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ORCIDJournal of Chemical Information and Modeling, Volume 49
Volume 49, Number 1, January 2009
- Anton J. Hopfinger, Emilio Xavier Esposito
, Antonio Llinàs, Robert C. Glen, Jonathan M. Goodman:
Findings of the Challenge To Predict Aqueous Solubility. 1-5
- Felix Reisen, Gisbert Schneider, Ewgenij Proschak:
Reaction-MQL: Line Notation for Functional Transformation. 6-12 - Yevgeniy Podolyan, George Karypis:
Common Pharmacophore Identification Using Frequent Clique Detection Algorithm. 13-21 - Adel Golovin, Kim Henrick:
Chemical Substructure Search in SQL. 22-27 - Christian Kramer, Christofer S. Tautermann, David J. Livingstone, David W. Salt, David C. Whitley, Bernd Beck, Timothy Clark:
Sharpening the Toolbox of Computational Chemistry: A New Approximation of Critical F-Values for Multiple Linear Regression. 28-34 - Ashutosh Kumar, Vinita Chaturvedi, Shalini Bhatnagar, Sudhir Sinha, Mohammad Imran Siddiqi:
Knowledge Based Identification of Potent Antitubercular Compounds Using Structure Based Virtual Screening and Structure Interaction Fingerprints. 35-42
- Poongavanam Vasanthanathan, Jozef Hritz, Olivier Taboureau, Lars Olsen, Flemming Steen Jørgensen, Nico P. E. Vermeulen, Chris Oostenbrink:
Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands. 43-52 - Ravi Shashi Nayana, Suneel Kumar Bommisetty, Kriti Singh, Santhosh Kumar Bairy, Sivakumari Nunna, Akula Pramod, Ravikumar Muttineni:
Structural Analysis of Carboline Derivatives As Inhibitors of MAPKAP K2 Using 3D QSAR and Docking Studies. 53-67 - Francesca Milletti, Loriano Storchi, Gianluca Sforna, Simon Cross, Gabriele Cruciani:
Tautomer Enumeration and Stability Prediction for Virtual Screening on Large Chemical Databases. 68-75
- Shailesh Sharma, Antonio Rosato:
Role of the N-Terminal Tail of Metal-Transporting P1B-type ATPases from Genome-Wide Analysis and Molecular Dynamics Simulations. 76-83 - Oliver Korb, Thomas Stützle, Thomas E. Exner:
Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS. 84-96
- Habibah A. Wahab, Yee-Siew Choong, Pazilah Ibrahim, Amirin Sadikun, Thomas Scior:
Elucidating Isoniazid Resistance Using Molecular Modeling. 97-107 - Andreas Bender, Jeremy L. Jenkins, Josef Scheiber, Sai Chetan K. Sukuru, Meir Glick, John W. Davies:
How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space. 108-119 - Guo Li, Kendra M. Haney, Glen E. Kellogg, Yan Zhang:
Comparative Docking Study of Anibamine as the First Natural Product CCR5 Antagonist in CCR5 Homology Models. 120-132
- Alexandre Varnek, Cédric Gaudin, Gilles Marcou, Igor I. Baskin, Anil Kumar Pandey, Igor V. Tetko:
Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients. 133-144
- Ting Zhou, Amedeo Caflisch:
Data Management System for Distributed Virtual Screening. 145-152
- Thomas Engel:
Book Review of Molecular Design (Concepts and Applications). 153
Volume 49, Number 2, February 2009
Chemical Information
- Chia-Wei Chu, John D. Holliday, Peter Willett:
Effect of Data Standardization on Chemical Clustering and Similarity Searching. 155-161 - Eugen Lounkine, Jürgen Bajorath:
Topological Fragment Index for the Analysis of Molecular Substructures and Their Topological Environment in Active Compounds. 162-168 - Sebastian G. Rohrer, Knut Baumann:
Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data. 169-184 - Jenny Chen, John D. Holliday, John Bradshaw:
A Machine Learning Approach to Weighting Schemes in the Data Fusion of Similarity Coefficients. 185-194 - George Papadatos, Anthony W. J. Cooper, Visakan Kadirkamanathan, Simon J. F. Macdonald, Iain M. McLay, Stephen D. Pickett, John Pritchard, Peter Willett, Valerie J. Gillet:
Analysis of Neighborhood Behavior in Lead Optimization and Array Design. 195-208 - Modest von Korff, Joël Freyss, Thomas Sander:
Comparison of Ligand- and Structure-Based Virtual Screening on the DUD Data Set. 209-231 - Thomas Sander, Joël Freyss, Modest von Korff, Jacqueline Renée Reich, Christian Rufener:
OSIRIS, an Entirely in-House Developed Drug Discovery Informatics System. 232-246 - Britta Nisius, Andreas H. Göller:
Similarity-Based Classifier Using Topomers to Provide a Knowledge Base for hERG Channel Inhibition. 247-256 - Andrew Smellie:
Compressed Binary Bit Trees: A New Data Structure For Accelerating Database Searching. 257-262 - Dazhi Jiao, David J. Wild:
Extraction of CYP Chemical Interactions from Biomedical Literature Using Natural Language Processing Methods. 263-269
- Uta F. Lessel, Bernd Wellenzohn, Markus Lilienthal, Holger Claussen:
Searching Fragment Spaces with Feature Trees. 270-279 - Fabrice Moriaud, Olivia Doppelt-Azeroual, Laetitia Martin, Ksenia Oguievetskaia, Kerstin Koch, Artem Vorotyntsev, Stewart A. Adcock, François Delfaud:
Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity. 280-294
- Christos A. Nicolaou, Joannis Apostolakis, Constantinos S. Pattichis:
De Novo Drug Design Using Multiobjective Evolutionary Graphs. 295-307 - Josef Scheiber, Bin Chen, Mariusz Milik, Sai Chetan K. Sukuru, Andreas Bender, Dmitri Mikhailov, Steven Whitebread, Jacques Hamon, Kamal Azzaoui, Laszlo Urban, Meir Glick, John W. Davies, Jeremy L. Jenkins:
Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis. 308-317
- Sarah L. Kinnings, Richard M. Jackson:
Binding Site Similarity Analysis for the Functional Classification of the Protein Kinase Family. 318-329
- Jamel Meslamani, François André, Michel Petitjean:
Assessing the Geometric Diversity of Cytochrome P450 Ligand Conformers by Hierarchical Clustering with a Stop Criterion. 330-337 - Andreas Steffen, Thierry Kogej, Christian Tyrchan, Ola Engkvist:
Comparison of Molecular Fingerprint Methods on the Basis of Biological Profile Data. 338-347 - Eelke van der Horst, Yasushi Okuno, Andreas Bender, Adriaan P. IJzerman:
Substructure Mining of GPCR Ligands Reveals Activity-Class Specific Functional Groups in an Unbiased Manner. 348-360 - Chern Chuang, Yuan-Chia Fan, Bih-Yaw Jin:
Generalized Classification Scheme of Toroidal and Helical Carbon Nanotubes. 361-368 - Arkadiusz Ciesielski, Tadeusz M. Krygowski, Michal Cyranski, Michal A. Dobrowolski, Alexandru T. Balaban:
Are Thermodynamic and Kinetic Stabilities Correlated? A Topological Index of Reactivity toward Electrophiles Used as a Criterion of Aromaticity of Polycyclic Benzenoid Hydrocarbons. 369-376
- Thomas A. Halgren:
Identifying and Characterizing Binding Sites and Assessing Druggability. 377-389 - Piotr Setny, Joanna Trylska:
Search for Novel Aminoglycosides by Combining Fragment-Based Virtual Screening and 3D-QSAR Scoring. 390-400
