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ORCIDJournal of Chemical Information and Modeling, Volume 51
Volume 51, Number 1, January 2011
- Petr Heneberg
:
On Bibliometric Analysis of Chinese Research on Cyclization, MALDI-TOF, and Antibiotics: Methodical Concerns. 1-2 - Jiang Li, Peter Willett:
Comments on "On Bibliometric Analysis of Chinese Research on Cyclization, MALDI-TOF, and Antibiotics: Methodological Concerns". 3
- Hamse Y. Mussa, Lezan Hawizy, Florian Nigsch, Robert C. Glen:
Classifying Large Chemical Data Sets: Using A Regularized Potential Function Method. 4-14 - Satoshi Niijima, Hiroaki Yabuuchi, Yasushi Okuno:
Cross-Target View to Feature Selection: Identification of Molecular Interaction Features in Ligand-Target Space. 15-24 - Ammar Abdo, Naomie Salim:
New Fragment Weighting Scheme for the Bayesian Inference Network in Ligand-Based Virtual Screening. 25-32 - Sundarapandian Thangapandian, Shalini John, Sugunadevi Sakkiah, Keun Woo Lee:
Molecular Docking and Pharmacophore Filtering in the Discovery of Dual-Inhibitors for Human Leukotriene A4 Hydrolase and Leukotriene C4 Synthase. 33-44
- Danilo A. Rodrigues, Nivan B. da Costa Jr., Ricardo Oliveira Freire:
Would the Pseudocoordination Centre Method Be Appropriate To Describe the Geometries of Lanthanide Complexes? 45-51 - Siavash Meshkat, Anthony E. Klon, Jinming Zou, Jeffrey S. Wiseman, Zenon Konteatis:
Transplant-Insert-Constrain-Relax-Assemble (TICRA): Protein-Ligand Complex Structure Modeling and Application to Kinases. 52-60 - Shigeru Saito, Takatsugu Hirokawa, Katsuhisa Horimoto:
Discovery of Chemical Compound Groups with Common Structures by a Network Analysis Approach (Affinity Prediction Method). 61-68 - Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang:
Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations. 69-82 - Fabian Rathke, Katja Hansen, Ulf Brefeld, Klaus-Robert Müller:
StructRank: A New Approach for Ligand-Based Virtual Screening. 83-92 - Steven K. Burger, David C. Thompson, Paul W. Ayers:
Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in Cytochrome c Peroxidase. 93-101 - John C. Shelley, David Calkins, Arron P. Sullivan:
Comments on the Article "Evaluation of pKa Estimation Methods on 211 Druglike Compounds". 102-104
- Se-Han Lee, Kwang-Hwi Cho, Chang-Joon Lee, Go-Eun Kim, Chul Hee Na, Youngyong In, Kyoung Tai No:
Calculation of the Solvation Free Energy of Neutral and Ionic Molecules in Diverse Solvents. 105-114 - Preethi Badrinarayan, G. Narahari Sastry:
Sequence, Structure, and Active Site Analyses of p38 MAP Kinase: Exploiting DFG-out Conformation as a Strategy to Design New Type II Leads. 115-129
- Sergio R. Ribone, Mario A. Quevedo, Marcela Madrid, Margarita C. Brinón:
Rational Approaches for the Design of Effective Human Immunodeficiency Virus Type 1 Nonnucleoside Reverse Transcriptase Inhibitors. 130-138 - Alfonso Lam, Supriyo Bhattacharya, Kevin Patel, Spencer Hall, Allen Mao, Nagarajan Vaidehi:
Importance of Receptor Flexibility in Binding of Cyclam Compounds to the Chemokine Receptor CXCR4. 139-147 - Taiji Oashi, Ashley L. Ringer, E. Prabhu Raman, Alexander D. MacKerell Jr.:
Automated Selection of Compounds with Physicochemical Properties To Maximize Bioavailability and Druglikeness. 148-158
- Philip V. Toukach:
Bacterial Carbohydrate Structure Database 3: Principles and Realization. 159-170 - George E. Chlipala, Aleksej Krunic, Shunyan Mo, Megan Sturdy, Jimmy Orjala:
CYANOS: A Data Management System for Natural Product Drug Discovery Efforts Using Cultured Microorganisms. 171-180 - Vladimir V. Diky, Robert D. Chirico, Andrei F. Kazakov, Chris Muzny, Joseph W. Magee, Ilmutdin Abdulagatov, Jeong Won Kang, Kenneth Kroenlein, Michael Frenkel:
ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 5. Experiment Planning and Product Design. 181-194
Volume 51, Number 2, February 2011
- William L. Jorgensen:
Letter from the Editor - January 2011. 195
- Izhar Wallach, Ryan H. Lilien:
Virtual Decoy Sets for Molecular Docking Benchmarks. 196-202
- Georg Hinselmann, Lars Rosenbaum, Andreas Jahn, Nikolas Fechner, Claude Ostermann, Andreas Zell:
Large-Scale Learning of Structure-Activity Relationships Using a Linear Support Vector Machine and Problem-Specific Metrics. 203-213 - Yat T. Tang, Garland R. Marshall:
PHOENIX: A Scoring Function for Affinity Prediction Derived Using High-Resolution Crystal Structures and Calorimetry Measurements. 214-228 - Tiejun Cheng, Qingliang Li, Yanli Wang, Stephen H. Bryant:
Binary Classification of Aqueous Solubility Using Support Vector Machines with Reduction and Recombination Feature Selection. 229-236 - Thorsten Meinl, Claude Ostermann, Michael R. Berthold:
Maximum-Score Diversity Selection for Early Drug Discovery. 237-247 - Ye Hu, Jürgen Bajorath:
Combining Horizontal and Vertical Substructure Relationships in Scaffold Hierarchies for Activity Prediction. 248-257 - Dilyana Dimova, Mathias Wawer, Anne Mai Wassermann, Jürgen Bajorath:
Design of Multitarget Activity Landscapes That Capture Hierarchical Activity Cliff Distributions. 258-266
- Anton Lindström, Lotta Edvinsson, Andreas Johansson, C. David Andersson, Ida E. Andersson, Florian Raubacher, Anna Linusson:
Postprocessing of Docked Protein-Ligand Complexes Using Implicit Solvation Models. 267-282 - Maciej Roman, Jan Cz. Dobrowolski, Malgorzata Baranska:
Theoretical Modeling of Molecular Spectra Parameters of Disubstituted Diacetylenes. 283-295 - Toshiyuki Harada, Yoshiaki Nakagawa, Takehiko Ogura, Yutaka Yamada, Takehiro Ohe, Hisashi Miyagawa:
Virtual Screening for Ligands of the Insect Molting Hormone Receptor. 296-305 - Li Gao, Yaoquan Tu, Pia Wegman, Sten Wingren, Leif A. Eriksson:
Conformational Enantiomerization and Estrogen Receptor α Binding of Anti-Cancer Drug Tamoxifen and Its Derivatives. 306-314 - Vignir Ísberg, Thomas Balle, Tommy Sander, Flemming Steen Jørgensen, David E. Gloriam:
G Protein- and Agonist-Bound Serotonin 5-HT2A Receptor Model Activated by Steered Molecular Dynamics Simulations. 315-325 - Zhenming Liu, Bo Li, Xia Li, Liang Ren Zhang, Luhua Lai:
Identification of Small-Molecule Inhibitors against Human Leukocyte Antigen-Death Receptor 4 (HLA-DR4) Through a Comprehensive Strategy. 326-334
- Neha Gandhi, Ricardo L. Mancera:
Molecular Dynamics Simulations of CXCL-8 and Its Interactions with a Receptor Peptide, Heparin Fragments, and Sulfated Linked Cyclitols. 335-358 - Lin-tai Da, Yun-Dong Wu:
Theoretical Studies on the Interactions and Interferences of HIV-1 Glycoprotein gp120 and Its Coreceptor CCR5. 359-369 - Carles Pons, David Talavera, Xavier de la Cruz, Modesto Orozco, Juan Fernández-Recio:
Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein-Protein Docking. 370-377
- Fumiyoshi Yamashita, Chunlai Feng, Shuya Yoshida, Takayuki Itoh, Mitsuru Hashida:
Automated Information Extraction and Structure-Activity Relationship Analysis of Cytochrome P450 Substrates. 378-385 - Qiancheng Shen, Bing Xiong, Mingyue Zheng, Xiaomin Luo, Cheng Luo, Xian Liu, Yun Du, Jing Li, Weiliang Zhu, Jingkang Shen, Hualiang Jiang:
Knowledge-Based Scoring Functions in Drug Design: 2. Can the Knowledge Base Be Enriched? 386-397 - Kuei-Chung Shih, Chun-Yuan Lin, Jiayi Zhou, Hsiao-Chieh Chi, Ting-Shou Chen, Chun-Chung Wang, Hsiang-Wen Tseng, Chuan Yi Tang:
Development of Novel 3D-QSAR Combination Approach for Screening and Optimizing B-Raf Inhibitors in silico. 398-407 - Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne:
A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing. 408-419 - Soo-Kyung Kim, Youyong Li, Ravinder Abrol, Jiyoung Heo, William A. Goddard III:
Predicted Structures and Dynamics for Agonists and Antagonists Bound to Serotonin 5-HT2B and 5-HT2C Receptors. 420-433 - Patrizia Crivori, Giulia Pennella, Miriam Magistrelli, Pietro Grossi, Anna Maria Giusti:
Predicting Myelosuppression of Drugs from in Silico Models. 434-445 - Mattia Mori, Fabrizio Manetti, Maurizio Botta:
Predicting the Binding Mode of Known NCp7 Inhibitors To Facilitate the Design of Novel Modulators. 446-454 - Marcin Nowosielski, Marcin Hoffmann, Lucjan Stanislaw Wyrwicz, Piotr Stepniak, Dariusz Plewczynski, Michal Lazniewski, Krzysztof Ginalski, Leszek Rychlewski:
Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine. 455-462 - Serdar Durdagi, Henry J. Duff, Sergei Yu Noskov:
Combined Receptor and Ligand-Based Approach to the Universal Pharmacophore Model Development for Studies of Drug Blockade to the hERG1 Pore Domain. 463-474 - Somisetti V. Sambasivarao, Orlando Acevedo:
Computational Insight into Small Molecule Inhibition of Cyclophilins. 475-482 - Cristian Obiol-Pardo, Julio Gomis-Tena, Ferran Sanz, Javier Saiz, Manuel Pastor:
A Multiscale Simulation System for the Prediction of Drug-Induced Cardiotoxicity. 483-492
- Jeremy Esque, Christophe Oguey, Alexandre G. de Brevern:
Comparative Analysis of Threshold and Tessellation Methods for Determining Protein Contacts. 493-507
- Anne Mai Wassermann, Britta Nisius, Martin Vogt, Jürgen Bajorath:
Correction to Identification of Descriptors Capturing Compound Class-Specific Features by Mutual Information Analysis. 508-509
Volume 51, Number 3, March 2011
- Wei Deng, Steven J. Berthel, W. Venus So:
Intuitive Patent Markush Structure Visualization Tool for Medicinal Chemists. 511-520 - Chao Ma, Lirong Wang, Xiang-Qun Xie:
Ligand Classifier of Adaptively Boosting Ensemble Decision Stumps (LiCABEDS) and Its Application on Modeling Ligand Functionality for 5HT-Subtype GPCR Families. 521-531 - Preeti Iyer, Ye Hu, Jürgen Bajorath:
SAR Monitoring of Evolving Compound Data Sets Using Activity Landscapes. 532-540
- Melvin J. Yu:
Natural Product-Like Virtual Libraries: Recursive Atom-Based Enumeration. 541-557 - Hemant Kumar Srivastava, Mukesh Chourasia, Devesh Kumar, G. Narahari Sastry:
Comparison of Computational Methods to Model DNA Minor Groove Binders. 558-571 - Tao Ye, Ruchu Xu, Wenqi Huang:
Global Optimization of Binary Lennard-Jones Clusters Using Three Perturbation Operators. 572-577 - Mark McGann:
FRED Pose Prediction and Virtual Screening Accuracy. 578-596 - Thomas Greve Kristensen, Jesper Buus Nielsen, Christian N. S. Pedersen:
Using Inverted Indices for Accelerating LINGO Calculations. 597-600 - Lucía Díaz, Jordi Bujons, Antonio Delgado, Hugo Gutiérrez-de-Terán, Johan Åqvist:
Computational Prediction of Structure-Activity Relationships for the Binding of Aminocyclitols to β-Glucocerebrosidase. 601-611 - Valérie Campagna-Slater, Man Wai Mok, Kong T. Nguyen, Miklos Feher, Rafael Najmanovich, Matthieu Schapira:
Structural Chemistry of the Histone Methyltransferases Cofactor Binding Site. 612-623
- Sarah L. Kinnings, Richard M. Jackson:
ReverseScreen3D: A Structure-Based Ligand Matching Method To Identify Protein Targets. 624-634 - Mohamed A. Helal, Amar G. Chittiboyina, Mitchell A. Avery:
New Insights into the Binding Mode of Melanin Concentrating Hormone Receptor-1 Antagonists: Homology Modeling and Explicit Membrane Molecular Dynamics Simulation Study. 635-646 - Mutasem O. Taha, Maha Habash, Zeina Al-Hadidi, Amal Al-Bakri, Khaled Younis, Suhaib Sisan:
Docking-Based Comparative Intermolecular Contacts Analysis as New 3-D QSAR Concept for Validating Docking Studies and in Silico Screening: NMT and GP Inhibitors as Case Studies. 647-669 - Verena Schattel, Georg Hinselmann, Andreas Jahn, Andreas Zell, Stefan Laufer:
Modeling and Benchmark Data Set for the Inhibition of c-Jun N-terminal Kinase-3. 670-679 - Ying Yang, Jin Qin, Huanxiang Liu, Xiaojun Yao:
Molecular Dynamics Simulation, Free Energy Calculation and Structure-Based 3D-QSAR Studies of B-RAF Kinase Inhibitors. 680-692 - Mengang Xu, Markus A. Lill:
Significant Enhancement of Docking Sensitivity Using Implicit Ligand Sampling. 693-706 - Christian Kramer, Peter Gedeck:
Global Free Energy Scoring Functions Based on Distance-Dependent Atom-Type Pair Descriptors. 707-720
- M. Michael Gromiha, Kazuhiko Fukui:
Scoring Function Based Approach for Locating Binding Sites and Understanding Recognition Mechanism of Protein-DNA Complexes. 721-729 - Claudia Andreini, Ivano Bertini, Gabriele Cavallaro, Leonardo Decaria, Antonio Rosato:
A Simple Protocol for the Comparative Analysis of the Structure and Occurrence of Biochemical Pathways Across Superkingdoms. 730-738
- Daniel M. Lowe, Peter T. Corbett, Peter Murray-Rust, Robert C. Glen:
Chemical Name to Structure: OPSIN, an Open Source Solution. 739-753
Volume 51, Number 4, April 2011
- Liwei Li, May Khanna, Inha Jo, Fang Wang, Nicole M. Ashpole, Andy Hudmon, Samy O. Meroueh:
Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation. 755-759
- Alessio Andronico, Arlo Z. Randall, Ryan W. Benz, Pierre Baldi:
Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. 760-776 - Jesús M. Planesas, Rosa M. Claramunt, Jordi Teixidó, José I. Borrell, Violeta I. Pérez-Nueno:
Improving VEGFR-2 Docking-Based Screening by Pharmacophore Postfiltering and Similarity Search Postprocessing. 777-787 - Ramesh Hariharan, Anand Janakiraman, Ramaswamy Nilakantan, Bhupender Singh, Sajith Varghese, Gregory A. Landrum, Ansgar Schuffenhauer:
MultiMCS: A Fast Algorithm for the Maximum Common Substructure Problem on Multiple Molecules. 788-806 - Lirong Wang, Zhaojun Xie, Peter Wipf, Xiang-Qun Xie:
Residue Preference Mapping of Ligand Fragments in the Protein Data Bank. 807-815 - Jian Jiao, Shi-Miao Tan, Rui-Ming Luo, Yan-Ping Zhou:
A Robust Boosting Regression Tree with Applications in Quantitative Structure-Activity Relationship Studies of Organic Compounds. 816-828 - Fergal J. Duffy, Mélanie Verniere, Marc Devocelle, Elise Bernard, Denis C. Shields, Anthony J. Chubb:
CycloPs: Generating Virtual Libraries of Cyclized and Constrained Peptides Including Nonnatural Amino Acids. 829-836 - Peter Ripphausen, Britta Nisius, Mathias Wawer, Jürgen Bajorath:
Rationalizing the Role of SAR Tolerance for Ligand-Based Virtual Screening. 837-842
- Bernd Wendt, Ulrike Uhrig, Fabian Bös:
Capturing Structure-Activity Relationships from Chemogenomic Spaces. 843-851 - Falgun Shah, Prasenjit Mukherjee, Jiri Gut, Jennifer Legac, Philip J. Rosenthal, Babu L. Tekwani, Mitchell A. Avery:
Identification of Novel Malarial Cysteine Protease Inhibitors Using Structure-Based Virtual Screening of a Focused Cysteine Protease Inhibitor Library. 852-864 - Oliver Korb, Thomas Stützle, Thomas E. Exner:
Accelerating Molecular Docking Calculations Using Graphics Processing Units. 865-876 - E. Prabhu Raman, Wenbo Yu, Olgun Guvench, Alexander D. MacKerell Jr.:
Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations. 877-896 - Robin Taylor:
Short Nonbonded Contact Distances in Organic Molecules and Their Use as Atom-Clash Criteria in Conformer Validation and Searching. 897-908 - Mette Alstrup Lie, René Thomsen, Christian N. S. Pedersen, Birgit Schiøtt, Mikael H. Christensen:
Molecular Docking with Ligand Attached Water Molecules. 909-917
- Andrei L. Lomize, Irina D. Pogozheva, Henry I. Mosberg:
Anisotropic Solvent Model of the Lipid Bilayer. 1. Parameterization of Long-Range Electrostatics and First Solvation Shell Effects. 918-929 - Andrei L. Lomize, Irina D. Pogozheva, Henry I. Mosberg:
Anisotropic Solvent Model of the Lipid Bilayer. 2. Energetics of Insertion of Small Molecules, Peptides, and Proteins in Membranes. 930-946 - Samuel Genheden, Ingemar Nilsson, Ulf Ryde:
Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA. 947-958
- Haoliang Yuan, Tao Lu, Ting Ran, Haichun Liu, Shuai Lu, Wenting Tai, Ying Leng, Weiwei Zhang, Jian Wang, Yadong Chen:
Novel Strategy for Three-Dimensional Fragment-Based Lead Discovery. 959-974
Volume 51, Number 5, May 2011
- Claire M. Ellison, Richard Sherhod, Mark T. D. Cronin, Steven J. Enoch, Judith C. Madden, Philip N. Judson:
Assessment of Methods To Define the Applicability Domain of Structural Alert Models. 975-985 - Kristl V. Dorschner, David Toomey, Marian P. Brennan, Tim Heinemann, Fergal J. Duffy, Kevin B. Nolan, Dermot Cox, Mauro Adamo, Anthony J. Chubb:
TIN - A Combinatorial Compound Collection of Synthetically Feasible Multicomponent Synthesis Products. 986-995 - Feixiong Cheng, Yue Yu, Jie Shen, Lei Yang, Weihua Li, Guixia Liu, Philip W. Lee, Yun Tang:
Classification of Cytochrome P450 Inhibitors and Noninhibitors Using Combined Classifiers. 996-1011 - Yoshifumi Fukunishi, Haruki Nakamura:
Definition of Drug-Likeness for Compound Affinity. 1012-1016
- Quan Liao, Ji-Bo Wang, Ian A. Watson:
Accelerating Two Algorithms for Large-Scale Compound Selection on GPUs. 1017-1024
- Shao-Yong Lu, Yong-Jun Jiang, Jian-Wei Zou, Tian-Xing Wu:
Molecular Modeling and Molecular Dynamics Simulation Studies of the GSK3β/ATP/Substrate Complex: Understanding the Unique P+4 Primed Phosphorylation Specificity for GSK3β Substrates. 1025-1036 - Pekka A. Postila, Mikko Ylilauri, Olli T. Pentikäinen:
Full and Partial Agonism of Ionotropic Glutamate Receptors Indicated by Molecular Dynamics Simulations. 1037-1047 - Andrew Leach, Nathan J. Kidley:
Quantitatively Interpreted Enhanced Inhibition of Cytochrome P450s by Heteroaromatic Rings Containing Nitrogen. 1048-1063 - Daniel P. Oehme, David J. D. Wilson, Robert T. C. Brownlee:
Effect of Structural Stress on the Flexibility and Adaptability of HIV-1 Protease. 1064-1073 - Xuemei Wang, Shanshan Wu, Dingguo Xu, Daiqian Xie, Hua Guo:
Inhibitor and Substrate Binding by Angiotensin-Converting Enzyme: Quantum Mechanical/Molecular Mechanical Molecular Dynamics Studies. 1074-1082
- Yaxia Yuan, Jianfeng Pei, Luhua Lai:
LigBuilder 2: A Practical de Novo Drug Design Approach. 1083-1091 - Muhammad K. Haider, Hugues-Olivier Bertrand, Roderick E. Hubbard:
Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach. 1092-1105 - Sayan Ranu, Ambuj K. Singh:
Novel Method for Pharmacophore Analysis by Examining the Joint Pharmacophore Space. 1106-1121 - Dimitris K. Agrafiotis, John J. M. Wiener, Andrew Skalkin, Jeremy Kolpak:
Single R-Group Polymorphisms (SRPs) and R-Cliffs: An Intuitive Framework for Analyzing and Visualizing Activity Cliffs in a Single Analog Series. 1122-1131 - Senthil Natesan, Tiansheng Wang, Viera Lukacova, Vladimir Bartus, Akash Khandelwal, Stefan Balaz:
Rigorous Treatment of Multispecies Multimode Ligand-Receptor Interactions in 3D-QSAR: CoMFA Analysis of Thyroxine Analogs Binding to Transthyretin. 1132-1150 - Zhijun Wu, Victor J. Hruby:
Backbone Alignment Modeling of the Structure-Activity Relationships of Opioid Ligands. 1151-1164
- Björn Sommer, Tim Dingersen, Christian Gamroth, Sebastian Schneider, Sebastian Rubert, Jens Krüger, Karl-Josef Dietz:
CELLmicrocosmos 2.2 MembraneEditor: A Modular Interactive Shape-Based Software Approach To Solve Heterogeneous Membrane Packing Problems. 1165-1182 - Yoshihiro Yamanishi, Edouard Pauwels, Hiroto Saigo, Véronique Stoven:
Extracting Sets of Chemical Substructures and Protein Domains Governing Drug-Target Interactions. 1183-1194
- Sarah L. Kinnings, Nina Liu, Peter J. Tonge, Richard M. Jackson, Lei Xie, Philip E. Bourne:
Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing". 1195-1197
Volume 51, Number 6, June 2011
- Cristiano R. W. Guimarães, Brajesh K. Rai, Michael J. Munchhof, Shenping Liu, Jian Wang, Samit K. Bhattacharya, Leonard Buckbinder:
Understanding the Impact of the P-loop Conformation on Kinase Selectivity. 1199-1204
- Jintao Zhang, Gerald H. Lushington, Jun Huan:
Characterizing the Diversity and Biological Relevance of the MLPCN Assay Manifold and Screening Set. 1205-1215 - Gonzalo Cerruela García, Irene Luque Ruiz, Miguel Ángel Gómez-Nieto:
Analysis and Study of Molecule Data Sets Using Snowflake Diagrams of Weighted Maximum Common Subgraph Trees. 1216-1232 - Violeta I. Pérez-Nueno, David W. Ritchie:
Using Consensus-Shape Clustering To Identify Promiscuous Ligands and Protein Targets and To Choose the Right Query for Shape-Based Virtual Screening. 1233-1248 - Marta Pinto, Maria del Mar Orzaez, Laura Delgado-Soler, Juan Jesús Pérez, Jaime Rubio-Martinez:
Rational Design of New Class of BH3-Mimetics As Inhibitors of the Bcl-xL Protein. 1249-1258 - Austin B. Yongye, Kendall G. Byler, Radleigh Santos, Karina Martínez-Mayorga, Gerald M. Maggiora, José L. Medina-Franco:
Consensus Models of Activity Landscapes with Multiple Chemical, Conformer, and Property Representations. 1259-1270 - Sergii Novotarskyi, Iurii Sushko, Robert Körner, Anil Kumar Pandey, Igor V. Tetko:
A comparison of different QSAR approaches to modeling CYP450 1A2 inhibition. 1271-1280 - Preeti Iyer, Dagmar Stumpfe, Jürgen Bajorath:
Molecular Mechanism-Based Network-like Similarity Graphs Reveal Relationships between Different Types of Receptor Ligands and Structural Changes that Determine Agonistic, Inverse-Agonistic, and Antagonistic Effects. 1281-1286
- Min Wu, Elin Grahn, Leif A. Eriksson, Åke Strid:
Computational Evidence for the Role of Arabidopsis thaliana UVR8 as UV-B Photoreceptor and Identification of Its Chromophore Amino Acids. 1287-1295 - Zheng Zheng, Kenneth M. Merz Jr.:
Ligand Identification Scoring Algorithm (LISA). 1296-1306 - David Ryan Koes, Carlos J. Camacho:
Pharmer: Efficient and Exact Pharmacophore Search. 1307-1314 - Ricardo J. Ferreira, Daniel J. V. A. dos Santos, Maria-José U. Ferreira, Rita C. Guedes:
Toward a Better Pharmacophore Description of P-Glycoprotein Modulators, Based on Macrocyclic Diterpenes from Euphorbia Species. 1315-1324
- Nicolas Floquet, Jean-François Hernandez, Jean-Luc Boucher, Jean Martinez:
l-Arginine Binding to Human Inducible Nitric Oxide Synthase: An Antisymmetric Funnel Route toward Isoform-Specific Inhibitors? 1325-1335 - Tao Zhang, Limin Angela Liu, David F. V. Lewis, Dong-Qing Wei:
Long-Range Effects of a Peripheral Mutation on the Enzymatic Activity of Cytochrome P450 1A2. 1336-1346 - Yiyu Li, Brian T. Sutch, Huynh-Hoa Bui, Timothy K. Gallaher, Ian S. Haworth:
Modeling of the Water Network at Protein-RNA Interfaces. 1347-1352
- Sanna P. Niinivehmas, Salla I. Virtanen, Jukka V. Lehtonen, Pekka A. Postila, Olli T. Pentikäinen:
Comparison of Virtual High-Throughput Screening Methods for the Identification of Phosphodiesterase-5 Inhibitors. 1353-1363 - Ji-Xia Ren, Lin-Li Li, Ren-Lin Zheng, Huan-Zhang Xie, Zhi-Xing Cao, Shan Feng, You-Li Pan, Xin Chen, Yu-Quan Wei, Sheng-Yong Yang:
Discovery of Novel Pim-1 Kinase Inhibitors by a Hierarchical Multistage Virtual Screening Approach Based on SVM Model, Pharmacophore, and Molecular Docking. 1364-1375 - Prasenjit Mukherjee, Falgun Shah, Prashant V. Desai, Mitchell A. Avery:
Inhibitors of SARS-3CLpro: Virtual Screening, Biological Evaluation, and Molecular Dynamics Simulation Studies. 1376-1392 - Ruoli Bai, Tam Luong Nguyen, James C. Burnett, Onur Atasoylu, Murray H. G. Munro, George R. Pettit, Amos B. Smith III, Rick Gussio, Ernest Hamel:
Interactions of Halichondrin B and Eribulin with Tubulin. 1393-1404 - Kuldeep K. Roy, Anil K. Saxena:
Structural Basis for the β-Adrenergic Receptor Subtype Selectivity of the Representative Agonists and Antagonists. 1405-1422 - Andreas Spitzmüller, Hans F. G. Velec, Gerhard Klebe:
MiniMuDS: A New Optimizer using Knowledge-Based Potentials Improves Scoring of Docking Solutions. 1423-1430 - Jiansong Fang, Dane Huang, Wenxia Zhao, Hu Ge, Hai-Bin Luo, Jun Xu:
A New Protocol for Predicting Novel GSK-3β ATP Competitive Inhibitors. 1431-1438 - Sara E. Nichols, Riccardo Baron, Anthony Ivetac, James Andrew McCammon:
Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening. 1439-1446 - Zhi Wang, Yuanying Chen, Hu Liang, Andreas Bender, Robert C. Glen, Aixia Yan:
P-glycoprotein Substrate Models Using Support Vector Machines Based on a Comprehensive Data set. 1447-1456
- Motosuke Tsutsumi, Joji M. Otaki:
Parallel and Antiparallel β-Strands Differ in Amino Acid Composition and Availability of Short Constituent Sequences. 1457-1464 - Luis Fernández Pacios, Leticia Tordesillas, Arantxa Palacín, Rosa Sánchez-Monge, Gabriel Salcedo, Araceli Díaz-Perales:
LocaPep: Localization of Epitopes on Protein Surfaces Using Peptides from Phage Display Libraries. 1465-1473
- Yan Li, Yuan Zhao, Zhihai Liu, Renxiao Wang:
Automatic Tailoring and Transplanting: A Practical Method that Makes Virtual Screening More Useful. 1474-1491 - Santiago Melchor, Francisco J. Martin-Martinez, José A. Dobado Jimez:
CoNTub v2.0 - Algorithms for Constructing C3-Symmetric Models of Three-Nanotube Junctions. 1492-1505 - Kenneth Kroenlein, Chris Muzny, Vladimir V. Diky, Andrei F. Kazakov, Robert D. Chirico, Joseph W. Magee, Ilmutdin Abdulagatov, Michael Frenkel:
ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 6. Dynamic Web-Based Data Dissemination through the NIST Web Thermo Tables. 1506-1512
Volume 51, Number 7, July 2011
- Francesco Musiani, Matteo Bellucci, Stefano Ciurli:
Model Structures of Helicobacter pylori UreD(H) Domains: A Putative Molecular Recognition Platform. 1513-1520
- Chao Ma, Lirong Wang, Xiang-Qun Xie:
GPU Accelerated Chemical Similarity Calculation for Compound Library Comparison. 1521-1527 - Thibault Varin, Ansgar Schuffenhauer, Peter Ertl, Steffen Renner:
Mining for Bioactive Scaffolds with Scaffold Networks: Improved Compound Set Enrichment from Primary Screening Data. 1528-1538 - Robert Lowe, Hamse Y. Mussa, John B. O. Mitchell, Robert C. Glen:
Classifying Molecules Using a Sparse Probabilistic Kernel Binary Classifier. 1539-1544 - Vigneshwaran Namasivayam, Preeti Iyer, Jürgen Bajorath:
Extraction of Discontinuous Structure-Activity Relationships from Compound Data Sets through Particle Swarm Optimization. 1545-1551
- John R. Owen, Ian T. Nabney, José L. Medina-Franco, Fabian López-Vallejo:
Visualization of Molecular Fingerprints. 1552-1563 - Mosé Casalegno, Emilio Benfenati, Guido Sello:
Identification of Toxifying and Detoxifying Moieties for Mutagenicity Prediction by Priority Assessment. 1564-1574 - Andrew G. Mercader, Pablo Duchowicz, Francisco M. Fernández, Eduardo A. Castro:
Advances in the Replacement and Enhanced Replacement Method in QSAR and QSPR Theories. 1575-1581 - Li Xing, Robert Goulet, Kjell Johnson:
Statistical Analysis and Compound Selection of Combinatorial Libraries for Soluble Epoxide Hydrolase. 1582-1592 - Jamel Meslamani, Didier Rognan:
Enhancing the Accuracy of Chemogenomic Models with a Three-Dimensional Binding Site Kernel. 1593-1603
- Aqeel Ahmed, Friedrich Rippmann, Gerhard Barnickel, Holger Gohlke:
A Normal Mode-Based Geometric Simulation Approach for Exploring Biologically Relevant Conformational Transitions in Proteins. 1604-1622 - Esteban Lanzarotti, Rolf R. Biekofsky, Dario A. Estrin, Marcelo A. Marti, Adrian Gustavo Turjanski:
Aromatic-Aromatic Interactions in Proteins: Beyond the Dimer. 1623-1633 - Di Wu, Qin Wang, Rajeev S. Assary, Linda J. Broadbelt, Goran Krilov:
A Computational Approach To Design and Evaluate Enzymatic Reaction Pathways: Application to 1-Butanol Production from Pyruvate. 1634-1647 - Robert D. Malmstrom, Stanley J. Watowich:
Using Free Energy of Binding Calculations To Improve the Accuracy of Virtual Screening Predictions. 1648-1655 - Yaohang Li, Ionel Rata, Eric Jakobsson:
Sampling Multiple Scoring Functions Can Improve Protein Loop Structure Prediction Accuracy. 1656-1666
- Jed Zaretzki, Charles Bergeron, Patrik Rydberg, Tao-wei Huang, Kristin P. Bennett, Curt M. Breneman:
RS-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to CYP 3A4. 1667-1689 - Sílvia G. Estácio, Rui Moreira, Rita C. Guedes:
Characterizing the Dynamics and Ligand-Specific Interactions in the Human Leukocyte Elastase through Molecular Dynamics Simulations. 1690-1702 - Fang-Yu Lin, Yufeng J. Tseng:
Structure-Based Fragment Hopping for Lead Optimization Using Predocked Fragment Database. 1703-1715 - Mojca Brunskole Svegelj, Samo Turk, Boris Brus, Tea Lanisnik Rizner, Jure Stojan, Stanislav Gobec:
Novel Inhibitors of Trihydroxynaphthalene Reductase with Antifungal Activity Identified by Ligand-Based and Structure-Based Virtual Screening. 1716-1724
- Kalidas Yeturu, Nagasuma R. Chandra:
PocketAlign A Novel Algorithm for Aligning Binding Sites in Protein Structures. 1725-1736
- Zhenming Liu, Bo Li, Xia Li, Liang Ren Zhang, Luhua Lai:
Correction to Identification of Small-Molecule Inhibitors against Human Leukocyte Antigen-Death Receptor 4 (HLA-DR4) Through a Comprehensive Strategy. 1737
Volume 51, Number 8, August 2011
- Pedro J. Ballester, John B. O. Mitchell:
Comments on "Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets": Significance for the Validation of Scoring Functions. 1739-1741
- Ye Hu, Dagmar Stumpfe, Jürgen Bajorath:
Lessons Learned from Molecular Scaffold Analysis. 1742-1753
- Carleton R. Sage, Runtong Wang, Gareth Jones:
G-Protein Coupled Receptors Virtual Screening Using Genetic Algorithm Focused Chemical Space. 1754-1761 - Vincent Le Guilloux, Lionel Colliandre, Stéphane Bourg, Guillaume Guénegou, Julie Dubois-Chevalier, Luc Morin-Allory:
Visual Characterization and Diversity Quantification of Chemical Libraries: 1. Creation of Delimited Reference Chemical Subspaces. 1762-1774 - Takeshi Kawabata:
Build-Up Algorithm for Atomic Correspondence between Chemical Structures. 1775-1787 - Patrik L. Andersson, Jerker Fick, Stefan Rannar:
A Multivariate Chemical Similarity Approach to Search for Drugs of Potential Environmental Concern. 1788-1794 - Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Michal Kudera, David Sehnal, Tomás Bouchal, Ruben Abagyan, Heinrich J. Huber, Jaroslav Koca:
Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. 1795-1806 - Pu Liu, Dimitris K. Agrafiotis, Dmitrii N. Rassokhin, Eric Yang:
Accelerating Chemical Database Searching Using Graphics Processing Units. 1807-1816 - Izhar Wallach, Navdeep Jaitly, Kong T. Nguyen, Matthieu Schapira, Ryan H. Lilien:
Normalizing Molecular Docking Rankings using Virtually Generated Decoys. 1817-1830 - Kathrin Heikamp, Jürgen Bajorath:
Large-Scale Similarity Search Profiling of ChEMBL Compound Data Sets. 1831-1839 - Ola Spjuth, Martin Eklund, Ernst Ahlberg Helgee, Scott Boyer, Lars Carlsson:
Integrated Decision Support for Assessing Chemical Liabilities. 1840-1847 - Martin Vogt, Yun Huang, Jürgen Bajorath:
From Activity Cliffs to Activity Ridges: Informative Data Structures for SAR Analysis. 1848-1856 - Anne Mai Wassermann, Jürgen Bajorath:
A Data Mining Method To Facilitate SAR Transfer. 1857-1866
- Gianluca Rossato, Beat Ernst, Angelo Vedani, Martin Smiesko:
AcquaAlta: A Directional Approach to the Solvation of Ligand-Protein Complexes. 1867-1881 - Matteo Calvaresi, Francesco Zerbetto:
In Silico Carborane Docking to Proteins and Potential Drug Targets. 1882-1896
- Michael Bieler, Ralf Heilker, Herbert Köppen, Gisbert Schneider:
Assay Related Target Similarity (ARTS) - Chemogenomics Approach for Quantitative Comparison of Biological Targets. 1897-1905 - Mats Linder, Adam Johannes Johansson, Tjelvar S. G. Olsson, John W. Liebeschuetz, Tore Brinck:
Designing a New Diels-Alderase: A Combinatorial, Semirational Approach Including Dynamic Optimization. 1906-1917 - Carlos M. A. Guardia, Diego F. Gauto, Santiago Di Lella, Gabriel A. Rabinovich, Marcelo A. Marti, Dario A. Estrin:
An Integrated Computational Analysis of the Structure, Dynamics, and Ligand Binding Interactions of the Human Galectin Network. 1918-1930
- Barry C. Finzel, Ramprasad Akavaram, Aravind Ragipindi, Jeffrey R. Van Voorst, Matthew H. Cahn, Malcolm E. Davis, Matt E. Pokross, Steven Sheriff, Eric T. Baldwin:
Conserved Core Substructures in the Overlay of Protein-Ligand Complexes. 1931-1941 - Eric J. Martin, Prasenjit Mukherjee, David C. Sullivan, Johanna M. Jansen:
Profile-QSAR: A Novel meta-QSAR Method that Combines Activities across the Kinase Family To Accurately Predict Affinity, Selectivity, and Cellular Activity. 1942-1956 - Lingling Shen, Theresa L. Johnson, Susan Clugston, Hongwei Huang, Kenneth J. Butenhof, Robert V. Stanton:
Molecular Dynamics Simulation and Binding Energy Calculation for Estimation of Oligonucleotide Duplex Thermostability in RNA-Based Therapeutics. 1957-1965 - Shome S. Bhunia, Kuldeep K. Roy, Anil K. Saxena:
Profiling the Structural Determinants for the Selectivity of Representative Factor-Xa and Thrombin Inhibitors Using Combined Ligand-Based and Structure-Based Approaches. 1966-1985 - Anthony K. Felts, Krystal LaBarge, Joseph D. Bauman, Dishaben V. Patel, Daniel Himmel, Eddy Arnold, Michael A. Parniak, Ronald M. Levy:
Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies. 1986-1998 - Xiaoyan Huang, Zhi Jie Shan, Hong Lin Zhai, Lina Li, Xiaoyun Zhang:
Molecular Design of Anticancer Drug Leads Based on Three-Dimensional Quantitative Structure-Activity Relationship. 1999-2006
- Martin Brehm, Barbara Kirchner:
TRAVIS - A Free Analyzer and Visualizer for Monte Carlo and Molecular Dynamics Trajectories. 2007-2023
Volume 51, Number 9, September 2011
- Heather A. Carlson, James B. Dunbar Jr.:
A Call to Arms: What You Can Do for Computational Drug Discovery. 2025-2026
- Jui-Hua Hsieh, Shuangye Yin, Shubin Liu, Alexander Sedykh, Nikolay V. Dokholyan, Alexander Tropsha:
Combined Application of Cheminformatics- and Physical Force Field-Based Scoring Functions Improves Binding Affinity Prediction for CSAR Data Sets. 2027-2035
- James B. Dunbar Jr., Richard D. Smith, Chao-Yie Yang, Peter Man-Un Ung, Katrina W. Lexa, Nickolay A. Khazanov, Jeanne A. Stuckey, Shaomeng Wang, Heather A. Carlson:
CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. 2036-2046 - Obaidur Rahaman, Trilce Estrada, Douglas J. Doren, Michela Taufer, Charles L. Brooks III, Roger S. Armen:
Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy. 2047-2065 - Traian Sulea, Qizhi Cui, Enrico O. Purisima:
Solvated Interaction Energy (SIE) for Scoring Protein-Ligand Binding Affinities. 2. Benchmark in the CSAR-2010 Scoring Exercise. 2066-2081 - Chaya Rapp, Chakrapani Kalyanaraman, Aviva Schiffmiller, Esther Leah Schoenbrun, Matthew P. Jacobson:
A Molecular Mechanics Approach to Modeling Protein-Ligand Interactions: Relative Binding Affinities in Congeneric Series. 2082-2089 - Fedor N. Novikov, Alexey A. Zeifman, Oleg V. Stroganov, Viktor S. Stroylov, Val Kulkov, Ghermes G. Chilov:
CSAR Scoring Challenge Reveals the Need for New Concepts in Estimating Protein-Ligand Binding Affinity. 2090-2096 - Sheng-You Huang, Xiaoqin Zou:
Scoring and Lessons Learned with the CSAR Benchmark Using an Improved Iterative Knowledge-Based Scoring Function. 2097-2106 - Sheng-You Huang, Xiaoqin Zou:
Construction and Test of Ligand Decoy Sets Using MDock: Community Structure-Activity Resource Benchmarks for Binding Mode Prediction. 2107-2114 - Richard D. Smith, James B. Dunbar Jr., Peter Man-Un Ung, Emilio Xavier Esposito, Chao-Yie Yang, Shaomeng Wang, Heather A. Carlson:
CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions. 2115-2131
- Liwei Li, Bo Wang, Samy O. Meroueh:
Support Vector Regression Scoring of Receptor-Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries. 2132-2138
- Christian Kramer, Peter Gedeck:
Three Descriptor Model Sets a High Standard for the CSAR-NRC HiQ Benchmark. 2139-2145
- James B. Dunbar Jr., Richard D. Smith, Chao-Yie Yang, Peter Man-Un Ung, Katrina W. Lexa, Nickolay A. Khazanov, Jeanne A. Stuckey, Shaomeng Wang, Heather A. Carlson:
Correction to CSAR Benchmark Exercise of 2010: Selection of the Protein-Ligand Complexes. 2146
- Wenxia Zhao, Qiong Gu, Ling Wang, Hu Ge, Jiabo Li, Jun Xu:
Three-Dimensional Pharmacophore Modeling of Liver-X Receptor Agonists. 2147-2155 - J. Robert Fischer, Uta F. Lessel, Matthias Rarey:
Improving Similarity-Driven Library Design: Customized Matching and Regioselective Feature Trees. 2156-2163 - Eric Beaser, Jennifer K. Schwartz, Caleb B. Bell III, Edward I. Solomon:
Hybrid Genetic Algorithm with an Adaptive Penalty Function for Fitting Multimodal Experimental Data: Application to Exchange-Coupled Non-Kramers Binuclear Iron Active Sites. 2164-2173 - Sarah R. Langdon, Nathan Brown, Julian Blagg:
Scaffold Diversity of Exemplified Medicinal Chemistry Space. 2174-2185 - William Lingran Chen, Burton A. Leland, Joseph L. Durant, David L. Grier, Bradley D. Christie, James G. Nourse, Keith T. Taylor:
Self-Contained Sequence Representation: Bridging the Gap between Bioinformatics and Cheminformatics. 2186-2208 - Matthew A. Kayala, Chloé-Agathe Azencott, Jonathan H. Chen, Pierre Baldi:
Learning to Predict Chemical Reactions. 2209-2222 - Julian E. Fuchs, Gudrun M. Spitzer, Ameera Javed, Adam Biela, Christoph Kreutz, Bernd Wellenzohn, Klaus R. Liedl:
Minor Groove Binders and Drugs Targeting Proteins Cover Complementary Regions in Chemical Shape Space. 2223-2232 - Masahiko Taniguchi, Hai Du, Jonathan S. Lindsey:
Virtual Libraries of Tetrapyrrole Macrocycles. Combinatorics, Isomers, Product Distributions, and Data Mining. 2233-2247 - Imran S. Haque, Vijay S. Pande:
Error Bounds on the SCISSORS Approximation Method. 2248-2253 - Kathrin Heikamp, Jürgen Bajorath:
How Do 2D Fingerprints Detect Structurally Diverse Active Compounds? Revealing Compound Subset-Specific Fingerprint Features through Systematic Selection. 2254-2265
- Trang Truc Nguyen, Binh Khanh Mai, Mai Suan Li:
Study of Tamiflu Sensitivity to Variants of A/H5N1 Virus Using Different Force Fields. 2266-2276 - Marijn P. A. Sanders, Stefan Verhoeven, Chris de Graaf, Luc Roumen, Bas Vroling, Sander B. Nabuurs, Jacob de Vlieg, Jan P. G. Klomp:
Snooker: A Structure-Based Pharmacophore Generation Tool Applied to Class A GPCRs. 2277-2292 - Li Gao, Yaoquan Tu, Pia Wegman, Sten Wingren, Leif A. Eriksson:
A Mechanistic Hypothesis for the Cytochrome P450-Catalyzed Cis-Trans Isomerization of 4-Hydroxytamoxifen: An Unusual Redox Reaction. 2293-2301 - Margaret R. McLellan, M. Dominic Ryan, Curt M. Breneman:
Rank Order Entropy: Why One Metric Is Not Enough. 2302-2319 - Nicola Chirico, Paola Gramatica:
Real External Predictivity of QSAR Models: How To Evaluate It? Comparison of Different Validation Criteria and Proposal of Using the Concordance Correlation Coefficient. 2320-2335 - Haiying Yu, Ralph Kühne, Ralf-Uwe Ebert, Gerrit Schüürmann:
Prediction of the Dissociation Constant pKa of Organic Acids from Local Molecular Parameters of Their Electronic Ground State. 2336-2344 - Imran S. Haque, Vijay S. Pande, W. Patrick Walters:
Anatomy of High-Performance 2D Similarity Calculations. 2345-2351
- Hoang T. Tran, Shuxing Zhang:
Accurate Prediction of the Bound Form of the Akt Pleckstrin Homology Domain Using Normal Mode Analysis To Explore Structural Flexibility. 2352-2360 - Guang Hu, Servaas Michielssens, Samuel L. C. Moors, Arnout Ceulemans:
Normal Mode Analysis of Trp RNA Binding Attenuation Protein: Structure and Collective Motions. 2361-2371
- Xiaofeng Liu, Hualiang Jiang, Honglin Li:
SHAFTS: A Hybrid Approach for 3D Molecular Similarity Calculation. 1. Method and Assessment of Virtual Screening. 2372-2385 - Minos-Timotheos Matsoukas, Panagiotis Zoumpoulakis, Theodore V. Tselios:
Conformational Analysis of Aliskiren, a Potent Renin Inhibitor, Using High-Resolution Nuclear Magnetic Resonance and Molecular Dynamics Simulations. 2386-2397 - Mitsuhito Wada, Eiji Kanamori, Haruki Nakamura, Yoshifumi Fukunishi:
Selection of In Silico Drug Screening Results for G-Protein-Coupled Receptors by Using Universal Active Probes. 2398-2407 - Markus Muehlbacher, Ahmed M. El Kerdawy, Christian Kramer, Brian Hudson, Timothy Clark:
Conformation-Dependent QSPR Models: logPOW. 2408-2416 - Sankar Manepalli, Laura M. Geffert, Christopher K. Surratt, Jeffry D. Madura:
Discovery of Novel Selective Serotonin Reuptake Inhibitors through Development of a Protein-Based Pharmacophore. 2417-2426 - José L. Medina-Franco, Austin B. Yongye, Jaime Pérez-Villanueva, Richard A. Houghten, Karina Martínez-Mayorga:
Multitarget Structure-Activity Relationships Characterized by Activity-Difference Maps and Consensus Similarity Measure. 2427-2439
- Tiejun Cheng, Qingliang Li, Yanli Wang, Stephen H. Bryant:
Identifying Compound-Target Associations by Combining Bioactivity Profile Similarity Search and Public Databases Mining. 2440-2448
Volume 51, Number 10, October 2011
- N. Yi Mok, Ruth Brenk:
Mining the ChEMBL Database: An Efficient Chemoinformatics Workflow for Assembling an Ion Channel-Focused Screening Library. 2449-2454 - G. Madhavi Sastry, Steven L. Dixon, Woody Sherman:
Rapid Shape-Based Ligand Alignment and Virtual Screening Method Based on Atom/Feature-Pair Similarities and Volume Overlap Scoring. 2455-2466 - Peter Ripphausen, Anne Mai Wassermann, Jürgen Bajorath:
REPROVIS-DB: A Benchmark System for Ligand-Based Virtual Screening Derived from Reproducible Prospective Applications. 2467-2473 - Hongmao Sun, Henrike Veith, Menghang Xia, Christopher P. Austin, Ruili Huang:
Predictive Models for Cytochrome P450 Isozymes Based on Quantitative High Throughput Screening Data. 2474-2481 - Feixiong Cheng, Yue Yu, Yadi Zhou, Zhonghua Shen, Wen Xiao, Guixia Liu, Weihua Li, Philip W. Lee, Yun Tang:
Insights into Molecular Basis of Cytochrome P450 Inhibitory Promiscuity of Compounds. 2482-2495 - Martin Vogt, Jürgen Bajorath:
Introduction of the Conditional Correlated Bernoulli Model of Similarity Value Distributions and its Application to the Prospective Prediction of Fingerprint Search Performance. 2496-2506 - Ruifang Li, Dagmar Stumpfe, Martin Vogt, Hanna Geppert, Jürgen Bajorath:
Development of a Method To Consistently Quantify the Structural Distance between Scaffolds and To Assess Scaffold Hopping Potential. 2507-2514
- Tanya Singh, D. Biswas, Bhyravabhotla Jayaram:
AADS - An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors. 2515-2527 - Jui-Chih Wang, Jung-Hsin Lin, Chung-Ming Chen, Alex L. Perryman, Arthur J. Olson:
Robust Scoring Functions for Protein-Ligand Interactions with Quantum Chemical Charge Models. 2528-2537 - Gabriela L. Borosky, Susana Lin:
Computational Modeling of the Catalytic Mechanism of Human Placental Alkaline Phosphatase (PLAP). 2538-2548 - Mahmoud A. A. Ibrahim:
Performance Assessment of Semiempirical Molecular Orbital Methods in Describing Halogen Bonding: Quantum Mechanical and Quantum Mechanical/Molecular Mechanical-Molecular Dynamics Study. 2549-2559 - Ming Hao, Yan Li, Yonghua Wang, Yulian Yan, Shuwei Zhang:
Combined 3D-QSAR, Molecular Docking, and Molecular Dynamics Study on Piperazinyl-Glutamate-Pyridines/Pyrimidines as Potent P2Y12 Antagonists for Inhibition of Platelet Aggregation. 2560-2572 - Jacob D. Durrant, Aaron J. Friedman, James Andrew McCammon:
CrystalDock: A Novel Approach to Fragment-Based Drug Design. 2573-2580
- Daniel Cappel, Rickard Wahlström, Ruth Brenk, Christoph A. Sotriffer:
Probing the Dynamic Nature of Water Molecules and Their Influences on Ligand Binding in a Model Binding Site. 2581-2594 - Alfonso T. García-Sosa, Sulev Sild, Kalev Takkis, Uko Maran:
Combined Approach Using Ligand Efficiency, Cross-Docking, and Antitarget Hits for Wild-Type and Drug-Resistant Y181C HIV-1 Reverse Transcriptase. 2595-2611 - Jing-Yuan Liu, Zhaomin Li, Huian Li, Jian-Ting Zhang:
Critical Residue That Promotes Protein Dimerization: A Story of Partially Exposed Phe25 in 14-3-3σ. 2612-2625 - Yuanhua Cheng, Fushi Zhang, Quan Chen, Jian Gao, Wei Cui, Mingjuan Ji, Chen-Ho Tung:
Structural Basis of Specific Binding between Aurora A and TPX2 by Molecular Dynamics Simulations. 2626-2635 - David W. Wright, Peter V. Coveney:
Resolution of Discordant HIV-1 Protease Resistance Rankings Using Molecular Dynamics Simulations. 2636-2649
- Simon M. Vogel, Matthias R. Bauer, Frank M. Boeckler:
DEKOIS: Demanding Evaluation Kits for Objective in Silico Screening - A Versatile Tool for Benchmarking Docking Programs and Scoring Functions. 2650-2665 - Ian R. Craig, Christopher Pfleger, Holger Gohlke, Jonathan W. Essex, Katrin Spiegel:
Pocket-Space Maps To Identify Novel Binding-Site Conformations in Proteins. 2666-2679 - Markus A. Lill, Jared J. Thompson:
Solvent Interaction Energy Calculations on Molecular Dynamics Trajectories: Increasing the Efficiency Using Systematic Frame Selection. 2680-2689 - Felix Hammann, Claudia Suenderhauf, Jörg Huwyler:
A Binary Ant Colony Optimization Classifier for Molecular Activities. 2690-2696 - Prasenjit Mukherjee, Eric J. Martin:
Development of a Minimal Kinase Ensemble Receptor (MKER) for Surrogate AutoShim. 2697-2705 - Seiji Hitaoka, Hiroshi Matoba, Masataka Harada, Tatsusada Yoshida, Daisuke Tsuji, Takatsugu Hirokawa, Kohji Itoh, Hiroshi Chuman:
Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures - LERE-QSAR Analysis (IV). 2706-2716 - Mohsen Shahlaei, Armin Madadkar-Sobhani, Afshin Fassihi, Lotfollah Saghaie:
Exploring a Model of a Chemokine Receptor/Ligand Complex in an Explicit Membrane Environment by Molecular Dynamics Simulation: The Human CCR1 Receptor. 2717-2730 - Gerd Neudert, Gerhard Klebe:
DSX: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes. 2731-2745 - Alfonso Pérez-Garrido, Aliuska Morales Helguera, Fernanda Borges, M. Natália Dias Soeiro Cordeiro, Virginia Rivero, Amalio Garrido Escudero:
Two New Parameters Based on Distances in a Receiver Operating Characteristic Chart for the Selection of Classification Models. 2746-2759
- Alexander M. Andrianov, Ivan V. Anishchenko, Alexander V. Tuzikov:
Discovery of Novel Promising Targets for Anti-AIDS Drug Developments by Computer Modeling: Application to the HIV-1 gp120 V3 Loop. 2760-2767
- Qi Huang, Lin-Li Li, Sheng-Yong Yang:
RASA: A Rapid Retrosynthesis-Based Scoring Method for the Assessment of Synthetic Accessibility of Drug-like Molecules. 2768-2777 - Roman A. Laskowski, Mark B. Swindells:
LigPlot+: Multiple Ligand-Protein Interaction Diagrams for Drug Discovery. 2778-2786
Volume 51, Number 11, November 2011
- Colin R. Groom:
Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre. 2787
- Tomoki Imada, Shunsuke Ota, Hiroshi Nagamochi, Tatsuya Akutsu:
Efficient Enumeration of Stereoisomers of Outerplanar Chemical Graphs Using Dynamic Programming. 2788-2807 - Charles Bergeron, Gregory M. Moore, Michael P. Krein, Curt M. Breneman, Kristin P. Bennett:
Exploiting Domain Knowledge for Improved Quantitative High-Throughput Screening Curve Fitting. 2808-2820 - Fei Wang, DongXiang Liu, Heyao Wang, Cheng Luo, Mingyue Zheng, Hong Liu, Weiliang Zhu, Xiaomin Luo, Jian Zhang, Hualiang Jiang:
Computational Screening for Active Compounds Targeting Protein Sequences: Methodology and Experimental Validation. 2821-2828 - Agata Krasowski, Daniel Muthas, Aurijit Sarkar, Stefan Schmitt, Ruth Brenk:
DrugPred: A Structure-Based Approach To Predict Protein Druggability Developed Using an Extensive Nonredundant Data Set. 2829-2842 - Pu Liu, Dimitris K. Agrafiotis, Dmitrii N. Rassokhin:
Power Keys: A Novel Class of Topological Descriptors Based on Exhaustive Subgraph Enumeration and their Application in Substructure Searching. 2843-2851 - Eric Yang, Pu Liu, Dmitrii N. Rassokhin, Dimitris K. Agrafiotis:
Stochastic Proximity Embedding on Graphics Processing Units: Taking Multidimensional Scaling to a New Scale. 2852-2859
- Hannes G. Wallnoefer, Klaus R. Liedl, Thomas Fox:
A GRID-Derived Water Network Stabilizes Molecular Dynamics Computer Simulations of a Protease. 2860-2867 - Ilaria Motto, Annalisa Bordogna, Anatoly A. Soshilov, Michael S. Denison, Laura Bonati:
New Aryl Hydrocarbon Receptor Homology Model Targeted To Improve Docking Reliability. 2868-2881 - Angelo D. Favia, Giovanni Bottegoni, Irene Nobeli, Paola Bisignano, Andrea Cavalli:
SERAPhiC: A Benchmark for in Silico Fragment-Based Drug Design. 2882-2896 - Jacob D. Durrant, James Andrew McCammon:
NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function. 2897-2903
- Yan Li, Dong Joon Kim, Weiya Ma, Ronald A. Lubet, Ann M. Bode, Zigang Dong:
Discovery of Novel Checkpoint Kinase 1 Inhibitors by Virtual Screening Based on Multiple Crystal Structures. 2904-2914 - Oliver Korb, Patrick McCabe, Jason C. Cole:
The Ensemble Performance Index: An Improved Measure for Assessing Ensemble Pose Prediction Performance. 2915-2919 - Julio Caballero, Jans H. Alzate-Morales, Ariela Vergara Jaque:
Investigation of the Differences in Activity between Hydroxycycloalkyl N1 Substituted Pyrazole Derivatives As Inhibitors of B-Raf Kinase by Using Docking, Molecular Dynamics, QM/MM, and Fragment-Based De Novo Design: Study of Binding Mode of Diastereomer Compounds. 2920-2931
- Anjali D. Ganjiwale, Gita Subba Rao, Sudha M. Cowsik:
Molecular Modeling of Neurokinin B and Tachykinin NK3 Receptor Complex. 2932-2938 - Shiliang Li, Yi Zhou, Weiqiang Lu, Ye Zhong, Wenlong Song, Kangdong Liu, Jin Huang, Zhenjiang Zhao, Yufang Xu, Xiaofeng Liu, Honglin Li:
Identification of Inhibitors against p90 Ribosomal S6 Kinase 2 (RSK2) through Structure-Based Virtual Screening with the Inhibitor-Constrained Refined Homology Model. 2939-2947 - Lei Du-Cuny, Lu Chen, Shuxing Zhang:
A Critical Assessment of Combined Ligand- and Structure-Based Approaches to hERG Channel Blocker Modeling. 2948-2960 - Sébastien Dilly, Jacqueline Scuvée-Moreau, Johan Wouters, Jean-François Liégeois:
The 5-HT1A Agonism Potential of Substituted Piperazine-Ethyl-Amide Derivatives Is Conserved in the Hexyl Homologues: Molecular Modeling and Pharmacological Evaluation. 2961-2966 - Matthew D. Segall, Edmund J. Champness, Chris Leeding, Ryan H. Lilien, Ramgopal R. Mettu, Brian W. Stevens:
