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ORCIDJournal of Computer-Aided Molecular Design, Volume 22
Volume 22, Number 1, January 2008
- Prashant Suresh Kharkar
, Maarten E. A. Reith, Aloke K. Dutta:
Three-dimensional quantitative structure-activity relationship (3D QSAR) and pharmacophore elucidation of tetrahydropyran derivatives as serotonin and norepinephrine transporter inhibitors. 1-17 - Marcela Colombres, José Antonio Garate, Carlos F. Lagos, Raúl Araya-Secchi, Patricia Norambuena, Soledad Quiroz, Luis Larrondo, Tomás Pérez-Acle, Jaime Eyzaguirre:
An eleven amino acid residue deletion expands the substrate specificity of acetyl xylan esterase II (AXE II) from Penicillium purpurogenum. 19-28 - Gary B. Fogel, Mars Cheung, Eric Pittman, David Hecht:
Modeling the inhibition of quadruple mutant Plasmodium falciparum dihydrofolate reductase by pyrimethamine derivatives. 29-38 - Christopher I. Williams, Miklos Feher:
The effect of numerical error on the reproducibility of molecular geometry optimizations. 39-51 - Erik Nordling, Yvonne Kallberg, Jan Johansson, Bengt Persson:
Molecular dynamics studies of α-helix stability in fibril-forming peptides. 53-58
Volume 22, Number 2, February 2008
- Andreas Schüller, Marcel Suhartono, Uli Fechner, Yusuf Tanrikulu, Sven Breitung, Ute Scheffer, Michael W. Göbel, Gisbert Schneider:
The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA. 59-68 - Nitin S. Sapre, Swagata Gupta, Nilanjana Pancholi, Neelima Sapre:
Molecular docking studies on tetrahydroimidazo-[4, 5, 1-jk][1, 4]-benzodiazepinone (TIBO) derivatives as HIV-1 NNRT inhibitors. 69-80 - Arthur M. Doweyko:
QSAR: dead or alive? 81-89 - Jitender Verma, Vijay M. Khedkar, Arati Prabhu, Santosh A. Khedkar, Alpeshkumar K. Malde, Evans C. Coutinho:
A comprehensive analysis of the thermodynamic events involved in ligand-receptor binding using CoRIA and its variants. 91-104 - Christopher J. R. Illingworth, Kevin E. B. Parkes, Christopher R. Snell, Christopher A. Reynolds:
Quantitative measurement of protease ligand conformation. 105-109 - Christof Gerlach, Howard Broughton, Andrea Zaliani:
FTree query construction for virtual screening: a statistical analysis. 111-118 - Yanhua Sun, Bin Shen, Zhonghua Lu, Zhong Jin, Xuebin Chi:
GridMol: a grid application for molecular modeling and visualization. 119-129
Volume 22, Numbers 3-4, March 2008
- Terry R. Stouch:
Editorial: Special Issue on "Evaluation of Computational Methods". 131 - Ajay N. Jain, Anthony Nicholls:
Recommendations for evaluation of computational methods. 133-139 - Robert D. Clark, Daniel J. Webster-Clark:
Managing bias in ROC curves. 141-146 - Ann E. Cleves, Ajay N. Jain:
Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery. 147-159 - Istvan J. Enyedy, William J. Egan:
Can we use docking and scoring for hit-to-lead optimization? 161-168 - Andrew C. Good, Tudor I. Oprea:
Optimization of CAMD techniques 3. Virtual screening enrichment studies: a help or hindrance in tool selection? 169-178 - Paul C. D. Hawkins, Gregory L. Warren, A. Geoffrey Skillman, Anthony Nicholls:
How to do an evaluation: pitfalls and traps. 179-190 - Paul C. D. Hawkins, Gregory L. Warren, A. Geoffrey Skillman, Anthony Nicholls:
How to do an evaluation: pitfalls and traps. 191-192 - John J. Irwin:
Community benchmarks for virtual screening. 193-199 - Ajay N. Jain:
Bias, reporting, and sharing: computational evaluations of docking methods. 201-212 - Johannes Kirchmair, Patrick Markt, Simona Distinto, Gerhard Wolber, Thierry Langer:
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes? 213-228 - John W. Liebeschuetz:
Evaluating docking programs: keeping the playing field level. 229-238 - Anthony Nicholls:
What do we know and when do we know it? 239-255 - Robert P. Sheridan, Georgia B. McGaughey, Wendy D. Cornell:
Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results. 257-265
Volume 22, Number 5, May 2008
- Terry R. Stouch:
Editorial: Contributions by Wendy Warr. 267 - Tuan A. Pham, Ajay N. Jain:
Customizing scoring functions for docking. 269-286 - Anna Maria Almerico, Marco Tutone, Antonino Lauria:
Docking and multivariate methods to explore HIV-1 drug-resistance: a comparative analysis. 287-297 - Chao-Bin Xue, Wan-Chun Luo, Qi Ding, Shou-Zhu Liu, Xing-Xiang Gao:
Quantitative structure-activity relationship studies of mushroom tyrosinase inhibitors. 299-309 - Giovanni Bottegoni, Irina Kufareva, Maxim Totrov, Ruben Abagyan:
A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). 311-325 - Wendy A. Warr:
RIP MDL information systems. Is this really the beginning of a new era? 327-331
Volume 22, Numbers 6-7, June 2008
- Robert D. Clark:
Preface to the special issue in memory of Phil Magee. 333 - Marvin Charton:
Philip S. Magee: a life in QSAR. 335-337 - Subhash C. Basak, Denise R. Mills, Douglas M. Hawkins:
Predicting allergic contact dermatitis: a hierarchical structure-activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors. 339-343 - Jianzhong Liu, Petra Kern, G. Frank Gerberick, Osvaldo Andrade Santos-Filho, Emilio Xavier Esposito, Anton J. Hopfinger, Yufeng J. Tseng:
Categorical QSAR models for skin sensitization based on local lymph node assay measures and both ground and excited state 4D-fingerprint descriptors. 345-366 - Rajarshi Guha, Stephan C. Schürer:
Utilizing high throughput screening data for predictive toxicology models: protocols and application to MLSCN assays. 367-384 - John H. Block, Douglas R. Henry:
Evaluation of descriptors and classification schemes to predict cytochrome substrates in terms of chemical information. 385-392 - Thomas C. Sparks, Gary D. Crouse, James E. Dripps, Peter Anzeveno, Jacek Martynow, Carl V. DeAmicis, James Gifford:
Neural network-based QSAR and insecticide discovery: spinetoram. 393-401 - Victor Kuzmin, Anatoly G. Artemenko, Eugene N. Muratov:
Hierarchical QSAR technology based on the Simplex representation of molecular structure. 403-421 - Isaac B. Bersuker:
QSAR without arbitrary descriptors: the electron-conformational method. 423-430 - Olga Obrezanova, Joelle M. R. Gola, Edmund J. Champness, Matthew D. Segall:
Automatic QSAR modeling of ADME properties: blood-brain barrier penetration and aqueous solubility. 431-440 - David T. Stanton:
On the importance of topological descriptors in understanding structure-property relationships. 441-460 - George D. Purvis:
Size-intensive descriptors. 461-468 - Daniele Dell'Orco, Pier Giuseppe De Benedetti:
Quantitative structure-activity relationship analysis of canonical inhibitors of serine proteases. 469-478 - Darryl Reid, Bashir Sadjad, Zsolt Zsoldos, Anikó Simon:
LASSO - ligand activity by surface similarity order: a new tool for ligand based virtual screening. 479-487 - Vladimir Potemkin, Maria A. Grishina:
A new paradigm for pattern recognition of drugs. 489-505 - Robert D. Clark:
A ligand's-eye view of protein binding. 507-521
Volume 22, Number 8, August 2008
- Yovani Marrero-Ponce, Alfredo Meneses-Marcel, Oscar Miguel Rivera-Borroto, Ramón García-Domenech, Jesús Vicente de Julián-Ortiz, Alina Montero-Torres, José Antonio Escario, Alicia Gómez Barrio, David Montero Pereira, Juan José Nogal, Ricardo Grau, Francisco Torrens, Christian Vogel, Vicente J. Arán:
Bond-based linear indices in QSAR: computational discovery of novel anti-trichomonal compounds. 523-540 - Bernd Wendt, Richard D. Cramer:
Quantitative Series Enrichment Analysis (QSEA): a novel procedure for 3D-QSAR analysis. 541-551 - Meng Cui, Mihaly Mezei, Roman Osman:
Modeling dimerizations of transmembrane proteins using Brownian dynamics simulations. 553-561 - Mary Hongying Cheng, Robert D. Coalson, Michael Cascio, Maria G. Kurnikova:
Computational prediction of ion permeation characteristics in the glycine receptor modified by photo-sensitive compounds. 563-570 - Sung Jin Cho, Yaxiong Sun:
Visual exploration of structure-activity relationship using maximum common framework. 571-578 - Duangkamol Gleeson:
A theoretical study of cis - trans isomerisation in H-ZSM5: probing the impact of cluster size and zeolite framework on energetics and structure. 579-585 - Wendy A. Warr:
A grand vision for configurable science and minimizing the loss model. 587-591
Volume 22, Number 9, September 2008
- Jui-Hua Hsieh, Xiang S. Wang, Denise G. Teotico, Alexander Golbraikh, Alexander Tropsha:
Differentiation of AmpC beta-lactamase binders vs. decoys using classification k NN QSAR modeling and application of the QSAR classifier to virtual screening. 593-609 - P. Aparoy, R. N. Reddy, Lalitha Guruprasad, M. Rami Reddy, P. Reddanna:
Homology modeling of 5-lipoxygenase and hints for better inhibitor design. 611-619 - Shashidhar N. Rao, Paul C. Sanschagrin, Jeremy R. Greenwood, Matthew P. Repasky, Woody Sherman, Ramy Farid:
Improving database enrichment through ensemble docking. 621-627 - Xinyuan Zhang, Nan Zheng, Gus R. Rosania:
Simulation-based cheminformatic analysis of organelle-targeted molecules: lysosomotropic monobasic amines. 629-645 - Preyesh Stephen, Ramachandran Vijayan, Audesh Bhat, Naidu Subbarao, R. N. K. Bamezai:
Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors. 647-660 - Fang Zheng, Chang-Guo Zhan:
Rational design of an enzyme mutant for anti-cocaine therapeutics. 661-671 - Yong Zhao, Michel F. Sanner:
Protein-ligand docking with multiple flexible side chains. 673-679 - Roman J. Dorfman, Karl M. Smith, Brian B. Masek, Robert D. Clark:
A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers. 681-691 - Rommie E. Amaro, Riccardo Baron, James Andrew McCammon:
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. 693-705
Volume 22, Number 10, October 2008
- Wendy A. Warr:
Future structural genomics initiatives: an interview with Helen Berman, director of the Protein Data Bank. 707-710 - Beilei Lei, Juan Du, Shuyan Li, Huanxiang Liu, Yueying Ren, Xiaojun Yao:
Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of thiazolone derivatives as hepatitis C virus NS5B polymerase allosteric inhibitors. 711-725 - Michael G. Lerner, Kristin L. Meagher, Heather A. Carlson:
Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. 727-736 - Rajni Garg, Barun Bhhatarai:
Possible allosteric interactions of monoindazole-substituted P2 cyclic urea analogues with wild-type and mutant HIV-1 protease. 737-745 - Victor Kuzmin, Eugene N. Muratov, Anatoly G. Artemenko, Leonid Gorb, Mo Qasim, Jerzy Leszczynski:
The effects of characteristics of substituents on toxicity of the nitroaromatics: HiT QSAR study. 747-759 - David C. Thompson, Rajiah Aldrin Denny, Ramaswamy Nilakantan, Christine Humblet, Diane Joseph-McCarthy, Eric Feyfant:
CONFIRM: connecting fragments found in receptor molecules. 761-772
Volume 22, Number 11, November 2008
- Jingchuan Zhu, Jie Cheng, Zhouxiong Liao, Zhonghong Lai, Bo Liu:
Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics. 773-781 - Dominik Gront, Andrzej Kolinski:
Fast and accurate methods for predicting short-range constraints in protein models. 783-788 - Keigo Gohda, Toshio Hakoshima:
A molecular mechanism of P-loop pliability of Rho-kinase investigated by molecular dynamic simulation. 789-797 - Ami Yi-Ching Yang, Ricardo L. Mancera:
Molecular dynamics simulations of ligand-induced backbone conformational changes in the binding site of the periplasmic lysine-, arginine-, ornithine-binding protein. 799-814 - Arun Prasad Pandurangan, Gautham Namasivayam:
A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling. 815-829 - Joseph Rebehmed, Florent Barbault, Cátia Teixeira, François Maurel:
2D and 3D QSAR studies of diarylpyrimidine HIV-1 reverse transcriptase inhibitors. 831-841 - Haiyan Li, Jin Sun, Xiaowen Fan, Xiaofan Sui, Lan Zhang, Yongjun Wang, Zhonggui He:
Considerations and recent advances in QSAR models for cytochrome P450-mediated drug metabolism prediction. 843-855
Volume 22, Number 12, December 2008
- Rajarshi Guha:
On the interpretation and interpretability of quantitative structure-activity relationship models. 857-871 - Dong Sun Park, Jae Min Kim, Young Bok Lee, Chang Ho Ahn:
QSID Tool: a new three-dimensional QSAR environmental tool. 873-883 - Omar Deeb, Brian W. Clare:
QSAR of heterocyclic antifungal agents by flip regression. 885-895 - Anders Poulsen, Anthony William, Angeline Lee, Stéphanie Blanchard, Eeling Teo, Weiping Deng, Noah Tu, Evelyn Tan, Eric Sun, Kay Lin Goh, Wai Chung Ong, Chee Pang Ng, Kee Chuan Goh, Zahid Bonday:
Structure-based design of Aurora A & B inhibitors. 897-906 - Alonso Aguirre-Valderrama, José A. Dobado:
CAL3JHH: a Java program to calculate the vicinal coupling constants (3 J H, H) of organic molecules. 907-914 - Li-Chu Tsai, Yi-Ning Chen, Lie-Fen Shyur:
Structural modeling of glucanase-substrate complexes suggests a conserved tyrosine is involved in carbohydrate recognition in plant 1, 3-1, 4-β-d-glucanases. 915-923 - Kavitha Bharatham, Nagakumar Bharatham, Yong Jung Kwon, Keun Woo Lee:
Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling. 925-933
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