- Matteo Mozzicafreddo, Massimiliano Cuccioloni, Valentina Cecarini, Anna Maria Eleuteri, Mauro Angeletti:
Homology Modeling and Docking Analysis of the Interaction between Polyphenols and Mammalian 20S Proteasomes. 401-409 - Janos Nadas, Chenglong Li, Peng George Wang:
Computational Structure Activity Relationship Studies on the CD1d/Glycolipid/TCR Complex Using AMBER and AUTODOCK. 410-423 - Holly Freedman, J. Torin Huzil, Tyler Luchko, Richard F. Luduena, Jack A. Tuszynski:
Identification and Characterization of an Intermediate Taxol Binding Site Within Microtubule Nanopores and a Mechanism for Tubulin Isotype Binding Selectivity. 424-436 - Min-Sun Park, Axel L. Dessal, Alan V. Smrcka, Harry A. Stern:
Evaluating Docking Methods for Prediction of Binding Affinities of Small Molecules to the G Protein βγ Subunits. 437-443
- Kirk E. Hevener, Wei Zhao, David M. Ball, Kerim Babaoglu, Jianjun Qi, Stephen W. White, Richard E. Lee:
Validation of Molecular Docking Programs for Virtual Screening against Dihydropteroate Synthase. 444-460 - Hao Tang, Xiang S. Wang, Xi-Ping Huang, Bryan L. Roth, Kyle V. Butler, Alan P. Kozikowski, Mira Jung, Alexander Tropsha:
Novel Inhibitors of Human Histone Deacetylase (HDAC) Identified by QSAR Modeling of Known Inhibitors, Virtual Screening, and Experimental Validation. 461-476 - José L. Medina-Franco, Karina Martínez-Mayorga, Andreas Bender, Ray M. Marín, Marc A. Giulianotti, Clemencia Pinilla, Richard A. Houghten:
Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs. 477-491
- Mikko J. Vainio, J. Santeri Puranen, Mark S. Johnson:
ShaEP: Molecular Overlay Based on Shape and Electrostatic Potential. 492-502 - Vladimir V. Diky, Robert D. Chirico, Andrei F. Kazakov, Chris Muzny, Michael Frenkel:
ThermoData Engine (TDE): Software Implementation of the Dynamic Data Evaluation Concept. 3. Binary Mixtures. 503-517
Volume 49, Number 3, March 2009
- Roger A. Sayle:
Foreign Language Translation of Chemical Nomenclature by Computer. 519-530 - Mark Johnson, Veer Shanmugasundaram, Gordon Bundy, Darryl Chapman, Robert Kilkuskie:
Chemotypic Coverage: A New Basis for Constructing Screening Sublibraries. 531-542 - Cornel Catana:
Simple Idea to Generate Fragment and Pharmacophore Descriptors and Their Implications in Chemical Informatics. 543-548 - Nikolas Fechner, Andreas Jahn, Georg Hinselmann, Andreas Zell:
Atomic Local Neighborhood Flexibility Incorporation into a Structured Similarity Measure for QSAR. 549-560 - Eugen Lounkine, Ye Hu, José Batista, Jürgen Bajorath:
Relevance of Feature Combinations for Similarity Searching Using General or Activity Class-Directed Molecular Fingerprints. 561-570 - Junmei Wang, Tingjun Hou, Xiaojie Xu:
Aqueous Solubility Prediction Based on Weighted Atom Type Counts and Solvent Accessible Surface Areas. 571-581 - Anne Mai Wassermann, Hanna Geppert, Jürgen Bajorath:
Searching for Target-Selective Compounds Using Different Combinations of Multiclass Support Vector Machine Ranking Methods, Kernel Functions, and Fingerprint Descriptors. 582-592
- James Law, Zsolt Zsoldos, Anikó Simon, Darryl Reid, Yang Liu, Sing Yoong Khew, A. Peter Johnson, Sarah Major, Robert A. Wade, Howard Y. Ando:
Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation. 593-602 - Hongming Chen, Ulf Borjesson, Ola Engkvist, Thierry Kogej, Mats Svensson, Niklas Blomberg, Dirk Weigelt, Jeremy N. Burrows, Tim Lange:
ProSAR: A New Methodology for Combinatorial Library Design. 603-614 - Takahiro Kosugi, Isao Nakanishi, Kazuo Kitaura:
Binding Free Energy Calculations of Adenosine Deaminase Inhibitor and the Effect of Methyl Substitution in Inhibitors. 615-622 - Shay Bar-Haim, Ayelet Aharon, Tal Ben-Moshe, Yael Marantz, Hanoch Senderowitz:
SeleX-CS: A New Consensus Scoring Algorithm for Hit Discovery and Lead Optimization. 623-633 - Polina V. Oliferenko, Alexander A. Oliferenko, Gennadiy Poda, Vladimir A. Palyulin, Nikolai S. Zefirov, Alan R. Katritzky:
New Developments in Hydrogen Bonding Acidity and Basicity of Small Organic Molecules for the Prediction of Physical and ADMET Properties. Part 2. The Universal Solvation Equation. 634-646 - R. S. K. Vijayan, Prabu Manoharan, Nahren Manuel Mascarenhas, Nanda Ghoshal:
Hybrid Structure-Based Virtual Screening Protocol for the Identification of Novel BACE1 Inhibitors. 647-657 - Rikke Bergmann, Tommy Liljefors, Morten Dahl Sørensen, Ismael Zamora:
SHOP: Receptor-Based Scaffold HOPping by GRID-Based Similarity Searches. 658-669 - Matthew Paul Gleeson, Duangkamol Gleeson:
QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena? 670-677 - Johannes Kirchmair, Simona Distinto, Patrick Markt, Daniela Schuster, Gudrun M. Spitzer, Klaus R. Liedl, Gerhard Wolber:
How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. 678-692
- Tatsuya Yoshikawa, Koki Tsukamoto, Yuichiro Hourai, Kazuhiko Fukui:
Improving the Accuracy of an Affinity Prediction Method by Using Statistics on Shape Complementarity between Proteins. 693-703
- Ruchi R. Mittal, Lisa Harris, Ross A. McKinnon, Michael J. Sorich:
Partial Charge Calculation Method Affects CoMFA QSAR Prediction Accuracy. 704-709 - Frank R. Burden, Mitchell J. Polley, David A. Winkler:
Toward Novel Universal Descriptors: Charge Fingerprints. 710-715 - Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan:
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes. 716-725 - Constantinos Potamitis, Maria Zervou, Vassilis Katsiaras, Panagiotis Zoumpoulakis, Serdar Durdagi, Manthos G. Papadopoulos, Joseph M. Hayes, Simona Golic Grdadolnik, Ioanna Kyrikou, Dimitris Argyropoulos, Georgia Vatougia, Thomas M. Mavromoustakos:
Antihypertensive Drug Valsartan in Solution and at the AT1 Receptor: Conformational Analysis, Dynamic NMR Spectroscopy, in Silico Docking, and Molecular Dynamics Simulations. 726-739
- Igor V. Filippov, Marc C. Nicklaus:
Optical Structure Recognition Software To Recover Chemical Information: OSRA, An Open Source Solution. 740-743
Volume 49, Number 4, April 2009
- Ning Yu, Gregory A. Bakken:
Efficient Exploration of Large Combinatorial Chemistry Spaces by Monomer-Based Similarity Searching. 745-755 - S. Joshua Swamidass, Chloé-Agathe Azencott, Ting-Wan Lin, Hugo Gramajo, Shiou-Chuan Tsai, Pierre Baldi:
Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method. 756-766 - Hanna Geppert, Jens Humrich, Dagmar Stumpfe, Thomas Gärtner, Jürgen Bajorath:
Ligand Prediction from Protein Sequence and Small Molecule Information Using Support Vector Machines and Fingerprint Descriptors. 767-779 - Aniko T. Valko, A. Peter Johnson:
CLiDE Pro: The Latest Generation of CLiDE, a Tool for Optical Chemical Structure Recognition. 780-787 - Daniel R. Albaugh, L. Mark Hall, Dennis W. Hill, Tzipporah M. Kertesz, Marc Parham, Lowell H. Hall, David F. Grant:
Prediction of HPLC Retention Index Using Artificial Neural Networks and IGroup E-State Indices. 788-799 - Jochen Schlosser, Matthias Rarey:
Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds. 800-809 - Violeta I. Pérez-Nueno, Sofia Pettersson, David W. Ritchie, José I. Borrell, Jordi Teixidó:
Discovery of Novel HIV Entry Inhibitors for the CXCR4 Receptor by Prospective Virtual Screening. 810-823 - Mohammad Goodarzi, Matheus P. Freitas, Richard Jensen:
Feature Selection and Linear/Nonlinear Regression Methods for the Accurate Prediction of Glycogen Synthase Kinase-3β Inhibitory Activities. 824-832
- Jernej Stare, Neil J. Henson, Juergen Eckert:
Mechanistic Aspects of Propene Epoxidation by Hydrogen Peroxide. Catalytic Role of Water Molecules, External Electric Field, and Zeolite Framework of TS-1. 833-846 - Chittima Laohpongspaisan, Thanyada Rungrotmongkol, Pathumwadee Intharathep, Maturos Malaisree, Panita Decha, Ornjira Aruksakunwong, Pornthep Sompornpisut, Supot Hannongbua:
Why Amantadine Loses Its Function in Influenza M2 Mutants: MD Simulations. 847-852 - Kazuya Yasuo, Noriyuki Yamaotsu, Hiroaki Gouda, Hideki Tsujishita, Shuichi Hirono:
Structure-Based CoMFA As a Predictive Model - CYP2C9 Inhibitors As a Test Case. 853-864 - Ori Kalid, Nir Ben-Tal:
Study of MDM2 Binding to p53-Analogues: Affinity, Helicity, and Applicability to Drug Design. 865-876 - Chin Yee Liew, Xiao Hua Ma, Xianghui Liu, Chun Wei Yap:
SVM Model for Virtual Screening of Lck Inhibitors. 877-885 - Jans H. Alzate-Morales, Julio Caballero, Ariela Vergara Jaque, Fernando D. González Nilo:
Insights into the Structural Basis of N2 and O6 Substituted Guanine Derivatives as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors: Prediction of the Binding Modes and Potency of the inhibitors by Docking and ONIOM Calculations. 886-899 - Antonio Macchiarulo, Roberto Nuti, Gokcen Eren, Roberto Pellicciari:
Charting the Chemical Space of Target Sites: Insights into the Binding Modes of Amine and Amidine Groups. 900-912 - Pedro Fong, Jonathan P. McNamara, Ian H. Hillier, Richard A. Bryce:
Assessment of QM/MM Scoring Functions for Molecular Docking to HIV-1 Protease. 913-924 - Yoshifumi Fukunishi, Tadaaki Mashimo, Masaya Orita, Kazuki Ohno, Haruki Nakamura:
In Silico Fragment Screening by Replica Generation (FSRG) Method for Fragment-Based Drug Design. 925-933 - Matthew Clark, Siavash Meshkat, Jeffrey S. Wiseman:
Grand Canonical Free-Energy Calculations of Protein-Ligand Binding. 934-943 - Robert S. Paton, Jonathan M. Goodman:
Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions. 944-955 - Johannes Schwöbel, Ralf-Uwe Ebert, Ralph Kühne, Gerrit Schüürmann:
Prediction of the Intrinsic Hydrogen Bond Acceptor Strength of Organic Compounds by Local Molecular Parameters. 956-962
- Marius Retegan, Anne Milet, Hélene Jamet:
Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach. 963-971 - Francesco Pietra:
Docking and MD Simulations of the Interaction of the Tarantula Peptide Psalmotoxin-1 with ASIC1a Channels Using a Homology Model. 972-977
