohamed, Ilaria Zanotti, Federica Vacondio, Silvia Rivara, Marco Mor, Alessio Lodola:
Combining Ligand- and Structure-Based Approaches for the Discovery of New Inhibitors of the EPHA2-ephrin-A1 Interaction. 2621-2626
- Matthew J. Harvey, Nicholas J. Mason, Henry S. Rzepa:
Digital Data Repositories in Chemistry and Their Integration with Journals and Electronic Notebooks. 2627-2635 - Anthony R. Bradley, Ian D. Wall, Darren V. S. Green, Charlotte M. Deane, Brian D. Marsden:
OOMMPPAA: A Tool To Aid Directed Synthesis by the Combined Analysis of Activity and Structural Data. 2636-2646 - Jonathan Alvarsson, Martin Eklund, Ola Engkvist, Ola Spjuth, Lars Carlsson, Jarl E. S. Wikberg, Tobias Noeske:
Ligand-Based Target Prediction with Signature Fingerprints. 2647-2653 - Antonio de la Vega de León, Jürgen Bajorath:
Prediction of Compound Potency Changes in Matched Molecular Pairs Using Support Vector Regression. 2654-2663 - Sheng Tian, Huiyong Sun, Peichen Pan, Dan Li, Xuechu Zhen, Youyong Li, Tingjun Hou:
Assessing an Ensemble Docking-Based Virtual Screening Strategy for Kinase Targets by Considering Protein Flexibility. 2664-2679
- K. Shawn Watts, Pranav Dalal, Andrew J. Tebben, Daniel L. Cheney, John C. Shelley:
Macrocycle Conformational Sampling with MacroModel. 2680-2696 - Paulette A. Greenidge, Christian Kramer, Jean-Christophe Mozziconacci, Woody Sherman:
Improving Docking Results via Reranking of Ensembles of Ligand Poses in Multiple X-ray Protein Conformations with MM-GBSA. 2697-2717 - Fabienne Dioury, Arthur F. Duprat, Gérard Dreyfus, Clotilde Ferroud, Janine Cossy:
QSPR Prediction of the Stability Constants of Gadolinium(III) Complexes for Magnetic Resonance Imaging. 2718-2731 - Pankaj R. Daga, Willma E. Polgar, Nurulain T. Zaveri:
Structure-Based Virtual Screening of the Nociceptin Receptor: Hybrid Docking and Shape-Based Approaches for Improved Hit Identification. 2732-2743 - Spandana Makeneni, Bethany Lachele Foley, Robert J. Woods:
BFMP: A Method for Discretizing and Visualizing Pyranose Conformations. 2744-2750 - Nobuyoshi Sugaya:
Ligand Efficiency-Based Support Vector Regression Models for Predicting Bioactivities of Ligands to Drug Target Proteins. 2751-2763 - Alessio Atzori, Neil J. Bruce, Kepa K. Burusco, Berthold Wroblowski, Pascal Bonnet, Richard A. Bryce:
Exploring Protein Kinase Conformation Using Swarm-Enhanced Sampling Molecular Dynamics. 2764-2775 - Lukács J. Németh, Zsófia Hegedüs, Tamás A. Martinek:
Predicting Order and Disorder for β-Peptide Foldamers in Water. 2776-2783 - Ashutosh Kumar, Akihiro Ito, Mikako Hirohama, Minoru Yoshida, Kam Y. J. Zhang:
Identification of Sumoylation Inhibitors Targeting a Predicted Pocket in Ubc9. 2784-2793 - Paulius Mikulskis, Samuel Genheden, Ulf Ryde:
A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities. 2794-2806 - Joffrey Gabel, Jérémy Desaphy, Didier Rognan:
Beware of Machine Learning-Based Scoring Functions - On the Danger of Developing Black Boxes. 2807-2815 - Usha Viswanathan, Suzanne M. Tomlinson, John M. Fonner, Stephen A. Mock, Stanley J. Watowich:
Identification of a Novel Inhibitor of Dengue Virus Protease through Use of a Virtual Screening Drug Discovery Web Portal. 2816-2825
- Shujun Zhang, Yefei Wang, Xiangfei Song, Jingbo Hong, Yu Zhang, Lishan Yao:
Improving Trichoderma reesei Cel7B Thermostability by Targeting the Weak Spots. 2826-2833 - Adel Hamza, Jonathan M. Wagner, Ning-Ning Wei, Stefan Kwiatkowski, Chang-Guo Zhan, David S. Watt, Konstantin V. Korotkov:
Application of the 4D Fingerprint Method with a Robust Scoring Function for Scaffold-Hopping and Drug Repurposing Strategies. 2834-2845 - Davide Sabbadin, Antonella Ciancetta, Stefano Moro:
Perturbation of Fluid Dynamics Properties of Water Molecules during G Protein-Coupled Receptor-Ligand Recognition: The Human A2A Adenosine Receptor as a Key Study. 2846-2855 - Jacopo Sgrignani, Marta Bon, Giorgio Colombo, Alessandra Magistrato:
Computational Approaches Elucidate the Allosteric Mechanism of Human Aromatase Inhibition: A Novel Possible Route to Small-Molecule Regulation of CYP450s Activities? 2856-2868 - Danielle M. McHarris, Daniel A. Barr:
Truncated Variants of the GCN4 Transcription Activator Protein Bind DNA with Dramatically Different Dynamical Motifs. 2869-2875 - Ram Kumar Mishra, Reshma Alokam, Sarthak Mohan Singhal, Geethasai Srivathsav, Dharamarajan Sriram, Neerja Kaushik-Basu, Dinesh Manvar, Perumal Yogeeswari:
Design of Novel Rho Kinase Inhibitors Using Energy Based Pharmacophore Modeling, Shape-Based Screening, in Silico Virtual Screening, and Biological Evaluation. 2876-2886
- Jadel M. Kratz, Daniela Schuster, Michael Edtbauer, Priyanka Saxena, Christina E. Mair, Julia Kirchebner, Barbara Matuszczak, Igor Baburin, Steffen Hering, Judith M. Rollinger:
Experimentally Validated hERG Pharmacophore Models as Cardiotoxicity Prediction Tools. 2887-2901 - Eslam Pourbasheer, Reza Aalizadeh, Samira Shokouhi Tabar, Mohammad Reza Ganjali, Parviz Norouzi, Javad Shadmanesh:
2D and 3D Quantitative Structure-Activity Relationship Study of Hepatitis C Virus NS5B Polymerase Inhibitors by Comparative Molecular Field Analysis and Comparative Molecular Similarity Indices Analysis Methods. 2902-2914 - Nathalie Lagarde, Jean-François Zagury, Matthieu Montès:
Importance of the Pharmacological Profile of the Bound Ligand in Enrichment on Nuclear Receptors: Toward the Use of Experimentally Validated Decoy Ligands. 2915-2944 - Ernst Ahlberg Helgee, Lars Carlsson, Scott Boyer:
Computational Derivation of Structural Alerts from Large Toxicology Data Sets. 2945-2952 - Laura Caboni, María Gálvez-Llompart, Jorge Gálvez, Fernando Blanco, Jaime Rubio-Martinez, Darren Fayne, David G. Lloyd:
Molecular Topology Applied to the Discovery of 1-Benzyl-2-(3-fluorophenyl)-4-hydroxy-3-(3-phenylpropanoyl)-2H-pyrrole-5-one as a Non-Ligand-Binding-Pocket Antiandrogen. 2953-2966 - Arben Kojtari, Vishal Shah, Jacob S. Babinec, Catherine Yang, Hai-Feng Ji:
Structure-Based Drug Design of Diphenyl α-Aminoalkylphosphonates as Prostate-Specific Antigen Antagonists. 2967-2979 - Tiziano Tuccinardi, Giulio Poli, Veronica Romboli, Antonio Giordano, Adriano Martinelli:
Extensive Consensus Docking Evaluation for Ligand Pose Prediction and Virtual Screening Studies. 2980-2986 - Ying Yang, Bingjie Hu, Markus A. Lill:
Analysis of Factors Influencing Hydration Site Prediction Based on Molecular Dynamics Simulations. 2987-2995 - Nadia K. Litterman, Christopher A. Lipinski, Barry A. Bunin, Sean Ekins:
Computational Prediction and Validation of an Expert's Evaluation of Chemical Probes. 2996-3004 - Srinivasaraghavan Kannan, Jelena Melesina, Alexander-Thomas Hauser, Alokta Chakrabarti, Tino Heimburg, Karin Schmidtkunz, Alexandra Walter, Martin Marek, Raymond J. Pierce, Christophe Romier, Manfred Jung, Wolfgang Sippl:
Discovery of Inhibitors of Schistosoma mansoni HDAC8 by Combining Homology Modeling, Virtual Screening, and in Vitro Validation. 3005-3019
- Ryan L. Stafford, Erik S. Zimmerman, Trevor J. Hallam, Aaron K. Sato:
A General Sequence Processing and Analysis Program for Protein Engineering. 3020-3032
- Badi Abdul-Wahid, Haoyun Feng, Dinesh Rajan, Ronan Costaouec, Eric Darve, Douglas Thain, Jesús A. Izaguirre:
AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble. 3033-3043
Volume 54, Number 11, November 2014
- Kenneth M. Merz Jr.:
New Manuscript Type: Application Note. 3045
- Yan Wang, Wai-Kit Law, Jian-Shu Hu, Huang-Quan Lin, Tsz-Ming Ip, David Chi-Cheong Wan:
Discovery of FDA-Approved Drugs as Inhibitors of Fatty Acid Binding Protein 4 Using Molecular Docking Screening. 3046-3050 - Ifedayo Victor Ogungbe, Rebecca A. Crouch, Teresa Demeritte:
(-) Arctigenin and (+) Pinoresinol Are Antagonists of the Human Thyroid Hormone Receptor β. 3051-3055
- Ye Hu, Jürgen Bajorath:
Influence of Search Parameters and Criteria on Compound Selection, Promiscuity, and Pan Assay Interference Characteristics. 3056-3066 - Mélaine A. Kuenemann, Laura M. L. Bourbon, Céline M. Labbé, Bruno O. Villoutreix, Olivier Sperandio:
Which Three-Dimensional Characteristics Make Efficient Inhibitors of Protein-Protein Interactions? 3067-3079
- Sandhya Kortagere, Jimmy P. Xu, Marie K. Mankowski, Roger G. Ptak, Simon Cocklin:
Structure-Activity Relationships of a Novel Capsid Targeted Inhibitor of HIV-1 Replication. 3080-3090 - Ilenia Giangreco, Tjelvar S. G. Olsson, Jason C. Cole, Martin J. Packer:
Assessment of a Cambridge Structural Database-Driven Overlay Program. 3091-3098
- Nai-Wan Hsiao, Tien-Sheng Tseng, Yu-Ching Lee, Wang-Chuan Chen, Hui-Hsiung Lin, Yun-Ru Chen, Yeng-Tseng Wang, Hung-Ju Hsu, Keng-Chang Tsai:
Serendipitous Discovery of Short Peptides from Natural Products as Tyrosinase Inhibitors. 3099-3111 - Robert Szczelina, Krzysztof Murzyn:
DMG-α - A Computational Geometry Library for Multimolecular Systems. 3112-3123 - Anna Maria Capelli, Gabriele Costantino:
Unbinding Pathways of VEGFR2 Inhibitors Revealed by Steered Molecular Dynamics. 3124-3136 - Prasad Chaskar, Vincent Zoete, Ute F. Röhrig:
Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function. 3137-3152 - Miwa Sato, Takatsugu Hirokawa:
Extended Template-Based Modeling and Evaluation Method Using Consensus of Binding Mode of GPCRs for Virtual Screening. 3153-3161 - Jingwei Zhou, Hujun Xie, Zhihong Liu, Hai-Bin Luo, Ruibo Wu:
Structure-Function Analysis of the Conserved Tyrosine and Diverse π-Stacking among Class I Histone Deacetylases: A QM (DFT)/MM MD Study. 3162-3171
- Alfonso T. García-Sosa, Uko Maran:
Improving the Use of Ranking in Virtual Screening against HIV-1 Integrase with Triangular Numbers and Including Ligand Profiling with Antitargets. 3172-3185 - Ling Wang, Xiu Le, Long Li, Yingchen Ju, Zhongxiang Lin, Qiong Gu, Jun Xu:
Discovering New Agents Active against Methicillin-Resistant Staphylococcus aureus with Ligand-Based Approaches. 3186-3197 - Eric Therrien, Nathanael Weill, Anna Tomberg, Christopher R. Corbeil, Devin Lee, Nicolas Moitessier:
Docking Ligands into Flexible and Solvated Macromolecules, 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy. 3198-3210 - Jonathan Alvarsson, Martin Eklund, Claes R. Andersson, Lars Carlsson, Ola Spjuth, Jarl E. S. Wikberg:
Benchmarking Study of Parameter Variation When Using Signature Fingerprints Together with Support Vector Machines. 3211-3217 - Tobias Linder, Priyanka Saxena, Eugen N. Timin, Steffen Hering, Anna Stary-Weinzinger:
Structural Insights into Trapping and Dissociation of Small Molecules in K+ Channels. 3218-3228 - Timo Krotzky, Thomas Rickmeyer, Thomas Fober, Gerhard Klebe:
Extraction of Protein Binding Pockets in Close Neighborhood of Bound Ligands Makes Comparisons Simple Due to Inherent Shape Similarity. 3229-3237 - Anders Poulsen, Harish Nagaraj, Angeline Lee, Stéphanie Blanchard, Chang Kai Soh, Dizhong Chen, Haishan Wang, Stefan Hart, Kee Chuan Goh, Brian Dymock, Meredith Williams:
Structure and Ligand-Based Design of mTOR and PI3-Kinase Inhibitors Leading to the Clinical Candidates VS-5584 (SB2343) and SB2602. 3238-3250
- Obaid Aftab, Mikael K. R. Engskog, Jakob Haglöf, Albert Elmsjö, Torbjörn Arvidsson, Curt Pettersson, Ulf Hammerling, Mats G. Gustafsson:
NMR Spectroscopy-Based Metabolic Profiling of Drug-Induced Changes In Vitro Can Discriminate between Pharmacological Classes. 3251-3258
Volume 54, Number 12, December 2014
- Yoshifumi Fukunishi, Takashi Kurosawa, Yoshiaki Mikami, Haruki Nakamura:
Prediction of Synthetic Accessibility Based on Commercially Available Compound Databases. 3259-3267 - Cerys Willoughby, Colin L. Bird, Simon J. Coles, Jeremy G. Frey:
Creating Context for the Experiment Record. User-Defined Metadata: Investigations into Metadata Usage in the LabTrove ELN. 3268-3283 - Antoine Daina, Olivier Michielin, Vincent Zoete:
iLOGP: A Simple, Robust, and Efficient Description of n-Octanol/Water Partition Coefficient for Drug Design Using the GB/SA Approach. 3284-3301 - Sonny Gan, David A. Cosgrove, Eleanor J. Gardiner, Valerie J. Gillet:
Investigation of the Use of Spectral Clustering for the Analysis of Molecular Data. 3302-3319 - Igor V. Tetko, Yurii Sushko, Sergii Novotarskyi, Luc Patiny, Ivan Kondratov, Alexander E. Petrenko, Larisa Charochkina, Abdullah M. Asiri:
How Accurately Can We Predict the Melting Points of Drug-like Compounds? 3320-3329
- Riccardo Concu, Martin Perez, M. Natália Dias Soeiro Cordeiro, Manuel Azenha:
Molecular Dynamics Simulations of Complex Mixtures Aimed at the Preparation of Naproxen-Imprinted Xerogels. 3330-3343 - Camilo Velez-Vega, Daniel J. J. McKay, Vibhas Aravamuthan, Robert Pearlstein, José S. Duca:
Time-Averaged Distributions of Solute and Solvent Motions: Exploring Proton Wires of GFP and PfM2DH. 3344-3361
- Umraan Hendricks, Werner Crous, Kevin J. Naidoo:
Computational Rationale for the Selective Inhibition of the Herpes Simplex Virus Type 1 Uracil-DNA Glycosylase Enzyme. 3362-3372 - Roberto Nuti, Marco Gargaro, Davide Matino, Daniela Dolciami, Ursula Grohmann, Paolo Puccetti, Francesca Fallarino, Antonio Macchiarulo:
Ligand Binding and Functional Selectivity of l-Tryptophan Metabolites at the Mouse Aryl Hydrocarbon Receptor (mAhR). 3373-3383 - Urska Zelenko, Milan Hodoscek, Damjana Rozman, Simona Golic Grdadolnik:
Structural Insight into the Unique Binding Properties of Pyridylethanol(phenylethyl)amine Inhibitor in Human CYP51. 3384-3395
- Ahmad Alzghoul, Amjad Alhalaweh, Denny Mahlin, Christel A. S. Bergström:
Experimental and Computational Prediction of Glass Transition Temperature of Drugs. 3396-3403 - Ann-Beth Nørholm, Pierre Francotte, Eric Goffin, Iuliana Botez, Laurence Danober, Pierre Lestage, Bernard Pirotte, Jette S. Kastrup, Lars Olsen, Chris Oostenbrink:
Thermodynamic Characterization of New Positive Allosteric Modulators Binding to the Glutamate Receptor A2 Ligand-Binding Domain: Combining Experimental and Computational Methods Unravels Differences in Driving Forces. 3404-3416
- Akhil Kumar, Costas D. Maranas:
CLCA: Maximum Common Molecular Substructure Queries within the MetRxn Database. 3417-3438 - Hamidreza Khataee, Alan Wee-Chung Liew:
Computational Modeling of Kinesin Stepping. 3439-3445
- Kyle I. Diller, David J. Diller:
VSViewer3D: A Tool for Interactive Data Mining of Three-Dimensional Virtual Screening Data. 3446-3452
- Matthias Dietzen, Elena Zotenko, Andreas Hildebrandt, Thomas Lengauer:
Correction to On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking. 3453
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