Applying Medicinal Chemistry Transformations and Multiparameter Optimization to Guide the Search for High-Quality Leads and Candidates. 2967-2976 - Masataka Takarabe, Daichi Shigemizu, Masaaki Kotera, Susumu Goto, Minoru Kanehisa:
Network-Based Analysis and Characterization of Adverse Drug-Drug Interactions. 2977-2985 - Hwangseo Park, Okyung Chi, Jinhee Kim, Sungwoo Hong:
Identification of Novel Inhibitors of Tropomyosin-Related Kinase A through the Structure-Based Virtual Screening with Homology-Modeled Protein Structure. 2986-2993 - Mingyue Zheng, Bing Xiong, Cheng Luo, Shanshan Li, Xian Liu, Qiancheng Shen, Jing Li, Weiliang Zhu, Xiaomin Luo, Hualiang Jiang:
Knowledge-Based Scoring Functions in Drug Design: 3. A Two-Dimensional Knowledge-Based Hydrogen-Bonding Potential for the Prediction of Protein-Ligand Interactions. 2994-3004
- Rosalba Lepore, Silvia Simeoni, Domenico Raimondo, Antonia Caroli, Anna Tramontano, Allegra Via:
Identification of the Schistosoma mansoni Molecular Target for the Antimalarial Drug Artemether. 3005-3016 - Benny Kneissl, Sabine C. Mueller, Christofer S. Tautermann, Andreas Hildebrandt:
String Kernels and High-Quality Data Set for Improved Prediction of Kinked Helices in α-Helical Membrane Proteins. 3017-3025
- Preeti Iyer, Ye Hu, Jürgen Bajorath:
SAR Monitoring of Evolving Compound Data Sets Using Activity Landscapes. 3026 - Ming Hao, Yan Li, Yonghua Wang, Yulian Yan, Shuwei Zhang, Guohui Li, Ling Yang:
Combined 3D-QSAR, Molecular Docking, and Molecular Dynamics Study on Piperazinyl-Glutamate-Pyridines/Pyrimidines as Potent P2Y12 Antagonists for Inhibition of Platelet Aggregation. 3027
Volume 51, Number 12, December 2011
- Pierre Baldi:
Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response to the Letter by the Cambridge Crystallographic Data Centre. 3029
- Lili X. Peng, Lei Yu, Stephen B. Howell, David A. Gough:
Aggregation Properties of a Polymeric Anticancer Therapeutic: A Coarse-Grained Modeling Study. 3030-3035
- Oscar Miguel Rivera-Borroto, Yovani Marrero-Ponce, José Manuel García de la Vega, Ricardo del Corazón Grau-Ábalo:
Comparison of Combinatorial Clustering Methods on Pharmacological Data Sets Represented by Machine Learning-Selected Real Molecular Descriptors. 3036-3049 - Antoine Le Roux, Igor Kuzmanovski, Damien Habrant, Stéphane Meunier, Pierre Bischoff, Brice Nadal, Sophie A.-L. Thetiot-Laurent, Thierry Le Gall, Alain Wagner, Marjana Novic:
Design and Synthesis of New Antioxidants Predicted by the Model Developed on a Set of Pulvinic Acid Derivatives. 3050-3059 - Maykel Cruz-Monteagudo, Fernanda Borges, M. Natália Dias Soeiro Cordeiro:
Jointly Handling Potency and Toxicity of Antimicrobial Peptidomimetics by Simple Rules from Desirability Theory and Chemoinformatics. 3060-3077 - Hao Fan, Dina Schneidman-Duhovny, John J. Irwin, Guang Qiang Dong, Brian K. Shoichet, Andrej Sali:
Statistical Potential for Modeling and Ranking of Protein-Ligand Interactions. 3078-3092 - Markus Hartenfeller, Martin Eberle, Peter Meier, Cristina Nieto-Oberhuber, Karl-Heinz Altmann, Gisbert Schneider, Edgar Jacoby, Steffen Renner:
A Collection of Robust Organic Synthesis Reactions for In Silico Molecule Design. 3093-3098 - Michael C. Hutter:
Determining the Degree of Randomness of Descriptors in Linear Regression Equations with Respect to the Data Size. 3099-3104 - Lorenz C. Blum, Ruud van Deursen, Sonia Bertrand, Milena Mayer, Justus J. Bürgi, Daniel Bertrand, Jean-Louis Reymond:
Discovery of α7-Nicotinic Receptor Ligands by Virtual Screening of the Chemical Universe Database GDB-13. 3105-3112 - Dimitris K. Agrafiotis, Victor S. Lobanov, Maxim Shemanarev, Dmitrii N. Rassokhin, Sergei Izrailev, Edward P. Jaeger, Simson Alex, Michael Farnum:
Efficient Substructure Searching of Large Chemical Libraries: The ABCD Chemical Cartridge. 3113-3130 - Dagmar Stumpfe, Jürgen Bajorath:
Assessing the Confidence Level of Public Domain Compound Activity Data and the Impact of Alternative Potency Measurements on SAR Analysis. 3131-3137 - Ye Hu, Jürgen Bajorath:
Target Family-Directed Exploration of Scaffolds with Different SAR Profiles. 3138-3148 - Alex M. Clark:
Accurate Specification of Molecular Structures: The Case for Zero-Order Bonds and Explicit Hydrogen Counting. 3149-3157 - Eugen Lounkine, Florian Nigsch, Jeremy L. Jenkins, Meir Glick:
Activity-Aware Clustering of High Throughput Screening Data and Elucidation of Orthogonal Structure-Activity Relationships. 3158-3168
- Sorin I. Avram, Liliana M. Pacureanu, Edward Seclaman, Alina Bora, Ludovic Kurunczi:
PLS-DA - Docking Optimized Combined Energetic Terms (PLSDA-DOCET) Protocol: A Brief Evaluation. 3169-3179 - Bernd Kuhn, Julian E. Fuchs, Michael Reutlinger, Martin Stahl, Neil R. Taylor:
Rationalizing Tight Ligand Binding through Cooperative Interaction Networks. 3180-3198 - Sascha Urbaczek, Adrian Kolodzik, J. Robert Fischer, Tobias Lippert, Stefan Heuser, Inken Groth, Tanja Schulz-Gasch, Matthias Rarey:
NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats. 3199-3207
- Alok Jain, Ramasubbu Sankararamakrishnan:
Dynamics of Noncovalent Interactions in All-α and All-β Class Proteins: Implications for the Stability of Amyloid Aggregates. 3208-3216 - Jue Li, Dong-Qing Wei, Jing-Fang Wang, Yi-Xue Li:
A Negative Cooperativity Mechanism of Human CYP2E1 Inferred from Molecular Dynamics Simulations and Free Energy Calculations. 3217-3225 - Nguyen Hoa My, Hajime Hirao, Dang Ung Van, Keiji Morokuma:
Computational Studies of Bacterial Resistance to β-Lactam Antibiotics: Mechanism of Covalent Inhibition of the Penicillin-Binding Protein 2a (PBP2a). 3226-3234
- Ying Yang, Yulin Shen, Huanxiang Liu, Xiaojun Yao:
Molecular Dynamics Simulation and Free Energy Calculation Studies of the Binding Mechanism of Allosteric Inhibitors with p38α MAP Kinase. 3235-3246 - Anna L. Bowman, Alexandros Makriyannis:
Approximating Protein Flexibility through Dynamic Pharmacophore Models: Application to Fatty Acid Amide Hydrolase (FAAH). 3247-3253 - Shan He, Luhua Lai:
Molecular Docking and Competitive Binding Study Discovered Different Binding Modes of Microsomal Prostaglandin E Synthase-1 Inhibitors. 3254-3261 - Soo-Kyung Kim, Peter Fristrup, Ravinder Abrol, William A. Goddard III:
Structure-Based Prediction of Subtype Selectivity of Histamine H3 Receptor Selective Antagonists in Clinical Trials. 3262-3274 - Michael D. Hack, Dmitrii N. Rassokhin, Christophe Buyck, Mark Seierstad, Andrew Skalkin, Peter ten Holte, Todd K. Jones, Taraneh Mirzadegan, Dimitris K. Agrafiotis:
Library Enhancement through the Wisdom of Crowds. 3275-3286
- Fei Guo, Shuai Cheng Li, Lusheng Wang:
Protein-Protein Binding Sites Prediction by 3D Structural Similarities. 3287-3294
- Barry K. Lavine:
Electronic van der Waals Surface Property Descriptors and Genetic Algorithms for Developing Structure-Activity Correlations in Olfactory Databases. 3295
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