- Areej M. Abu Hammad, Mutasem O. Taha:
Pharmacophore Modeling, Quantitative Structure-Activity Relationship Analysis, and Shape-Complemented in Silico Screening Allow Access to Novel Influenza Neuraminidase Inhibitors. 978-996 - Christopher R. Corbeil, Nicolas Moitessier:
Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs. 997-1009 - Narender Singh, Rajarshi Guha, Marc A. Giulianotti, Clemencia Pinilla, Richard A. Houghten, José L. Medina-Franco:
Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products, and Molecular Libraries Small Molecule Repository. 1010-1024 - Timothy J. Ritchie, Christopher N. Luscombe, Simon J. F. Macdonald:
Analysis of the Calculated Physicochemical Properties of Respiratory Drugs: Can We Design for Inhaled Drugs Yet? 1025-1032 - Xing-long Zhang, Xun Li, Renxiao Wang:
Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA Method and the X-Score Scoring Function. 1033-1048 - Nathanael Weill, Didier Rognan:
Development and Validation of a Novel Protein-Ligand Fingerprint To Mine Chemogenomic Space: Application to G Protein-Coupled Receptors and Their Ligands. 1049-1062 - Gudrun M. Spitzer, Bernd Wellenzohn, Patrick Markt, Johannes Kirchmair, Thierry Langer, Klaus R. Liedl:
Hydrogen-Bonding Patterns of Minor Groove-Binder-DNA Complexes Reveal Criteria for Discovery of New Scaffolds. 1063-1069 - Carolina Horta Andrade, Kerly F. M. Pasqualoto, Elizabeth I. Ferreira, Anton J. Hopfinger:
Rational Design and 3D-Pharmacophore Mapping of 5′-Thiourea-Substituted α-Thymidine Analogues as Mycobacterial TMPK Inhibitors. 1070-1078 - Tiejun Cheng, Xun Li, Yan Li, Zhihai Liu, Renxiao Wang:
Comparative Assessment of Scoring Functions on a Diverse Test Set. 1079-1093 - Agnieszka A. Kaczor, Urszula A. Kijkowska-Murak, Christiane Kronbach, Klaus Unverferth, Dariusz Matosiuk:
Modeling of Glutamate GluR6 Receptor and Its Interactions with Novel Noncompetitive Antagonists. 1094-1104 - David Hecht, Gary B. Fogel:
A Novel In Silico Approach to Drug Discovery via Computational Intelligence. 1105-1121
- Daichi Shigemizu, Michihiro Araki, Shujiro Okuda, Susumu Goto, Minoru Kanehisa:
Extraction and Analysis of Chemical Modification Patterns in Drug Development. 1122-1129 - M. Michael Gromiha:
Multiple Contact Network Is a Key Determinant to Protein Folding Rates. 1130-1135
- Tim Claridge:
Software Review of MNova: NMR Data Processing, Analysis, and Prediction Software. 1136-1137
Volume 49, Number 5, May 2009
- Serdar Durdagi, Claudiu T. Supuran, T. Amanda Strom, Nadjmeh Doostdar, Mananjali K. Kumar, Andrew R. Barron, Thomas M. Mavromoustakos, Manthos G. Papadopoulos:
In Silico Drug Screening Approach for the Design of Magic Bullets: A Successful Example with Anti-HIV Fullerene Derivatized Amino Acids. 1139-1143
- Yan-Ping Zhou, Li-Juan Tang, Jian Jiao, Dandan Song, Jian-Hui Jiang, Ru-Qin Yu:
Modified Particle Swarm Optimization Algorithm for Adaptively Configuring Globally Optimal Classification and Regression Trees. 1144-1153 - Mark D. Mackey, James L. Melville:
Better than Random? The Chemotype Enrichment Problem. 1154-1162 - Hina Patel, Michael J. Bodkin, Beining Chen, Valerie J. Gillet:
Knowledge-Based Approach to de Novo Design Using Reaction Vectors. 1163-1184