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ORCIDJournal of Chemical Information and Modeling, Volume 50
Volume 50, Number 1, January 2010
- J. Robert Fischer, Uta F. Lessel, Matthias Rarey
:
LoFT: Similarity-Driven Multiobjective Focused Library Design. 1-21
- Jiang Li, Peter Willett:
Bibliometric Analysis of Chinese Research on Cyclization, MALDI-TOF, and Antibiotics. 22-29 - Stefan Rannar, Patrik L. Andersson:
A Novel Approach Using Hierarchical Clustering To Select Industrial Chemicals for Environmental Impact Assessment. 30-36 - Alex M. Clark:
2D Depiction of Fragment Hierarchies. 37-46 - Yingyao Zhou, Bin Zhou, Shumei Jiang, Frederick J. King:
Chemical-Text Hybrid Search Engines. 47-54 - Junmei Wang, Tingjun Hou:
Drug and Drug Candidate Building Block Analysis. 55-67 - Eugen Lounkine, Mathias Wawer, Anne Mai Wassermann, Jürgen Bajorath:
SARANEA: A Freely Available Program To Mine Structure-Activity and Structure-Selectivity Relationship Information in Compound Data Sets. 68-78 - José Batista, Lu Tan, Jürgen Bajorath:
Atom-Centered Interacting Fragments and Similarity Search Applications. 79-86
- Glenn I. Hawe, Ibon Alkorta, Paul L. A. Popelier:
Prediction of the Basicities of Pyridines in the Gas Phase and in Aqueous Solution. 87-96 - Renato F. Freitas, Renato de Lima Bauab, Carlos A. Montanari:
Novel Application of 2D and 3D-Similarity Searches To Identify Substrates among Cytochrome P450 2C9, 2D6, and 3A4. 97-109
- Jans H. Alzate-Morales, Julio Caballero:
Computational Study of the Interactions between Guanine Derivatives and Cyclin-Dependent Kinase 2 (CDK2) by CoMFA and QM/MM. 110-122 - Nathanael Weill, Didier Rognan:
Alignment-Free Ultra-High-Throughput Comparison of Druggable Protein-Ligand Binding Sites. 123-135
- Ming Han, John Z. H. Zhang:
Class I Phospho-inositide-3-kinases (PI3Ks) Isoform-Specific Inhibition Study by the Combination of Docking and Molecular Dynamics Simulation. 136-145 - Rita Santos, Jozef Hritz, Chris Oostenbrink:
Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6. 146-154 - Simone Sciabola, Robert V. Stanton, James E. J. Mills, Maria M. Flocco, Massimo Baroni, Gabriele Cruciani, Francesca Perruccio, Jonathan S. Mason:
High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields. 155-169 - Tomohiro Sato, Teruki Honma, Shigeyuki Yokoyama:
Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening. 170-185 - Manuel Rueda, Giovanni Bottegoni, Ruben Abagyan:
Recipes for the Selection of Experimental Protein Conformations for Virtual Screening. 186-193 - Suman Sirimulla, Maricarmen Lerma, William C. Herndon:
Prediction of Partial Molar Volumes of Amino Acids and Small Peptides: Counting Atoms versus Topological Indices. 194-204
Volume 50, Number 2, February 2010
- Hanna Geppert, Martin Vogt, Jürgen Bajorath:
Current Trends in Ligand-Based Virtual Screening: Molecular Representations, Data Mining Methods, New Application Areas, and Performance Evaluation. 205-216
- Michael Seitz, Nicola Alzakhem:
Computational Estimation of Lanthanoid-Water Bond Lengths by Semiempirical Methods. 217-220
- Frédéric Pennerath, Gilles Niel, Philippe Vismara, Philippe Jauffret, Claude Laurenço, Amedeo Napoli:
Graph-Mining Algorithm for the Evaluation of Bond Formability. 221-239 - Xialan Dong, Jerry Osagie Ebalunode, Sung Jin Cho, Weifan Zheng:
A Novel Structure-Based Multimode QSAR Method Affords Predictive Models for Phosphodiesterase Inhibitors. 240-250 - Jim Downing, Matt J. Harvey, Peter B. Morgan, Peter Murray-Rust, Henry S. Rzepa, Diana C. Stewart, Alan P. Tonge, Joe Townsend:
SPECTRa-T: Machine-Based Data Extraction and Semantic Searching of Chemistry e-Theses. 251-261
- Sheng-You Huang, Xiaoqin Zou:
Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions. 262-273 - Jörg Bentzien, Eugene R. Hickey, Raymond A. Kemper, Mark L. Brewer, Jane D. Dyekjær, Stephen P. East, Mark Whittaker:
An in Silico Method for Predicting Ames Activities of Primary Aromatic Amines by Calculating the Stabilities of Nitrenium Ions. 274-297 - Sourav Das, Michael P. Krein, Curt M. Breneman:
Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures. 298-308
- Mark Vere Culp, Kjell Johnson, George Michailidis:
The Ensemble Bridge Algorithm: A New Modeling Tool for Drug Discovery Problems. 309-316 - Qingye Zhang, Ding Li, Pei Wei, Jie Zhang, Jian Wan, Yangliang Ren, Zhigang Chen, Deli Liu, Ziniu Yu, Lingling Feng:
Structure-Based Rational Screening of Novel Hit Compounds with Structural Diversity for Cytochrome P450 Sterol 14α-Demethylase from Penicillium digitatum. 317-325
- Milan Randic:
Book Review of Molecular Descriptors for Chemoinformatics - Second, Revised and Enlarged Edition (Volume I: Alphabetical Listing; Volume II: Appendices, Bibliography). 326
Volume 50, Number 3, March 2010
- Akio Tanaka, Hideho Okamoto, Malcolm Bersohn:
Construction of Functional Group Reactivity Database under Various Reaction Conditions Automatically Extracted from Reaction Database in a Synthesis Design System. 327-338 - Jameed Hussain, Ceara Rea:
Computationally Efficient Algorithm to Identify Matched Molecular Pairs (MMPs) in Large Data Sets. 339-348
- Michael Devereux, Markus Meuwly:
Force Field Optimization using Dynamics and Ensemble Averaged Data: Vibrational Spectra and Relaxation in Bound MbCO. 349-357 - Valérie Campagna-Slater, Andrew G. Arrowsmith, Yong Zhao, Matthieu Schapira:
Pharmacophore Screening of the Protein Data Bank for Specific Binding Site Chemistry. 358-367
- Slimane Doudou, Raman Sharma, Richard H. Henchman, David W. Sheppard, Neil A. Burton:
Inhibitors of PIM-1 Kinase: A Computational Analysis of the Binding Free Energies of a Range of Imidazo [1, 2-b] Pyridazines. 368-379 - Wei Cui, Zhuo Wei, Quan Chen, Yuanhua Cheng, Lingling Geng, Jian Zhang, Jianhua Chen, Tingjun Hou, Mingjuan Ji:
Structure-Based Design of Peptides against G3BP with Cytotoxicity on Tumor Cells. 380-387 - Nikolaos Dimitropoulos, Athanasios Papakyriakou, Georgios A. Dalkas, Edward D. Sturrock, Georgios Spyroulias:
A Computational Approach to the Study of the Binding Mode of Dual ACE/NEP Inhibitors. 388-396 - Ignasi Buch, Matt J. Harvey, Toni Giorgino, David P. Anderson, Gianni De Fabritiis:
High-Throughput All-Atom Molecular Dynamics Simulations Using Distributed Computing. 397-403
- Christian Kramer, Bernd Beck, Timothy Clark:
Insolubility Classification with Accurate Prediction Probabilities Using a MetaClassifier. 404-414 - Ramasamy Thilagavathi, Ricardo L. Mancera:
Ligand-Protein Cross-Docking with Water Molecules. 415-421 - Jana Sopkova-de Oliveira Santos, Aurélien Lesnard, Jean-Hugues Agondanou, Nathalie Dupont, Anne-Marie Godard, Silvia Stiebing, Christophe Rochais, Frédéric Fabis, Patrick Dallemagne, Ronan Bureau, Sylvain Rault:
Virtual Screening Discovery of New Acetylcholinesterase Inhibitors Issued from CERMN Chemical Library. 422-428 - Christian Kramer, Bernd Beck, Timothy Clark:
A Surface-Integral Model for Log POW. 429-436 - Anwar Rayan, David Marcus, Amiram Goldblum:
Predicting Oral Druglikeness by Iterative Stochastic Elimination. 437-445 - Alban Lepailleur, Stéphane Lemaître, Xiao Feng, Jana Sopkova-de Oliveira Santos, Philippe Delagrange, Jean Boutin, Pierre Renard, Ronan Bureau, Sylvain Rault:
Receptor- and Ligand-Based Study on Novel 2, 2′-Bithienyl Derivatives as Non-Peptidic AANAT Inhibitors. 446-460
Volume 50, Number 4, April 2010
- Kevin Theisen, Berend Smit, Maciej Haranczyk:
Chemical Hieroglyphs: Abstract Depiction of Complex Void Space Topology of Nanoporous Materials. 461-469 - Alexander Chuprina, Oleg Lukin, Robert Demoiseaux, Alexander Buzko, Alexander Shivanyuk:
Drug- and Lead-likeness, Target Class, and Molecular Diversity Analysis of 7.9 Million Commercially Available Organic Compounds Provided by 29 Suppliers. 470-479 - Sara Núñez, Jennifer Venhorst, Chris G. Kruse:
Assessment of a Novel Scoring Method Based on Solvent Accessible Surface Area Descriptors. 480-486 - Hany E. A. Ahmed, Martin Vogt, Jürgen Bajorath:
Design and Evaluation of Bonded Atom Pair Descriptors. 487-499 - Ye Hu, Jürgen Bajorath:
Molecular Scaffolds with High Propensity to Form Multi-Target Activity Cliffs. 500-510
- Ian R. Craig, Jonathan W. Essex, Katrin Spiegel:
Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments. 511-524 - Jason G. Kettle, Richard A. Ward:
Toward the Comprehensive Systematic Enumeration and Synthesis of Novel Kinase Inhibitors Based on a 4-Anilinoquinazoline Binding Mode. 525-533 - K. Shawn Watts, Pranav Dalal, Robert B. Murphy, Woody Sherman, Richard A. Friesner, John C. Shelley:
ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers. 534-546 - Cristiano Ruch Werneck Guimarães, Alan M. Mathiowetz:
Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations. 547-559 - Imran S. Haque, Vijay S. Pande, W. Patrick Walters:
SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on GPUs and CPUs. 560-564 - John Manchester, Grant Walkup, Olga Rivin, Zhiping You:
Evaluation of pKa Estimation Methods on 211 Druglike Compounds. 565-571 - Paul C. D. Hawkins, A. Geoffrey Skillman, Gregory L. Warren, Benjamin A. Ellingson, Matthew T. Stahl:
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database. 572-584 - Anitha Ramraj, Ian H. Hillier:
Binding of Pollutant Aromatics on Carbon Nanotubes and Graphite. 585-588
- Ryan G. Coleman, Kim A. Sharp:
Protein Pockets: Inventory, Shape, and Comparison. 589-603 - Martin Sippel, Christoph A. Sotriffer:
Molecular Dynamics Simulations of the HIV-1 Integrase Dimerization Interface: Guidelines for the Design of a Novel Class of Integrase Inhibitors. 604-614 - Zhi Chen, Guanghui Tian, Zhen Wang, Hualiang Jiang, Jingshan Shen, Weiliang Zhu:
Multiple Pharmacophore Models Combined with Molecular Docking: A Reliable Way for Efficiently Identifying Novel PDE4 Inhibitors with High Structural Diversity. 615-625 - Fiona M. McRobb, Ben Capuano, Ian T. Crosby, David K. Chalmers, Elizabeth Yuriev:
Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors. 626-637 - Mattia Mori, Ursula Dietrich, Fabrizio Manetti, Maurizio Botta:
Molecular Dynamics and DFT Study on HIV-1 Nucleocapsid Protein-7 in Complex with Viral Genome. 638-650
- Xiaohua Zhang, Alan C. Gibbs, Charles H. Reynolds, Martin B. Peters, Lance M. Westerhoff:
Quantum Mechanical Pairwise Decomposition Analysis of Protein Kinase B Inhibitors: Validating a New Tool for Guiding Drug Design. 651-661 - Ira Musmuca, Antonia Caroli, Antonello Mai, Neerja Kaushik-Basu, Payal Arora, Rino Ragno:
Combining 3-D Quantitative Structure-Activity Relationship with Ligand Based and Structure Based Alignment Procedures for in Silico Screening of New Hepatitis C Virus NS5B Polymerase Inhibitors. 662-676 - Ernst Ahlberg Helgee, Lars Carlsson, Scott Boyer, Ulf Norinder:
Evaluation of Quantitative Structure-Activity Relationship Modeling Strategies: Local and Global Models. 677-689
- Joji M. Otaki, Motosuke Tsutsumi, Tomonori Gotoh, Haruhiko Yamamoto:
Secondary Structure Characterization Based on Amino Acid Composition and Availability in Proteins. 690-700
Volume 50, Number 5, May 2010
- Leo Ghemtio, Marie-Dominique Devignes, Malika Smaïl-Tabbone, Michel Souchet, Vincent Leroux, Bernard Maigret:
Comparison of Three Preprocessing Filters Efficiency in Virtual Screening: Identification of New Putative LXRβ Regulators As a Test Case. 701-715 - Shivani Agarwal, Deepak Dugar, Shiladitya Sengupta:
Ranking Chemical Structures for Drug Discovery: A New Machine Learning Approach. 716-731 - Joo-Young Choi, Melissa J. Davis, Andrew F. Newman, Mark A. Ragan:
A Semantic Web Ontology for Small Molecules and Their Biological Targets. 732-741 - David Rogers, Mathew Hahn:
Extended-Connectivity Fingerprints. 742-754 - Punnaivanam Sankar, Alain Krief, Gnanasekaran Aghila:
Model Tool to Describe Chemical Structures in XML Format Utilizing Structural Fragments and Chemical Ontology. 755-770 - G. Madhavi Sastry, Jeffrey F. Lowrie, Steven L. Dixon, Woody Sherman:
Large-Scale Systematic Analysis of 2D Fingerprint Methods and Parameters to Improve Virtual Screening Enrichments. 771-784 - Ghanima Al-Sharrah:
Ranking Using the Copeland Score: A Comparison with the Hasse Diagram. 785-791
- Paul Labute:
LowModeMD - Implicit Low-Mode Velocity Filtering Applied to Conformational Search of Macrocycles and Protein Loops. 792-800 - Miriam López-Ramos, Francesca Perruccio:
HPPD: Ligand- and Target-Based Virtual Screening on a Herbicide Target. 801-814 - Kazuki Ohno, Yuichi Nagahara, Kazuhisa Tsunoyama, Masaya Orita:
Are There Differences between Launched Drugs, Clinical Candidates, and Commercially Available Compounds? 815-821 - I-Jen Chen, Nicolas Foloppe:
Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst. 822-839 - Sandhya Kortagere, William J. Welsh, Joanne M. Morrisey, Thomas Daly, Ijeoma Ejigiri, Photini Sinnis, Akhil B. Vaidya, Lawrence W. Bergman:
Structure-based Design of Novel Small-Molecule Inhibitors of Plasmodium falciparum. 840-849 - Tatsusada Yoshida, Yohei Munei, Seiji Hitaoka, Hiroshi Chuman:
Correlation Analyses on Binding Affinity of Substituted Benzenesulfonamides with Carbonic Anhydrase Using ab Initio MO Calculations on Their Complex Structures. 850-860 - Jiazhong Li, Paola Gramatica:
Classification and Virtual Screening of Androgen Receptor Antagonists. 861-874
- Ying Wang, Dongqing Wei, Jing-Fang Wang:
Molecular Dynamics Studies on T1 Lipase: Insight into a Double-Flap Mechanism. 875-878 - René Meier, Martin Pippel, Frank Brandt, Wolfgang Sippl, Carsten Baldauf:
ParaDockS: A Framework for Molecular Docking with Population-Based Metaheuristics. 879-889 - S. Kashif Sadiq, David W. Wright, Owain Kenway, Peter V. Coveney:
Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases. 890-905
- Prasenjit Mukherjee, Prashant V. Desai, Yu-Dong Zhou, Mitchell A. Avery:
Targeting the BH3 Domain Mediated Protein-Protein Interaction of Bcl-xL through Virtual Screening. 906-923
- Alberto Rolo-Naranjo, Edelsys Codorniu-Hernández, Noel Ferro:
Quantum Chemical Associations Ligand-Residue: Their Role to Predict Flavonoid Binding Sites in Proteins. 924-933 - Yusuke Ishida, Yuki Kato, Liang Zhao, Hiroshi Nagamochi, Tatsuya Akutsu:
Branch-and-Bound Algorithms for Enumerating Treelike Chemical Graphs with Given Path Frequency Using Detachment-Cut. 934-946 - Jeremy Esque, Christophe Oguey, Alexandre G. de Brevern:
A Novel Evaluation of Residue and Protein Volumes by Means of Laguerre Tessellation. 947-960
Volume 50, Number 6, June 2010
- Lisa Michielan, Stefano Moro:
Pharmaceutical Perspectives of Nonlinear QSAR Strategies. 961-978
- Yevgeniy Podolyan, Michael A. Walters, George Karypis:
Assessing Synthetic Accessibility of Chemical Compounds Using Machine Learning Methods. 979-991 - David Giganti, Hélène Guillemain, Jean-Louis Spadoni, Michael Nilges, Jean-François Zagury, Matthieu Montès:
Comparative Evaluation of 3D Virtual Ligand Screening Methods: Impact of the Molecular Alignment on Enrichment. 992-1004 - Salla I. Virtanen, Olli T. Pentikäinen:
Efficient Virtual Screening Using Multiple Protein Conformations Described as Negative Images of the Ligand-Binding Site. 1005-1011 - Ammar Abdo, Beining Chen, Christoph Müller, Naomie Salim, Peter Willett:
Ligand-Based Virtual Screening Using Bayesian Networks. 1012-1020 - Lisa Peltason, Preeti Iyer, Jürgen Bajorath:
Rationalizing Three-Dimensional Activity Landscapes and the Influence of Molecular Representations on Landscape Topology and the Formation of Activity Cliffs. 1021-1033 - Jie Shen, Feixiong Cheng, You Xu, Weihua Li, Yun Tang:
Estimation of ADME Properties with Substructure Pattern Recognition. 1034-1041 - Lu Tan, José Batista, Jürgen Bajorath:
Rationalization of the Performance and Target Dependence of Similarity Searching Incorporating Protein-Ligand Interaction Information. 1042-1052
- Olga Obrezanova, Matthew D. Segall:
Gaussian Processes for Classification: QSAR Modeling of ADMET and Target Activity. 1053-1061 - Francesca Milletti, Anna Vulpetti:
Tautomer Preference in PDB Complexes and its Impact on Structure-Based Drug Discovery. 1062-1074 - Imran S. Haque, Vijay S. Pande:
SCISSORS: A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities. 1075-1088
- Xiaoying Hu, Aixia Yan, Tianwei Tan, Oliver Sacher, Johann Gasteiger:
Similarity Perception of Reactions Catalyzed by Oxidoreductases and Hydrolases Using Different Classification Methods. 1089-1100 - Jans H. Alzate-Morales, Ariela Vergara Jaque, Julio Caballero:
Computational Study on the Interaction of N1 Substituted Pyrazole Derivatives with B-Raf Kinase: An Unusual Water Wire Hydrogen-Bond Network and Novel Interactions at the Entrance of the Active Site. 1101-1112 - Luciana Gavernet, Jose L. Gonzalez Funes, Luis Bruno Blanch, Guillermina Estiu, Alfonso Maresca, Claudiu T. Supuran:
Affinity of Sulfamates and Sulfamides to Carbonic Anhydrase II Isoform: Experimental and Molecular Modeling Approaches. 1113-1122
- Kristi Yi Fan, Raymond J. Unwalla, Rajiah Aldrin Denny, Li Di, Edward H. Kerns, David J. Diller, Christine Humblet:
Insights for Predicting Blood-Brain Barrier Penetration of CNS Targeted Molecules Using QSPR Approaches. 1123-1133 - Yaozong Li, Jie Shen, Xianqiang Sun, Weihua Li, Guixia Liu, Yun Tang:
Accuracy Assessment of Protein-Based Docking Programs against RNA Targets. 1134-1146 - Rajendra Kumar, Ranajit Nivrutti Shinde, Dara Ajay, Masilamani Elizabeth Sobhia:
Probing Interaction Requirements in PTP1B Inhibitors: A Comparative Molecular Dynamics Study. 1147-1158 - Brett R. Beno, David R. Langley:
MORPH: A New Tool for Ligand Design. 1159-1164 - Mark Sandor, Robert Kiss, György M. Keserü:
Virtual Fragment Docking by Glide: a Validation Study on 190 Protein-Fragment Complexes. 1165-1172 - Toshimasa Itoh, Hitomi Takemura, Kayoko Shimoi, Keiko Yamamoto:
A 3D Model of CYP1B1 Explains the Dominant 4-Hydroxylation of Estradiol. 1173-1178
- Michael Fernández, Shandar Ahmad, Akinori Sarai:
Proteochemometric Recognition of Stable Kinase Inhibition Complexes Using Topological Autocorrelation and Support Vector Machines. 1179-1188
Volume 50, Number 7, July 2010
- Denis Fourches, Eugene N. Muratov, Alexander Tropsha:
Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research. 1189-1204
- Pierre Baldi, Ramzi Nasr:
When is Chemical Similarity Significant? The Statistical Distribution of Chemical Similarity Scores and Its Extreme Values. 1205-1222 - Torsten Thalheim, Armin Vollmer, Ralf-Uwe Ebert, Ralph Kühne, Gerrit Schüürmann:
Tautomer Identification and Tautomer Structure Generation Based on the InChI Code. 1223-1232 - Yoshifumi Fukunishi, Kazuki Ohno, Masaya Orita, Haruki Nakamura:
Selection of In Silico Drug Screening Results by Using Universal Active Probes (UAPs). 1233-1240 - Gudrun M. Spitzer, Mathias Heiss, Martina Mangold, Patrick Markt, Johannes Kirchmair, Gerhard Wolber, Klaus R. Liedl:
One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space. 1241-1247