default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDJournal of Chemical Information and Modeling, Volume 52
Volume 52, Number 1, January 2012
- Edgar A. Gatica, Claudio N. Cavasotto
:
Ligand and Decoy Sets for Docking to G Protein-Coupled Receptors. 1-6
- Kuei-Jen Lee:
Molecular Dynamics Simulations of a Hyperthermophilic and a Mesophilic Protein L30e. 7-15 - Jui-Hua Hsieh, Shuangye Yin, Xiang S. Wang, Shubin Liu, Nikolay V. Dokholyan, Alexander Tropsha:
Cheminformatics Meets Molecular Mechanics: A Combined Application of Knowledge-Based Pose Scoring and Physical Force Field-Based Hit Scoring Functions Improves the Accuracy of Structure-Based Virtual Screening. 16-28 - S. Joshua Swamidass, Bradley T. Calhoun, Joshua A. Bittker, Nicole E. Bodycombe, Paul A. Clemons:
Utility-Aware Screening with Clique-Oriented Prioritization. 29-37 - Xia Ning, Michael A. Walters, George Karypis:
Improved Machine Learning Models for Predicting Selective Compounds. 38-50 - Roger A. Sayle, Paul Hongxing Xie, Sorel Muresan:
Improved Chemical Text Mining of Patents with Infinite Dictionaries and Automatic Spelling Correction. 51-62
- Jing Shi, Xiong-Yi Huang, Hua-Jing Wang, Yao Fu:
Hydride Dissociation Energies of Six-Membered Heterocyclic Organic Hydrides Predicted by ONIOM-G4Method. 63-75 - Wasinee Khuntawee, Thanyada Rungrotmongkol, Supot Hannongbua:
Molecular Dynamic Behavior and Binding Affinity of Flavonoid Analogues to the Cyclin Dependent Kinase 6/cyclin D Complex. 76-83 - Eric L. First, Chrysanthos E. Gounaris, Christodoulos A. Floudas:
Stereochemically Consistent Reaction Mapping and Identification of Multiple Reaction Mechanisms through Integer Linear Optimization. 84-92 - Sadhana Kumbhar, Frank D. Fischer, Mark P. Waller:
Assessment of Weak Intermolecular Interactions Across QM/MM Noncovalent Boundaries. 93-98 - Sebastian A. Andujar, Rodrigo D. Tosso, Fernando D. Suvire, Emilio Angelina, Nelida Peruchena, Nuria Cabedo, Diego Cortes, Ricardo D. Enriz:
Searching the "Biologically Relevant"Conformation of Dopamine: A Computational Approach. 99-112
- M. Victoria Ruiz-Pérez, Almudena Pino-Ángeles, Miguel Angel Medina, Francisca Sánchez-Jiménez, Aurelio A. Moya-García:
Structural Perspective on the Direct Inhibition Mechanism of EGCG on Mammalian Histidine Decarboxylase and DOPA Decarboxylase. 113-119 - Alexander Metz, Christopher Pfleger, Hannes Kopitz, Stefania Pfeiffer-Marek, Karl-Heinz Baringhaus, Holger Gohlke:
Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein-Protein Interface. 120-133
- Zoltán Simon, Ágnes Peragovics, Margit Vigh-Smeller, Gábor Csukly, László Tombor, Zhenhui Yang, Gergely Zahoránszky-Köhalmi, László Végner, Balázs Jelinek, Péter Hári, Csaba Hetényi, István Bitter, Pál Czobor, András Málnási-Csizmadia:
Drug Effect Prediction by Polypharmacology-Based Interaction Profiling. 134-145 - Kuei-Chung Shih, Chun-Yuan Lin, Hsiao-Chieh Chi, Chrong-Shiong Hwang, Ting-Shou Chen, Chuan Yi Tang, Naiwan Hsiao:
Design of Novel FLT-3 Inhibitors Based on Dual-Layer 3D-QSAR Model and Fragment-Based Compounds in Silico. 146-155 - Eric J. Martin, Prasenjit Mukherjee:
Kinase-Kernel Models: Accurate In silico Screening of 4 Million Compounds Across the Entire Human Kinome. 156-170 - Zhaomin Liu, A. Michael Crider, Daniel Ansbro, Christina Hayes, Maria Kontoyianni:
A Structure-Based Approach to Understanding Somatostatin Receptor-4 Agonism (sst4). 171-186 - Mengang Xu, Markus A. Lill:
Utilizing Experimental Data for Reducing Ensemble Size in Flexible-Protein Docking. 187-198 - David R. Hall, Chi-Ho Ngan, Brandon S. Zerbe, Dima Kozakov, Sandor Vajda:
Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery. 199-209 - Eric Therrien, Pablo Englebienne, Andrew G. Arrowsmith, Rodrigo Mendoza-Sanchez, Christopher R. Corbeil, Nathanael Weill, Valérie Campagna-Slater, Nicolas Moitessier:
Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery. 210-224 - Fredrik Svensson, Anders Karlén, Christian Sköld:
Virtual Screening Data Fusion Using Both Structure- and Ligand-Based Methods. 225-232 - Robert Kiss, Mark Sandor, Anikó Gere, Éva Schmidt, György Balogh, Béla Kiss, László Molnár, Christian Lemmen, György M. Keserü:
Discovery of Novel Histamine H4 and Serotonin Transporter Ligands Using the Topological Feature Tree Descriptor. 233-242 - Varnavas D. Mouchlis, Vasiliki Michopoulou, Violetta Constantinou-Kokotou, Thomas M. Mavromoustakos, Edward A. Dennis, George Kokotos:
Binding Conformation of 2-Oxoamide Inhibitors to Group IVA Cytosolic Phospholipase A2 Determined by Molecular Docking Combined with Molecular Dynamics. 243-254
- Márton Münz, Philip C. Biggin:
JGromacs: A Java Package for Analyzing Protein Simulations. 255-259 - Vladimir V. Diky, Robert D. Chirico, Chris Muzny, Andrei F. Kazakov, Kenneth Kroenlein, Joseph W. Magee, Ilmutdin M. Abdulagatov, Jeong Won Kang, Michael Frenkel:
ThermoData Engine (TDE) Software Implementation of the Dynamic Data Evaluation Concept. 7. Ternary Mixtures. 260-276
Volume 52, Number 2, February 2012
Editorial
- Wendy A. Warr:
Ninth International Conference on Chemical Structures, June 5-9, 2011, Noordwijkerhout, The Netherlands. 277
- Man-Ling Lee, Ignacio Aliagas, Jennafer Dotson, Jianwen A. Feng, Alberto Gobbi, Timothy Heffron:
DEGAS: Sharing and Tracking Target Compound Ideas with External Collaborators. 278-284 - Alberto Gobbi, Man-Ling Lee:
Handling of Tautomerism and Stereochemistry in Compound Registration. 285-292 - Felix Rudolphi, Lukas J. Goossen:
Electronic Laboratory Notebook: The Academic Point of View. 293-301 - Paolo Tosco, Thomas Balle:
A 3D-QSAR-Driven Approach to Binding Mode and Affinity Prediction. 302-307 - Richard L. Martin, Berend Smit, Maciej Haranczyk:
Addressing Challenges of Identifying Geometrically Diverse Sets of Crystalline Porous Materials. 308-318 - Pekka Tiikkainen, Lutz Franke:
Analysis of Commercial and Public Bioactivity Databases. 319-326 - Lionel Colliandre, Vincent Le Guilloux, Stéphane Bourg, Luc Morin-Allory:
Visual Characterization and Diversity Quantification of Chemical Libraries: 2. Analysis and Selection of Size-Independent, Subspace-Specific Diversity Indices. 327-342 - David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koca:
SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. 343-359 - Andrea Volkamer, Daniel Kuhn, Thomas Grombacher, Friedrich Rippmann, Matthias Rarey:
Combining Global and Local Measures for Structure-Based Druggability Predictions. 360-372 - Uta F. Lessel, Bernd Wellenzohn, J. Robert Fischer, Matthias Rarey:
Design of Combinatorial Libraries for the Exploration of Virtual Hits from Fragment Space Searches with LoFT. 373-379
- Modest von Korff, Joël Freyss, Thomas Sander, Christoph Boss, Claire-Lise Ciana:
Fighting High Molecular Weight in Bioactive Molecules with Sub-Pharmacophore-Based Virtual Screening. 380-390
- Jennifer A. Bayron, Amy M. Deveau, John M. Stubbs:
Conformational Analysis of 6α- and 6β-Naltrexol and Derivatives and Relationship to Opioid Receptor Affinity. 391-395
- Kunal Roy, Indrani Mitra, Supratik Kar, Probir Kumar Ojha, Rudra Narayan Das, Humayun Kabir:
Comparative Studies on Some Metrics for External Validation of QSPR Models. 396-408
- Jacob Poehlsgaard, Kasper Harpsøe, Flemming Steen Jørgensen, Lars Olsen:
A Robust Force Field Based Method for Calculating Conformational Energies of Charged Drug-Like Molecules. 409-419 - Jogoth Ali, Patrick Camilleri, Marc B. Brown, Andrew J. Hutt, Stewart B. Kirton:
Revisiting the General Solubility Equation: In Silico Prediction of Aqueous Solubility Incorporating the Effect of Topographical Polar Surface Area. 420-428 - Jana Sopkova-de Oliveira Santos, Anne Sophie Voisin-Chiret, Gregory Burzicki, Laure Sebaoun, Muriel Sebban, Jean-François Lohier, Rémi Legay, Hassan Oulyadi, Ronan Bureau, Sylvain Rault:
Structural Characterizations of Oligopyridyl Foldamers, α-Helix Mimetics. 429-439 - Se-Han Lee, Kwang-Hwi Cho, William E. Acree Jr., Kyoung Tai No:
Development of Surface-SFED Models for Polar Solvents. 440-448
- Jianzhuang Yao, Yuzhuo Chu, Ran An, Hong Guo:
Understanding Product Specificity of Protein Lysine Methyltransferases from QM/MM Molecular Dynamics and Free Energy Simulations: The Effects of Mutation on SET7/9 beyond the Tyr/Phe Switch. 449-456 - Johanna Jyrkkärinne, Jenni Küblbeck, Juha Pulkkinen, Paavo Honkakoski, Reino Laatikainen, Antti Poso, Tuomo Laitinen:
Molecular Dynamics Simulations for Human CAR Inverse Agonists. 457-464 - Diana Lousa, António M. Baptista, Cláudio M. Soares:
Analyzing the Molecular Basis of Enzyme Stability in Ethanol/Water Mixtures Using Molecular Dynamics Simulations. 465-473 - Luisa Di Paola, Paola Paci, Daniele Santoni, Micol De Ruvo, Alessandro Giuliani:
Proteins as Sponges: A Statistical Journey along Protein Structure Organization Principles. 474-482 - Matteo Chioccioli, Simone Marsili, Claudia Bonaccini, Piero Procacci, Paola Gratteri:
Insights into the Conformational Switching Mechanism of the Human Vascular Endothelial Growth Factor Receptor Type 2 Kinase Domain. 483-491
- Mohamed Diwan M. AbdulHameed, Sidhartha Chaudhury, Narender Singh, Hongmao Sun, Anders Wallqvist, Gregory J. Tawa:
Exploring Polypharmacology Using a ROCS-Based Target Fishing Approach. 492-505 - Ying-Ting Lin, Guan-Yu Chen:
A Scaffold-Independent Subcellular Event-Based Analysis: Characterization of Significant Structural Modifications. 506-514 - Horrick Sharma, Xiaolin Cheng, John K. Buolamwini:
Homology Model-Guided 3D-QSAR Studies of HIV-1 Integrase Inhibitors. 515-544
- Francesco Bettella, Dawid Rasinski, Ernst-Walter Knapp:
Protein Secondary Structure Prediction with SPARROW. 545-556 - Satoshi Yamasaki, Shugo Nakamura, Kazuhiko Fukui:
Prospects for Tertiary Structure Prediction of RNA Based on Secondary Structure Information. 557-567 - Valère Lounnas, Gert Vriend:
AsteriX: A Web Server To Automatically Extract Ligand Coordinates from Figures in PDF Articles. 568-576 - Michael Binns, Sam P. de Visser, Constantinos Theodoropoulos:
Modeling Flexible Pharmacophores with Distance Geometry, Scoring, and Bound Stretching. 577-588 - Subha Kalyaanamoorthy, Yi-Ping Phoebe Chen:
Exploring Inhibitor Release Pathways in Histone Deacetylases Using Random Acceleration Molecular Dynamics Simulations. 589-603 - Janez Konc, Tomo Cesnik, Joanna Trykowska Konc, Matej Penca, Dusanka Janezic:
ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of PDB Structures. 604-612
- Matthew C. Swain:
chemicalize.org. 613-615
Volume 52, Number 3, March 2012
- Johannes Kirchmair, Mark J. Williamson, Jonathan D. Tyzack, Lu Tan, Peter J. Bond, Andreas Bender, Robert C. Glen:
Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms. 617-648
- Stefano Alcaro, Adriana Bolasco, Roberto Cirilli, Rosella Ferretti, Rossella Fioravanti, Francesco Ortuso:
Computer-Aided Molecular Design of Asymmetric Pyrazole Derivatives with Exceptional Enantioselective Recognition toward the Chiralcel OJ-H Stationary Phase. 649-654
- Feixiong Cheng, Yutaka Ikenaga, Yadi Zhou, Yue Yu, Weihua Li, Jie Shen, Zheng Du, Lei Chen, Congying Xu, Guixia Liu, Philip W. Lee, Yun Tang:
In Silico Assessment of Chemical Biodegradability. 655-669 - Ye Hu, Jürgen Bajorath:
Exploration of 3D Activity Cliffs on the Basis of Compound Binding Modes and Comparison of 2D and 3D Cliffs. 670-677
- Tammy Biniashvili, Ehud Schreiber, Yossef Kliger:
Improving Classical Substructure-Based Virtual Screening to Handle Extrapolation Challenges. 678-685 - Ya-Wen Hsiao, Carl Petersson, Mats Svensson, Ulf Norinder:
A Pragmatic Approach Using First-Principle Methods to Address Site of Metabolism with Implications for Reactive Metabolite Formation. 686-695 - Falgun Shah, Jiri Gut, Jennifer Legac, Devleena Shivakumar, Woody Sherman, Philip J. Rosenthal, Mitchell A. Avery:
Computer-Aided Drug Design of Falcipain Inhibitors: Virtual Screening, Structure-Activity Relationships, Hydration Site Thermodynamics, and Reactivity Analysis. 696-710 - Varnavas D. Mouchlis, Georgia Melagraki, Thomas M. Mavromoustakos, George Kollias, Antreas Afantitis:
Molecular Modeling on Pyrimidine-Urea Inhibitors of TNF-α Production: An Integrated Approach Using a Combination of Molecular Docking, Classification Techniques, and 3D-QSAR CoMSIA. 711-723 - Miklos Feher, Christopher I. Williams:
Numerical Errors and Chaotic Behavior in Docking Simulations. 724-738
- Markus Sitzmann, Iwona E. Weidlich, Igor V. Filippov, Chenzhong Liao, Megan L. Peach, Wolf-Dietrich Ihlenfeldt, Rajeshri G. Karki, Yulia V. Borodina, Raul E. Cachau, Marc C. Nicklaus:
PDB Ligand Conformational Energies Calculated Quantum-Mechanically. 739-756
- Richard L. Martin, Eleanor J. Gardiner, Stefan Senger, Valerie J. Gillet:
Compression of Molecular Interaction Fields Using Wavelet Thumbnails: Application to Molecular Alignment. 757-769 - Karim M. ElSawy, Reidun Twarock, Chandra S. Verma, Leo S. D. Caves:
Peptide Inhibitors of Viral Assembly: A Novel Route to Broad-Spectrum Antivirals. 770-776 - Prashant Khare, Amit K. Gupta, Praveen K. Gajula, Krishna Y. Sunkari, Anil K. Jaiswal, Sanchita Das, Preeti Bajpai, Tushar K. Chakraborty, Anuradha Dube, Anil K. Saxena:
Identification of Novel S-Adenosyl-l-Homocysteine Hydrolase Inhibitors through Homology-Model-Based Virtual Screening, Synthesis, and Biological Evaluation. 777-791 - Bin Chen, Robert P. Sheridan, Viktor Hornak, Johannes H. Voigt:
Comparison of Random Forest and Pipeline Pilot Naïve Bayes in Prospective QSAR Predictions. 792-803 - Vojtech Spiwok, Katarína Hlat-Glembová, Igor Tvaroska, Blanka Králová:
Conformational Free Energy Modeling of Druglike Molecules by Metadynamics in the WHIM Space. 804-813 - Robert P. Sheridan:
Three Useful Dimensions for Domain Applicability in QSAR Models Using Random Forest. 814-823
- Maria Kontoyianni, Christopher B. Rosnick:
Functional Prediction of Binding Pockets. 824-833 - Hong Kang, Zhen Sheng, Ruixin Zhu, Qi Huang, Qi Liu, Zhiwei Cao:
Virtual Drug Screen Schema Based on Multiview Similarity Integration and Ranking Aggregation. 834-843 - Matthias Dietzen, Elena Zotenko, Andreas Hildebrandt, Thomas Lengauer:
On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking. 844-856 - Frank H. Allen, Colin R. Groom, John W. Liebeschuetz, David A. Bardwell, Tjelvar S. G. Olsson, Peter A. Wood:
The Hydrogen Bond Environments of 1H-Tetrazole and Tetrazolate Rings: The Structural Basis for Tetrazole-Carboxylic Acid Bioisosterism. 857-866
Volume 52, Number 4, April 2012
- Thomas Scior, Andreas Bender, Gary Tresadern, José L. Medina-Franco, Karina Martínez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras, Dimitris K. Agrafiotis:
Recognizing Pitfalls in Virtual Screening: A Critical Review. 867-881
- Cristiano R. W. Guimarães, Alan M. Mathiowetz, Marina Shalaeva, Gilles Goetz, Spiros Liras:
Use of 3D Properties to Characterize Beyond Rule-of-5 Property Space for Passive Permeation. 882-890
- Ramzi Nasr, Rares Vernica, Chen Li, Pierre Baldi:
Speeding Up Chemical Searches Using the Inverted Index: The Convergence of Chemoinformatics and Text Search Methods. 891-900 - Satoshi Niijima, Akira Shiraishi, Yasushi Okuno:
Dissecting Kinase Profiling Data to Predict Activity and Understand Cross-Reactivity of Kinase Inhibitors. 901-912 - Jianwei Che, Frederick J. King, Bin Zhou, Yingyao Zhou:
Chemical and Biological Properties of Frequent Screening Hits. 913-926 - Vigneshwaran Namasivayam, Jürgen Bajorath:
Searching for Coordinated Activity Cliffs Using Particle Swarm Optimization. 927-934 - Disha Gupta-Ostermann, Mathias Wawer, Anne Mai Wassermann, Jürgen Bajorath:
Graph Mining for SAR Transfer Series. 935-942 - Jamel Meslamani, Jiabo Li, Jon M. Sutter, Adrian Stevens, Hugues-Olivier Bertrand, Didier Rognan:
Protein-Ligand-Based Pharmacophores: Generation and Utility Assessment in Computational Ligand Profiling. 943-955
- Simon J. Cottrell, Tjelvar S. G. Olsson, Robin Taylor, Jason C. Cole, John W. Liebeschuetz:
Validating and Understanding Ring Conformations Using Small Molecule Crystallographic Data. 956-962 - Adel Hamza, Ning-Ning Wei, Chang-Guo Zhan:
Ligand-Based Virtual Screening Approach Using a New Scoring Function. 963-974 - Stefan Brandmaier, Ullrika Sahlin, Igor V. Tetko, Tomas Öberg:
PLS-Optimal: A Stepwise D-Optimal Design Based on Latent Variables. 975-983 - Jong Young Joung, Ky-Youb Nam, Kwang-Hwi Cho, Kyoung Tai No:
Ligand Aligning Method for Molecular Docking: Alignment of Property-Weighted Vectors. 984-995 - Qishi Du, Jing Gao, Yu-Tuo Wei, Li-Qin Du, Shu-Qing Wang, Ri-Bo Huang:
Structure-Based and Multiple Potential Three-Dimensional Quantitative Structure-Activity Relationship (SB-MP-3D-QSAR) for Inhibitor Design. 996-1004
- Zhiwei Feng, Tingjun Hou, Youyong Li:
Studies on the Interactions between β2 Adrenergic Receptor and Gs Protein by Molecular Dynamics Simulations. 1005-1014
- Tomohiro Sato, Hitomi Yuki, Daisuke Takaya, Shunta Sasaki, Akiko Tanaka, Teruki Honma:
Application of Support Vector Machine to Three-Dimensional Shape-Based Virtual Screening Using Comprehensive Three-Dimensional Molecular Shape Overlay with Known Inhibitors. 1015-1026 - Emanuele Perola, Lee Herman, Jonathan Weiss:
Development of a Rule-Based Method for the Assessment of Protein Druggability. 1027-1038 - György G. Ferenczy, György M. Keserü:
Thermodynamics of Fragment Binding. 1039-1045 - Bingjie Hu, Markus A. Lill:
Protein Pharmacophore Selection Using Hydration-Site Analysis. 1046-1060 - Ahmed M. El Kerdawy, Christian R. Wick, Matthias Hennemann, Timothy Clark:
Predicting the Sites and Energies of Noncovalent Intermolecular Interactions Using Local Properties. 1061-1071
- Jonas Feldt, Ricardo A. Mata, Johannes M. Dieterich:
Atomdroid: A Computational Chemistry Tool for Mobile Platforms. 1072-1078
Volume 52, Number 5, May 2012
- Puneet Kacker, Matteo Masetti, Martina Mangold, Giovanni Bottegoni, Andrea Cavalli:
Combining Dyad Protonation and Active Site Plasticity in BACE-1 Structure-Based Drug Design. 1079-1085
- Obdulia Rabal, Julen Oyarzabal:
Using Novel Descriptor Accounting for Ligand-Receptor Interactions To Define and Visually Explore Biologically Relevant Chemical Space. 1086-1102 - Guoping Hu, Guanglin Kuang, Wen Xiao, Weihua Li, Guixia Liu, Yun Tang:
Performance Evaluation of 2D Fingerprint and 3D Shape Similarity Methods in Virtual Screening. 1103-1113 - Meihua Tu, Brajesh K. Rai, Alan M. Mathiowetz, Mary Didiuk, Jeffrey A. Pfefferkorn, Angel Guzman-Perez, John Benbow, Cristiano R. W. Guimarães, Scot Mente, Matthew M. Hayward, Spiros Liras:
Exploring Aromatic Chemical Space with NEAT: Novel and Electronically Equivalent Aromatic Template. 1114-1123 - Edward O. Cannon:
New Benchmark for Chemical Nomenclature Software. 1124-1131 - Dongyue Cao, Junmei Wang, Rui Zhou, Youyong Li, Huidong Yu, Tingjun Hou:
ADMET Evaluation in Drug Discovery. 11. PharmacoKinetics Knowledge Base (PKKB): A Comprehensive Database of Pharmacokinetic and Toxic Properties for Drugs. 1132-1137 - Xiaoying Hu, Ye Hu, Martin Vogt, Dagmar Stumpfe, Jürgen Bajorath:
MMP-Cliffs: Systematic Identification of Activity Cliffs on the Basis of Matched Molecular Pairs. 1138-1145
- Jean-Paul Ebejer, Garrett M. Morris, Charlotte M. Deane:
Freely Available Conformer Generation Methods: How Good Are They? 1146-1158 - Frederico Pratas, Leonel Sousa, Johannes M. Dieterich, Ricardo A. Mata:
Computation of Induced Dipoles in Molecular Mechanics Simulations Using Graphics Processors. 1159-1166 - Markus Hartenfeller, Martin Eberle, Peter Meier, Cristina Nieto-Oberhuber, Karl-Heinz Altmann, Gisbert Schneider, Edgar Jacoby, Steffen Renner:
Probing the Bioactivity-Relevant Chemical Space of Robust Reactions and Common Molecular Building Blocks. 1167-1178 - Jarmila Husby, Alan K. Todd, Shozeb M. Haider, Giovanna Zinzalla, David E. Thurston, Stephen Neidle:
Molecular Dynamics Studies of the STAT3 Homodimer: DNA Complex: Relationships between STAT3 Mutations and Protein-DNA Recognition. 1179-1192 - Nina Sadlej-Sosnowska, Aleksander P. Mazurek:
Electron Density Distribution in Endohedral Complexes of Fullerene C60, Calculated Based on the Gauss Law. 1193-1198 - Junmei Wang, Tingjun Hou:
Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations. 1199-1212 - Gerald Zapata-Torres, Angelica Fierro, Sebastian Miranda-Rojas, Carlos Guajardo, Patricio Saez-Briones, J. Cristian Salgado, Cristian Celis-Barros:
Influence of Protonation on Substrate and Inhibitor Interactions at the Active Site of Human Monoamine Oxidase-A. 1213-1221 - L. Mark Hall, Lowell H. Hall, Tzipporah M. Kertesz, Dennis W. Hill, Thomas R. Sharp, Edward Z. Oblak, Ying W. Dong, David S. Wishart, Ming-Hui Chen, David F. Grant:
Development of Ecom50 and Retention Index Models for Nontargeted Metabolomics: Identification of 1, 3-Dicyclohexylurea in Human Serum by HPLC/Mass Spectrometry. 1222-1237
- Anna Edberg, Daniel Soeria-Atmadja, Jonas Laurila Bergman, Fredrik Johansson, Mats G. Gustafsson, Ulf Hammerling:
Assessing Relative Bioactivity of Chemical Substances Using Quantitative Molecular Network Topology Analysis. 1238-1249 - Sushil Kumar Mishra, Jan Adam, Michaela Wimmerová, Jaroslav Koca:
In Silico Mutagenesis and Docking Study of Ralstonia solanacearum RSL Lectin: Performance of Docking Software To Predict Saccharide Binding. 1250-1261 - Oliver Korb, Tjelvar S. G. Olsson, Simon Bowden, Richard J. Hall, Marcel L. Verdonk, John W. Liebeschuetz, Jason C. Cole:
Potential and Limitations of Ensemble Docking. 1262-1274 - Arghya Barman, Rajeev Prabhakar:
Protonation States of the Catalytic Dyad of β-Secretase (BACE1) in the Presence of Chemically Diverse Inhibitors: A Molecular Docking Study. 1275-1287 - Sai Lakshmana Vankayala, Jacqueline C. Hargis, H. Lee Woodcock III:
Unlocking the Binding and Reaction Mechanism of Hydroxyurea Substrates as Biological Nitric Oxide Donors. 1288-1297 - Hector Figueroa, Durgaprasad Peddi, Joshua M. Osborne, Brenan M. Wilson, Ranadheer Reddy Pesaru, Balakrishna Kurva, Swathi Ramaraju, Maria C. Milletti, Deborah L. Heyl:
Modeling the Interface between Islet Amyloid Polypeptide and Insulin-Based Aggregation Inhibitors: Correlation to Aggregation Kinetics and Membrane Damage. 1298-1307 - Özlem Demir, Rommie E. Amaro:
Elements of Nucleotide Specificity in the Trypanosoma brucei Mitochondrial RNA Editing Enzyme RET2. 1308-1318
- Alessandra Nurisso, Juan Bravo, Pierre-Alain Carrupt, Antoine Daina:
Molecular Docking Using the Molecular Lipophilicity Potential as Hydrophobic Descriptor: Impact on GOLD Docking Performance. 1319-1327 - Matthew A. Lardy, Laurie LeBrun, Drew Bullard, Charles Kissinger, Alberto Gobbi:
Building a Three-Dimensional Model of CYP2C9 Inhibition Using the Autocorrelator: An Autonomous Model Generator. 1328-1336 - María Gálvez-Llompart, Jorge Gálvez, Ramón García-Domenech, Lemont B. Kier:
Modeling Drug-Induced Anorexia by Molecular Topology. 1337-1344 - Kiran Mahasenan, Chenglong Li:
Novel Inhibitor Discovery through Virtual Screening against Multiple Protein Conformations Generated via Ligand-Directed Modeling: A Maternal Embryonic Leucine Zipper Kinase Example. 1345-1355 - Dane Huang, Qiong Gu, Hu Ge, Jiming Ye, Noeris K. Salam, Arnold T. Hagler, Hongzhuan Chen, Jun Xu:
On the Value of Homology Models for Virtual Screening: Discovering hCXCR3 Antagonists by Pharmacophore-Based and Structure-Based Approaches. 1356-1366 - Fung-Yi Chan, Marco A. C. Neves, Ning Sun, Man-Wah Tsang, Yun-Chung Leung, Tak-Hang Chan, Ruben Abagyan, Kwok-Yin Wong:
Validation of the AmpC β-Lactamase Binding Site and Identification of Inhibitors with Novel Scaffolds. 1367-1375 - Amit K. Gupta, Kanika Varshney, Anil K. Saxena:
Toward the Identification of a Reliable 3D QSAR Pharmacophore Model for the CCK2 Receptor Antagonism. 1376-1390 - Susanne von Grafenstein, Judit Mihaly-Bison, Gerhard Wolber, Valery N. Bochkov, Klaus R. Liedl, Daniela Schuster:
Identification of Novel Liver X Receptor Activators by Structure-Based Modeling. 1391-1400
- Praveen K. Madala, David P. Fairlie, Mikael Bodén:
Matching Cavities in G Protein-Coupled Receptors to Infer Ligand-Binding Sites. 1401-1410
- Xia Ning, Michael A. Walters, George Karypis:
Improved Machine Learning Models for Predicting Selective Compounds. 1411
Volume 52, Number 6, June 2012
- Alexandre Varnek, Igor I. Baskin:
Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis? 1413-1437
- Eric J. Baede, Ernest den Bekker, Jan-Willem Boiten, Deborah Cronin, Rob van Gammeren, Jacob de Vlieg:
Integrated Project Views: Decision Support Platform for Drug Discovery Project Teams. 1438-1449 - Martin Weisel, Hans-Marcus Bitter, François Diederich, W. Venus So, Rama Kondru:
PROLIX: Rapid Mining of Protein-Ligand Interactions in Large Crystal Structure Databases. 1450-1461 - Michal Jamróz, Joanna E. Rode, Slawomir Ostrowski, Piotr Lipinski, Jan Cz. Dobrowolski:
Chirality Measures of α-Amino Acids. 1462-1479 - Christian Tyrchan, Jonas Boström, Fabrizio Giordanetto, Jon Winter, Sorel Muresan:
Exploiting Structural Information in Patent Specifications for Key Compound Prediction. 1480-1489 - Ye Hu, Norbert Furtmann, Michael Gütschow, Jürgen Bajorath:
Systematic Identification and Classification of Three-Dimensional Activity Cliffs. 1490-1498
- Tanja Schulz-Gasch, Christin Schärfer, Wolfgang Guba, Matthias Rarey:
TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations. 1499-1512 - Plamen N. Penchev, Klaus-Peter Schulz, Morton E. Munk:
INFERCNMR: A 13C NMR Interpretive Library Search System. 1513-1528
- Maria Safi, Ryan H. Lilien:
Efficient a Priori Identification of Drug Resistant Mutations Using Dead-End Elimination and MM-PBSA. 1529-1541 - Georgios Leonis, Zaneta Czyznikowska, Grigorios Megariotis, Heribert Reis, Manthos G. Papadopoulos:
Computational Studies of Darunavir into HIV-1 Protease and DMPC Bilayer: Necessary Conditions for Effective Binding and the Role of the Flaps. 1542-1558 - Xiao Zhu, Pedro E. M. Lopes, Jihyun Shim, Alexander D. MacKerell Jr.:
Intrinsic Energy Landscapes of Amino Acid Side-Chains. 1559-1572 - Urban Bren, Chris Oostenbrink:
Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations. 1573-1582 - Antonija Tomic, Miguel González, Sanja Tomic:
The Large Scale Conformational Change of the Human DPP III-Substrate Prefers the "Closed" Form. 1583-1594 - Jacopo Sgrignani, Alessandra Magistrato:
Influence of the Membrane Lipophilic Environment on the Structure and on the Substrate Access/Egress Routes of the Human Aromatase Enzyme. A Computational Study. 1595-1606
- Marijn P. A. Sanders, Arménio Jorge Moura Barbosa, Barbara Zarzycka, Gerry A. F. Nicolaes, Jan P. G. Klomp, Jacob de Vlieg, Alberto Del Rio:
Comparative Analysis of Pharmacophore Screening Tools. 1607-1620 - Siegfried S. F. Leung, Jona Mijalkovic, Kenneth W. Borrelli, Matthew P. Jacobson:
Testing Physical Models of Passive Membrane Permeation. 1621-1636 - Jed Zaretzki, Patrik Rydberg, Charles Bergeron, Kristin P. Bennett, Lars Olsen, Curt M. Breneman:
RS-Predictor Models Augmented with SMARTCyp Reactivities: Robust Metabolic Regioselectivity Predictions for Nine CYP Isozymes. 1637-1659 - Bo-Han Su, Yi-shu Tu, Emilio Xavier Esposito, Yufeng J. Tseng:
Predictive Toxicology Modeling: Protocols for Exploring hERG Classification and Tetrahymena pyriformis End Point Predictions. 1660-1673 - Flavio Ballante, Rino Ragno:
3-D QSAutogrid/R: An Alternative Procedure To Build 3-D QSAR Models. Methodologies and Applications. 1674-1685 - Ines Filipa Martins, Ana L. Teixeira, Luis Pinheiro, André O. Falcão:
A Bayesian Approach to in Silico Blood-Brain Barrier Penetration Modeling. 1686-1697 - Ruifeng Liu, Jin Liu, Gregory J. Tawa, Anders Wallqvist:
2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes. 1698-1712
Volume 52, Number 7, July 2012
- Eelke van der Horst, Patricia Marqués-Gallego, Thea Mulder-Krieger, Jacobus van Veldhoven, Johannes W. Kruisselbrink, Alexander Aleman, Michael T. M. Emmerich, Johannes Brussee, Andreas Bender, Adriaan P. IJzerman:
Multi-Objective Evolutionary Design of Adenosine Receptor Ligands. 1713-1721 - Eduardo B. de Melo, Márcia M. C. Ferreira:
Four-Dimensional Structure-Activity Relationship Model to Predict HIV-1 Integrase Strand Transfer Inhibition using LQTA-QSAR Methodology. 1722-1732 - Ágnes Peragovics, Zoltán Simon, Ildikó Brandhuber, Balázs Jelinek, Péter Hári, Csaba Hetényi, Pál Czobor, András Málnási-Csizmadia:
Contribution of 2D and 3D Structural Features of Drug Molecules in the Prediction of Drug Profile Matching. 1733-1744 - Clara D. Christ, Matthias Zentgraf, Jan M. Kriegl:
Mining Electronic Laboratory Notebooks: Analysis, Retrosynthesis, and Reaction Based Enumeration. 1745-1756 - John J. Irwin, Teague Sterling, Michael M. Mysinger, Erin S. Bolstad, Ryan G. Coleman:
ZINC: A Free Tool to Discover Chemistry for Biology. 1757-1768 - Anne Mai Wassermann, Peter Haebel, Nils Weskamp, Jürgen Bajorath:
SAR Matrices: Automated Extraction of Information-Rich SAR Tables from Large Compound Data Sets. 1769-1776 - Mikko J. Vainio, Thierry Kogej, Florian Raubacher:
Automated Recycling of Chemistry for Virtual Screening and Library Design. 1777-1786 - Shawn Martin:
Lattice Enumeration for Inverse Molecular Design Using the Signature Descriptor. 1787-1797 - Hongmao Sun, Sampada Shahane, Menghang Xia, Christopher P. Austin, Ruili Huang:
Structure Based Model for the Prediction of Phospholipidosis Induction Potential of Small Molecules. 1798-1805 - Ye Hu, Jürgen Bajorath:
Extending the Activity Cliff Concept: Structural Categorization of Activity Cliffs and Systematic Identification of Different Types of Cliffs in the ChEMBL Database. 1806-1811
- Chang Sun Kong, Wei Luo, Sergiu Arapan, Pierre Villars, Shuichi Iwata, Rajeev Ahuja, Krishna Rajan:
Information-Theoretic Approach for the Discovery of Design Rules for Crystal Chemistry. 1812-1820 - Hui Sun Lee, Sunhwan Jo, Hyun-Suk Lim, Wonpil Im:
Application of Binding Free Energy Calculations to Prediction of Binding Modes and Affinities of MDM2 and MDMX Inhibitors. 1821-1832 - Ding Li, Jie Gui, Yongjian Li, Lingling Feng, Xinya Han, Yao Sun, Tinglin Sun, Zhigang Chen, Yi Cao, Yang Zhang, Li Zhou, Xiaopeng Hu, Yanliang Ren, Jian Wan:
Structure-Based Design and Screen of Novel Inhibitors for Class II 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase from Streptococcus Pneumoniae. 1833-1841
- James A. R. Dalton, Ori Kalid, Maya Schushan, Nir Ben-Tal, Jordi Villà-Freixa:
New Model of Cystic Fibrosis Transmembrane Conductance Regulator Proposes Active Channel-like Conformation. 1842-1853 - Svetoslav H. Slavov, Elizabeth L. Geesaman, Bruce A. Pearce, Laura K. Schnackenberg, Dan A. Buzatu, Jon G. Wilkes, Richard D. Beger:
13C NMR-Distance Matrix Descriptors: Optimal Abstract 3D Space Granularity for Predicting Estrogen Binding. 1854-1864 - Marco Pasi, Matteo Tiberti, Alberto Arrigoni, Elena Papaleo:
xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures. 1865-1874 - Jun Tan, Ravinder Abrol, Bartosz Trzaskowski, William A. Goddard III:
3D Structure Prediction of TAS2R38 Bitter Receptors Bound to Agonists Phenylthiocarbamide (PTC) and 6-n-Propylthiouracil (PROP). 1875-1885
- Ting-Lan Chiu, Elizabeth A. Amin:
Development of a Comprehensive, Validated Pharmacophore Hypothesis for Anthrax Toxin Lethal Factor (LF) Inhibitors Using Genetic Algorithms, Pareto Scoring, and Structural Biology. 1886-1897
- Eugene E. Kwan:
ACD/Spectrus Processor Review. 1898-1900
Volume 52, Number 8, August 2012
- Nick Spadaccini, Sydney R. Hall:
Extensions to the STAR File Syntax. 1901-1906 - Nick Spadaccini, Sydney R. Hall:
DDLm: A New Dictionary Definition Language. 1907-1916 - Nick Spadaccini, Ian R. Castleden, Douglas du Boulay, Sydney R. Hall:
dREL: A Relational Expression Language for Dictionary Methods. 1917-1925 - David Tai, Jianwen Fang:
SymDex: Increasing the Efficiency of Chemical Fingerprint Similarity Searches for Comparing Large Chemical Libraries by Using Query Set Indexing. 1926-1935 - David A. Cosgrove, Keith M. Green, Andrew Leach, Andrew R. Poirrette, Jon Winter:
A System for Encoding and Searching Markush Structures. 1936-1947 - Violeta I. Pérez-Nueno, Vishwesh Venkatraman, Lazaros Mavridis, David W. Ritchie:
Detecting Drug Promiscuity Using Gaussian Ensemble Screening. 1948-1961 - Preeti Iyer, Dilyana Dimova, Martin Vogt, Jürgen Bajorath:
Navigating High-Dimensional Activity Landscapes: Design and Application of the Ligand-Target Differentiation Map. 1962-1969 - Paulo J. Mendes, Tiago J. L. Silva, M. Helena Garcia, J. P. Prates Ramalho, A. J. Palace Carvalho:
Switchable Nonlinear Optical Properties of η5-Monocyclopentadienylmetal Complexes: A DFT Approach. 1970-1983 - Manuel Hechinger, Kai Leonhard, Wolfgang Marquardt:
What is Wrong with Quantitative Structure-Property Relations Models Based on Three-Dimensional Descriptors? 1984-1993 - Yong Wang, Jing Lu, Fei Wang, Qiancheng Shen, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, Hualiang Jiang, Kaixian Chen:
Estimation of Carcinogenicity Using Molecular Fragments Tree. 1994-2003
- Sarath Kumar Baskaran, Nabajyoti Goswami, Sudhagar Selvaraj, Velusamy Shanmuganathan Muthusamy, Baddireddi Subhadra Lakshmi:
Molecular Dynamics Approach to Probe the Allosteric Inhibition of PTP1B by Chlorogenic and Cichoric Acid. 2004-2012 - Adrian Kolodzik, Sascha Urbaczek, Matthias Rarey:
Unique Ring Families: A Chemically Meaningful Description of Molecular Ring Topologies. 2013-2021 - Thomas Klabunde, Clemens Giegerich, Andreas Evers:
MARS: Computing Three-Dimensional Alignments for Multiple Ligands Using Pairwise Similarities. 2022-2030 - David J. Wood, Jacob de Vlieg, Markus Wagener, Tina Ritschel:
Pharmacophore Fingerprint-Based Approach to Binding Site Subpocket Similarity and Its Application to Bioisostere Replacement. 2031-2043 - Nicola Chirico, Paola Gramatica:
Real External Predictivity of QSAR Models. Part 2. New Intercomparable Thresholds for Different Validation Criteria and the Need for Scatter Plot Inspection. 2044-2058 - Megumi Ikemori-Kawada, Atsushi Inoue, Masaki Goto, Yuan John Wang, Yoshiyuki Kawakami:
Docking Simulation Study and Kinase Selectivity of f152A1 and Its Analogs. 2059-2068 - Giuliano Berellini, Nigel J. Waters, Franco Lombardo:
In silico Prediction of Total Human Plasma Clearance. 2069-2078 - Samuel Genheden, Oliver Kuhn, Paulius Mikulskis, Daniel Hoffmann, Ulf Ryde:
The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant. 2079-2088
- Alexey Ishchenko, Zhijie Liu, Peter Lindblom, Guosheng Wu, Kam-Chuen Jim, Richard D. Gregg, David A. Claremon, Suresh B. Singh:
Structure-Based Design Technology Contour and Its Application to the Design of Renin Inhibitors. 2089-2097 - Richard D. Smith, Alaina L. Engdahl, James B. Dunbar Jr., Heather A. Carlson:
Biophysical Limits of Protein-Ligand Binding. 2098-2106 - Laura Delgado-Soler, Marta Pinto, Kaori Tanaka-Gil, Jaime Rubio-Martinez:
Molecular Determinants of Bim(BH3) Peptide Binding to Pro-Survival Proteins. 2107-2118 - Zhiwei Feng, Tingjun Hou, Youyong Li:
Concerted Movement in pH-Dependent Gating of FocA from Molecular Dynamics Simulations. 2119-2131 - Jian Liu, Jianfen Fan, Min Cen, Xuezeng Song, Dongyan Liu, Weiqun Zhou, Zhao Liu, Jianfeng Yan:
Dependences of Water Permeation through Cyclic Octa-peptide Nanotubes on Channel Length and Membrane Thickness. 2132-2138 - Stephanie B. A. De Beer, Harini Venkataraman, Daan P. Geerke, Chris Oostenbrink, Nico P. E. Vermeulen:
Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants. 2139-2148
- Michael Thormann, Andreas Klamt, Karin Wichmann:
COSMOsim3D: 3D-Similarity and Alignment Based on COSMO Polarization Charge Densities. 2149-2156 - Andreas Klamt, Michael Thormann, Karin Wichmann, Paolo Tosco:
COSMOsar3D: Molecular Field Analysis Based on Local COSMO σ-Profiles. 2157-2164 - Alfonso T. García-Sosa, Mare Oja, Csaba Hetényi, Uko Maran:
DrugLogit: Logistic Discrimination between Drugs and Nondrugs Including Disease-Specificity by Assigning Probabilities Based on Molecular Properties. 2165-2180 - Rajarshi Guha:
Exploring Uncharted Territories: Predicting Activity Clis in Structure-Activity Landscapes. 2181-2191 - Daniel N. Santiago, Yuri Pevzner, Ashley A. Durand, Minh Phuong Tran, Rachel R. Scheerer, Kenyon G. Daniel, Shen-Shu Sung, H. Lee Woodcock III, Wayne C. Guida, Wesley H. Brooks:
Virtual Target Screening: Validation Using Kinase Inhibitors. 2192-2203 - Michael Oberlin, Romano T. Kroemer, Vincent Mikol, Hervé Minoux, Erdogan Tastan, Nicolas Baurin:
Engineering Protein Therapeutics: Predictive Performances of a Structure-Based Virtual Affinity Maturation Protocol. 2204-2214 - Laura Silvestri, Flavio Ballante, Antonello Mai, Garland R. Marshall, Rino Ragno:
Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction. 2215-2235 - Brandon S. Zerbe, David R. Hall, Sandor Vajda, Adrian Whitty, Dima Kozakov:
Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces. 2236-2244 - Rima Chaudhuri, Hyun Lee, Lena Truong, Jaime Torres, Kavankumar Patel, Michael E. Johnson:
Identification of Non-Macrocyclic Small Molecule Inhibitors against the NS3/4A Serine Protease of Hepatitis C Virus through in Silico Screening. 2245-2256 - Naoya Nagata, Kentaro Kawai, Isao Nakanishi:
Subtle Structural Changes in Tetrahydroquinolines, A New Class of Nonsteroidal Selective Androgen Receptor Modulators, Induce Different Functions. 2257-2264 - Sandra Dreisigacker, Dorota Latek, Svenja Bockelmann, Markus Huss, Helmut Wieczorek, Slawomir Filipek, Holger Gohlke, Dirk Menche, Teresa Carlomagno:
Understanding the Inhibitory Effect of Highly Potent and Selective Archazolides Binding to the Vacuolar ATPase. 2265-2272
- Billur Engin, Ozlem Keskin, Ruth Nussinov, Attila Gürsoy:
A Strategy Based on Protein-Protein Interface Motifs May Help in Identifying Drug Off-Targets. 2273-2286
- Jérémy Desaphy, Karima Azdimousa, Esther Kellenberger, Didier Rognan:
Comparison and Druggability Prediction of Protein-Ligand Binding Sites from Pharmacophore-Annotated Cavity Shapes. 2287-2299 - Álvaro Cortés Cabrera, Javier Klett, Helena G. Dos Santos, Almudena Perona, Rubén Gil-Redondo, Sandrea M. Francis, Eva-Maria Priego, Federico Gago, Antonio Morreale:
CRDOCK: An Ultrafast Multipurpose Protein-Ligand Docking Tool. 2300-2309 - Iurii Sushko, Elena Salmina, Vladimir Potemkin, Gennadiy Poda, Igor V. Tetko:
ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions. 2310-2316
- Xiao Zhu, Pedro E. M. Lopes, Jihyun Shim, Alexander D. MacKerell Jr.:
Correction to Intrinsic Energy Landscapes of Amino Acid Side-Chains. 2317-2318
Volume 52, Number 9, September 2012
- Weizhuang Zhou, Efthimios Motakis, Gloria Fuentes, Chandra S. Verma:
Macrostate Identification from Biomolecular Simulations through Time Series Analysis. 2319-2324
- Aurélie de Luca, Dragos Horvath, Gilles Marcou, Vitaly P. Solov'ev, Alexandre Varnek:
Mining Chemical Reactions Using Neighborhood Behavior and Condensed Graphs of Reactions Approaches. 2325-2338 - Britta Nisius, Holger Gohlke:
Alignment-Independent Comparison of Binding Sites Based on DrugScore Potential Fields Encoded by 3D Zernike Descriptors. 2339-2347 - Dagmar Stumpfe, Jürgen Bajorath:
Frequency of Occurrence and Potency Range Distribution of Activity Cliffs in Bioactive Compounds. 2348-2353 - Kathrin Heikamp, Xiaoying Hu, Aixia Yan, Jürgen Bajorath:
Prediction of Activity Cliffs Using Support Vector Machines. 2354-2365
- Yunierkis Pérez-Castillo, Cosmin Lazar, Jonatan Taminau, Matheus Froeyen, Miguel Ángel Cabrera-Pérez, Ann Nowé:
GA(M)E-QSAR: A Novel, Fully Automatic Genetic-Algorithm-(Meta)-Ensembles Approach for Binary Classification in Ligand-Based Drug Design. 2366-2386 - Fernando Blanco, Billy Egan, Laura Caboni, José Elguero, John O'Brien, Thomas McCabe, Darren Fayne, Mary J. Meegan, David G. Lloyd:
Study of E/Z Isomerization in a Series of Novel Non-ligand Binding Pocket Androgen Receptor Antagonists. 2387-2397
- Shaoyong Lu, Wenkang Huang, Xiaobai Li, Zhimin Huang, Xinyi Liu, Yingyi Chen, Ting Shi, Jian Zhang:
Insights into the Role of Magnesium Triad in myo-Inositol Monophosphatase: Metal Mechanism, Substrate Binding, and Lithium Therapy. 2398-2409 - Noé Sturm, Jérémy Desaphy, Ronald J. Quinn, Didier Rognan, Esther Kellenberger:
Structural Insights into the Molecular Basis of the Ligand Promiscuity. 2410-2421 - Ying Wang, Xiaolin Wu, Dong-Qing Wei, Yi-Xue Li, Jing-Fang Wang:
Autoinhibitory Mechanism for the Mutation-Induced Impaired FGF9 Signaling. 2422-2429
- Prasenjit Mukherjee, Eric J. Martin:
Profile-QSAR and Surrogate AutoShim Protein-Family Modeling of Proteases. 2430-2440 - Stefan Güssregen, Hans Matter, Gerhard Hessler, Marco Müller, K. Friedemann Schmidt, Timothy Clark:
3D-QSAR Based on Quantum-Chemical Molecular Fields: Toward an Improved Description of Halogen Interactions. 2441-2453 - Austin B. Yongye, José L. Medina-Franco:
Data Mining of Protein-Binding Profiling Data Identifies Structural Modifications that Distinguish Selective and Promiscuous Compounds. 2454-2461 - Fabio Broccatelli:
QSAR Models for P-Glycoprotein Transport Based on a Highly Consistent Data Set. 2462-2470 - Valérie Campagna-Slater, Joshua Pottel, Eric Therrien, Louis-David Cantin, Nicolas Moitessier:
Development of a Computational Tool to Rival Experts in the Prediction of Sites of Metabolism of Xenobiotics by P450s. 2471-2483
- Svetoslav H. Slavov, Elizabeth L. Geesaman, Bruce A. Pearce, Laura K. Schnackenberg, Dan A. Buzatu, Jon G. Wilkes, Richard D. Beger:
Erratum: 13C NMR - Distance Matrix Descriptors: Optimal Abstract 3D Space Granularity for Predicting Estrogen Binding. 2484
Volume 52, Number 10, October 2012
- José L. Medina-Franco:
Scanning Structure-Activity Relationships with Structure-Activity Similarity and Related Maps: From Consensus Activity Cliffs to Selectivity Switches. 2485-2493
- Joe Townsend, Robert C. Glen, Hamse Y. Mussa:
Note on Naive Bayes Based on Binary Descriptors in Cheminformatics. 2494-2500 - Anshuman Dixit, Gennady Verkhivker:
Integrating Ligand-Based and Protein-Centric Virtual Screening of Kinase Inhibitors Using Ensembles of Multiple Protein Kinase Genes and Conformations. 2501-2515 - Nicholas C. Firth, Nathan Brown, Julian Blagg:
Plane of Best Fit: A Novel Method to Characterize the Three-Dimensionality of Molecules. 2516-2525 - Matthew A. Kayala, Pierre Baldi:
ReactionPredictor: Prediction of Complex Chemical Reactions at the Mechanistic Level Using Machine Learning. 2526-2540 - Nejc Carl, Milan Hodoscek, Blaz Vehar, Janez Konc, Bernard R. Brooks, Dusanka Janezic:
Correlating Protein Hot Spot Surface Analysis Using ProBiS with Simulated Free Energies of Protein-Protein Interfacial Residues. 2541-2549 - Ye Hu, Jürgen Bajorath:
Growth of Ligand-Target Interaction Data in ChEMBL Is Associated with Increasing and Activity Measurement-Dependent Compound Promiscuity. 2550-2558 - Narender Singh, Sidhartha Chaudhury, Ruifeng Liu, Mohamed Diwan M. AbdulHameed, Gregory J. Tawa, Anders Wallqvist:
QSAR Classification Model for Antibacterial Compounds and Its Use in Virtual Screening. 2559-2569 - Todd M. Martin, Paul Harten, Douglas M. Young, Eugene N. Muratov, Alexander Golbraikh, Hao Zhu, Alexander Tropsha:
Does Rational Selection of Training and Test Sets Improve the Outcome of QSAR Modeling? 2570-2578 - Disha Gupta-Ostermann, Jürgen Bajorath:
Identification of Multitarget Activity Ridges in High-Dimensional Bioactivity Spaces. 2579-2586
- Simon Cross, Massimo Baroni, Laura Goracci, Gabriele Cruciani:
GRID-Based Three-Dimensional Pharmacophores I: FLAPpharm, a Novel Approach for Pharmacophore Elucidation. 2587-2598 - Simon Cross, Francesco Ortuso, Massimo Baroni, Giosuè Costa, Simona Distinto, Federica Moraca, Stefano Alcaro, Gabriele Cruciani:
GRID-Based Three-Dimensional Pharmacophores II: PharmBench, a Benchmark Data Set for Evaluating Pharmacophore Elucidation Methods. 2599-2608 - Suman K. Chakravarti, Roustem D. Saiakhov, Gilles Klopman:
Optimizing Predictive Performance of CASE Ultra Expert System Models Using the Applicability Domains of Individual Toxicity Alerts. 2609-2618 - Maninder Kaur, Malkeet Singh Bahia, Om Silakari:
Exploring the Role of Water Molecules for Docking and Receptor Guided 3D-QSAR Analysis of Naphthyridine Derivatives as Spleen Tyrosine Kinase (Syk) Inhibitors. 2619-2630 - Patricia Saenz-Méndez, Ali Ateia Elmabsout, Helena Sävenstrand, Mohamed Khalid Alhaj Awadalla, Åke Strid, Allan Sirsjö, Leif A. Eriksson:
Homology Models of Human All-Trans Retinoic Acid Metabolizing Enzymes CYP26B1 and CYP26B1 Spliced Variant. 2631-2637 - Abhishek Singharoy, Harshad Joshi, Peter J. Ortoleva:
Multiscale Macromolecular Simulation: Role of Evolving Ensembles. 2638-2649 - Ariela Vergara Jaque, Horacio Poblete, Eric H. Lee, Klaus Schulten, Fernando D. González Nilo, Christophe Chipot:
Molecular Basis of Drug Resistance in A/H1N1 Virus. 2650-2656
- Thomas H. Schmidt, Christian Kandt:
LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations. 2657-2669 - Eleonora Gianti, Randy J. Zauhar:
Modeling Androgen Receptor Flexibility: A Binding Mode Hypothesis of CYP17 Inhibitors/Antiandrogens for Prostate Cancer Therapy. 2670-2683 - Wanding Zhou, Luay Nakhleh:
Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways. 2684-2696 - Sandro Cosconati, Luciana Marinelli, Francesco Saverio Di Leva, Valeria La Pietra, Angela De Simone, Francesca Mancini, Vincenza Andrisano, Ettore Novellino, David S. Goodsell, Arthur J. Olson:
Protein Flexibility in Virtual Screening: The BACE-1 Case Study. 2697-2704
- Manuel Rueda, Maxim Totrov, Ruben Abagyan:
ALiBERO: Evolving a Team of Complementary Pocket Conformations Rather than a Single Leader. 2705-2714 - Lin Li, Youyong Li, Liling Zhang, Tingjun Hou:
Theoretical Studies on the Susceptibility of Oseltamivir against Variants of 2009 A/H1N1 Influenza Neuraminidase. 2715-2729 - Ran Cao, Minyu Liu, Min Yin, Quanhai Liu, Yanli Wang, Niu Huang:
Discovery of Novel Tubulin Inhibitors via Structure-Based Hierarchical Virtual Screening. 2730-2740 - Lu Chen, George A. Calin, Shuxing Zhang:
Novel Insights of Structure-Based Modeling for RNA-Targeted Drug Discovery. 2741-2753 - Njabulo J. Gumede, Parvesh Singh, Myalowenkosy I. Sabela, Krishna Bisetty, Laura Escuder-Gilabert, María-José Medina-Hernández, Salvador Sagrado:
Experimental-Like Affinity Constants and Enantioselectivity Estimates from Flexible Docking. 2754-2759 - Serdar Durdagi, Sumukh Deshpande, Henry J. Duff, Sergei Yu Noskov:
Modeling of Open, Closed, and Open-Inactivated States of the hERG1 Channel: Structural Mechanisms of the State-Dependent Drug Binding. 2760-2774
- Nelson Alberto N. de Alencar, Paulo Robson M. Sousa, José Rogério A. Silva, Jerônimo Lameira, Cláudio Nahum Alves, Sergio Martí, Vicent Moliner:
Computational Analysis of Human OGA Structure in Complex with PUGNAc and NAG-Thiazoline Derivatives. 2775-2783 - Hui Sun Lee, Wonpil Im:
Identification of Ligand Templates using Local Structure Alignment for Structure-Based Drug Design. 2784-2795
- Tianhong Zhang, Hongli Li, Hualin Xi, Robert V. Stanton, Sergio H. Rotstein:
HELM: A Hierarchical Notation Language for Complex Biomolecule Structure Representation. 2796-2806
Volume 52, Number 11, November 2012
- Dennis M. Krüger, Gisela Jessen, Holger Gohlke:
How Good Are State-of-the-Art Docking Tools in Predicting Ligand Binding Modes in Protein-Protein Interfaces? 2807-2811
- Ksenia S. Egorova, Philip V. Toukach:
Critical Analysis of CCSD Data Quality. 2812-2814 - Ulf Norinder, Henrik Boström:
Introducing Uncertainty in Predictive Modeling - Friend or Foe? 2815-2822 - Amol Shivajirao Hukkerikar, Sawitree Kalakul, Bent Sarup, Douglas M. Young, Gürkan Sin, Rafiqul Gani:
Estimation of Environment-Related Properties of Chemicals for Design of Sustainable Processes: Development of Group-Contribution+ (GC+) Property Models and Uncertainty Analysis. 2823-2839 - Congying Xu, Feixiong Cheng, Lei Chen, Zheng Du, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang:
In silico Prediction of Chemical Ames Mutagenicity. 2840-2847 - Vigneshwaran Namasivayam, Jürgen Bajorath:
Multiobjective Particle Swarm Optimization: Automated Identification of Structure-Activity Relationship-Informative Compounds with Favorable Physicochemical Property Distributions. 2848-2855 - Alexandru T. Balaban:
Partitioned-Formula Periodic Tables for Diamond Hydrocarbons (Diamondoids). 2856-2863 - Lars Ruddigkeit, Ruud van Deursen, Lorenz C. Blum, Jean-Louis Reymond:
Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17. 2864-2875 - Antonio de la Vega de León, Jürgen Bajorath:
Design of a Three-Dimensional Multitarget Activity Landscape. 2876-2883
- Roberto Todeschini, Viviana Consonni, Hua Xiang, John D. Holliday, Paolo Massimo Buscema, Peter Willett:
Similarity Coefficients for Binary Chemoinformatics Data: Overview and Extended Comparison Using Simulated and Real Data Sets. 2884-2901 - Maciej Haranczyk, Piotr Urbaszek, Esmond G. Ng, Tomasz Puzyn:
Combinatorial × Computational × Cheminformatics (C3) Approach to Characterization of Congeneric Libraries of Organic Pollutants. 2902-2909 - Gunnar Brinkmann, Jan Goedgebeur, Brendan D. McKay:
The Generation of Fullerenes. 2910-2918 - Paul C. D. Hawkins, Anthony Nicholls:
Conformer Generation with OMEGA: Learning from the Data Set and the Analysis of Failures. 2919-2936 - Gregory A. Bakken, Andrew Bell, Markus Boehm, Jeremy R. Everett, Rosalia Gonzales, David Hepworth, Jacquelyn L. Klug-McLeod, Jeremy Lanfear, Jens Loesel, John Mathias, Terence P. Wood:
Shaping a Screening File for Maximal Lead Discovery Efficiency and Effectiveness: Elimination of Molecular Redundancy. 2937-2949 - Jogoth Ali, Patrick Camilleri, Marc B. Brown, Andrew J. Hutt, Stewart B. Kirton:
In Silico Prediction of Aqueous Solubility Using Simple QSPR Models: The Importance of Phenol and Phenol-like Moieties. 2950-2957
- R. S. K. Vijayan, Neha Trivedi, Sudipendra Nath Roy, Indrani Bera, Prabu Manoharan, Pavan V. Payghan, Dhananjay Bhattacharyya, Nanda Ghoshal:
Modeling the Closed and Open State Conformations of the GABAA Ion Channel - Plausible Structural Insights for Channel Gating. 2958-2969 - Mario Latendresse, Jeremiah P. Malerich, Mike Travers, Peter D. Karp:
Accurate Atom-Mapping Computation for Biochemical Reactions. 2970-2982 - Yiyu Li, Mámon M. Hatmal, Ralf Langen, Ian S. Haworth:
Idealized Models of Protofilaments of Human Islet Amyloid Polypeptide. 2983-2991 - Shunzhou Wan, Peter V. Coveney:
Regulation of JAK2 Activation by Janus Homology 2: Evidence from Molecular Dynamics Simulations. 2992-3000 - Bruno L. Victor, António M. Baptista, Cláudio M. Soares:
Structural Determinants for the Membrane Insertion of the Transmembrane Peptide of Hemagglutinin from Influenza Virus. 3001-3012 - Samuel Genheden:
Are Homology Models Sufficiently Good for Free-Energy Simulations? 3013-3021 - Maxime Louet, Landry Charlier, Jean Martinez, Nicolas Floquet:
Dissociation of Membrane-Anchored Heterotrimeric G-Protein Induced by Gα Subunit Binding to GTP. 3022-3027 - Niels Johan Christensen, Kasper P. Kepp:
Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol. 3028-3042 - Weihua Li, Jing Fu, Feixiong Cheng, Mingyue Zheng, Jian Zhang, Guixia Liu, Yun Tang:
Unbinding Pathways of GW4064 from Human Farnesoid X Receptor As Revealed by Molecular Dynamics Simulations. 3043-3052 - Sabina Berne, Barbara Podobnik, Neja Zupanec, Metka Novak, Nada Krasevec, Samo Turk, Branka Korosec, Ljerka Lah, Erika Suligoj, Jure Stojan, Stanislav Gobec, Radovan Komel:
Virtual Screening Yields Inhibitors of Novel Antifungal Drug Target, Benzoate 4-Monooxygenase. 3053-3063
- Yunde Xiao, Philip S. Hammond, Anatoly A. Mazurov, Daniel Yohannes:
Multiple Interaction Regions in the Orthosteric Ligand Binding Domain of the α7 Neuronal Nicotinic Acetylcholine Receptor. 3064-3073 - Richard Sherhod, Valerie J. Gillet, Philip N. Judson, Jonathan D. Vessey:
Automating Knowledge Discovery for Toxicity Prediction Using Jumping Emerging Pattern Mining. 3074-3087 - Hemant Kumar Srivastava, G. Narahari Sastry:
Molecular Dynamics Investigation on a Series of HIV Protease Inhibitors: Assessing the Performance of MM-PBSA and MM-GBSA Approaches. 3088-3098
- Feixiong Cheng, Weihua Li, Yadi Zhou, Jie Shen, Zengrui Wu, Guixia Liu, Philip W. Lee, Yun Tang:
admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties. 3099-3105
Volume 52, Number 12, December 2012
- Dusica Vidovic, Steven M. Muskal, Stephan C. Schürer:
Novel Kinase Inhibitors by Reshuffling Ligand Functionalities Across the Human Kinome. 3107-3115 - Christophe Muller, Gilles Marcou, Dragos Horvath, João Aires-de-Sousa, Alexandre Varnek:
Models for Identification of Erroneous Atom-to-Atom Mapping of Reactions Performed by Automated Algorithms. 3116-3122 - Obdulia Rabal, Julen Oyarzabal:
Biologically Relevant Chemical Space Navigator: From Patent and Structure-Activity Relationship Analysis to Library Acquisition and Design. 3123-3137 - Bijun Zhang, Anne Mai Wassermann, Martin Vogt, Jürgen Bajorath:
Systematic Assessment of Compound Series with SAR Transfer Potential. 3138-3143
- Kenno Vanommeslaeghe, Alexander D. MacKerell Jr.:
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing. 3144-3154 - Kenno Vanommeslaeghe, E. Prabhu Raman, Alexander D. MacKerell Jr.:
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges. 3155-3168 - Yan Yuan, Hugh A. Chipman, William J. Welch:
Harvesting Classification Trees for Drug Discovery. 3169-3180 - Hans-Christian Ehrlich, Andrea Volkamer, Matthias Rarey:
Searching for Substructures in Fragment Spaces. 3181-3189 - Haipeng Hu, James P. Snyder:
Models for Predicting IKKA and IKKB Blockade. 3190-3199 - Miklos Feher, Christopher I. Williams:
Numerical Errors in Minimization Based Binding Energy Calculations. 3200-3212 - Dima A. Sabbah, Jonathan L. Vennerstrom, Haizhen Zhong:
Binding Selectivity Studies of Phosphoinositide 3-Kinases Using Free Energy Calculations. 3213-3224 - Woong-Hee Shin, Chaok Seok:
GalaxyDock: Protein-Ligand Docking with Flexible Protein Side-chains. 3225-3232 - Paola Bisignano, Chiara Lambruschini, Manuele Bicego, Vittorio Murino, Angelo D. Favia, Andrea Cavalli:
In Silico Deconstruction of ATP-Competitive Inhibitors of Glycogen Synthase Kinase-3β. 3233-3244 - Laura De Luca, Francesca Morreale, Alba Chimirri:
Insight into the Fundamental Interactions between LEDGF Binding Site Inhibitors and Integrase Combining Docking and Molecular Dynamics Simulations. 3245-3254 - Jack Yang, Mark P. Waller:
JACOB: A Dynamic Database for Computational Chemistry Benchmarking. 3255-3262 - Thijs Beuming, Woody Sherman:
Current Assessment of Docking into GPCR Crystal Structures and Homology Models: Successes, Challenges, and Guidelines. 3263-3277
- Minsup Kim, Keun Woo Lee, Art E. Cho:
Elucidation of Allosteric Inhibition Mechanism of 2-Cys Human Peroxiredoxin by Molecular Modeling. 3278-3283
- Yoshihiro Yamanishi, Edouard Pauwels, Masaaki Kotera:
Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces. 3284-3292 - Eleni Vrontaki, Georgios Leonis, Manthos G. Papadopoulos, M. Simcic, Simona Golic Grdadolnik, Antreas Afantitis, Georgia Melagraki, S. K. Hadjikakou, Thomas M. Mavromoustakos:
Comparative Binding Effects of Aspirin and Anti-Inflammatory Cu Complex in the Active Site of LOX-1. 3293-3301 - Anthony F. Nastase, Donald B. Boyd:
Simple Structure-Based Approach for Predicting the Activity of Inhibitors of Beta-Secretase (BACE1) Associated with Alzheimer's Disease. 3302-3307 - Francesco Sirci, Enade P. Istyastono, Henry F. Vischer, Albert J. Kooistra, Saskia Nijmeijer, Martien Kuijer, Maikel Wijtmans, Raimund Mannhold, Rob Leurs, Iwan J. P. de Esch, Chris de Graaf:
Virtual Fragment Screening: Discovery of Histamine H3 Receptor Ligands Using Ligand-Based and Protein-Based Molecular Fingerprints. 3308-3324 - Mauricio E. Di Ianni, Andrea V. Enrique, Pablo H. Palestro, Luciana Gavernet, Alan Talevi, Luis Bruno Blanch:
Several New Diverse Anticonvulsant Agents Discovered in a Virtual Screening Campaign Aimed at Novel Antiepileptic Drugs to Treat Refractory Epilepsy. 3325-3330
- Humberto González Díaz, Pablo Riera-Fernández:
New Markov-Autocorrelation Indices for Re-evaluation of Links in Chemical and Biological Complex Networks used in Metabolomics, Parasitology, Neurosciences, and Epidemiology. 3331-3340 - Nédia Kamech, Damir Vukicevic, Ali Ladram, Christophe Piesse, Julie Vasseur, Viktor Bojovic, Juraj Simunic, Davor Juretic:
Improving the Selectivity of Antimicrobial Peptides from Anuran Skin. 3341-3351
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2026-03-05 22:28 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
