Software and Web Resources for Computer-Aided Molecular Modeling and Drug Discovery

[1]  Jaroslaw Polanski,et al.  Receptor dependent multidimensional QSAR for modeling drug--receptor interactions. , 2009, Current medicinal chemistry.

[2]  I. Eberini,et al.  In-silico studies in Chinese herbal medicines’ research: Evaluation of in-silico methodologies and phytochemical data sources, and a review of research to date , 2012, Journal of Ethnopharmacology.

[3]  Thomas Lengauer,et al.  Docking of hydrophobic ligands with interaction-based matching algorithms , 1999, German Conference on Bioinformatics.

[4]  F. Joubert,et al.  Antimalarial drug discovery: in silico structural biology and rational drug design. , 2009, Infectious disorders drug targets.

[5]  C. Venkatachalam,et al.  LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. , 2003, Journal of molecular graphics & modelling.

[6]  Matthew Clark,et al.  Generalized Fragment-Substructure Based Property Prediction Method , 2005, J. Chem. Inf. Model..

[7]  Haruki Nakamura,et al.  Noise Reduction Method for Molecular Interaction Energy: Application to in Silico Drug Screening and in Silico Target Protein Screening , 2006, J. Chem. Inf. Model..

[8]  M. Karelson,et al.  QSPR: the correlation and quantitative prediction of chemical and physical properties from structure , 1995 .

[9]  Feroz Khan,et al.  QSAR and docking based semi-synthesis and in vivo evaluation of artemisinin derivatives for antimalarial activity. , 2014, Current drug targets.

[10]  Valerie J. Gillet,et al.  SPROUT: A program for structure generation , 1993, J. Comput. Aided Mol. Des..

[11]  Shigeyuki Yokoyama,et al.  In silico functional profiling of small molecules and its applications. , 2008, Journal of medicinal chemistry.

[12]  P Willett,et al.  Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.

[13]  Jörg Lippert,et al.  From physicochemistry to absorption and distribution: predictive mechanistic modelling and computational tools , 2005, Expert opinion on drug metabolism & toxicology.

[14]  György M Keseru,et al.  Hit discovery and hit-to-lead approaches. , 2006, Drug discovery today.

[15]  M. Jambon,et al.  A new bioinformatic approach to detect common 3D sites in protein structures , 2003, Proteins.

[16]  Christoph Steinbeck,et al.  Classification and comparison of ligand-binding sites derived from grid-mapped knowledge-based potentials. , 2006, Journal of molecular graphics & modelling.

[17]  Zhan Deng,et al.  Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening. , 2005, Journal of medicinal chemistry.

[18]  Z. Deng,et al.  Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. , 2004, Journal of medicinal chemistry.

[19]  David A. Gough,et al.  Virtual Screen for Ligands of Orphan G Protein-Coupled Receptors , 2005, J. Chem. Inf. Model..

[20]  Incomplete protein packing as a selectivity filter in drug design. , 2005, Structure.

[21]  P. Khadikar,et al.  QSAR studies for the inhibition of the transmembrane carbonic anhydrase isozyme XIV with sulfonamides using PRECLAV software , 2009 .

[22]  Mark A. Murcko,et al.  Virtual screening : an overview , 1998 .

[23]  Richard D. Cramer,et al.  The inevitable QSAR renaissance , 2011, Journal of Computer-Aided Molecular Design.

[24]  Todd J. A. Ewing,et al.  Critical evaluation of search algorithms for automated molecular docking and database screening , 1997 .

[25]  Robert P Bywater,et al.  Recognition of privileged structures by G-protein coupled receptors. , 2004, Journal of medicinal chemistry.

[26]  Thierry Langer,et al.  Parallel Screening: A Novel Concept in Pharmacophore Modeling and Virtual Screening , 2006, J. Chem. Inf. Model..

[27]  M. Gleeson.  Generation of a set of simple, interpretable ADMET rules of thumb. , 2008, Journal of medicinal chemistry.

[28]  T. Kennedy.  Managing the drug discovery/development interface , 1997 .

[29]  John C Dearden,et al.  In silico prediction of ADMET properties: how far have we come? , 2007, Expert opinion on drug metabolism & toxicology.

[30]  Markus Lill,et al.  Virtual screening in drug design. , 2013, Methods in molecular biology.

[31]  Feroz Khan,et al.  QSAR, docking and ADMET studies of camptothecin derivatives as inhibitors of DNA topoisomerase‐I , 2013 .

[32]  Junmei Wang,et al.  Genetic Algorithm-Optimized QSPR Models for Bioavailability, Protein Binding, and Urinary Excretion , 2006, J. Chem. Inf. Model..

[33]  Feroz Khan,et al.  Pharmacophore modeling, molecular docking, QSAR, and in silico ADMET studies of gallic acid derivatives for immunomodulatory activity , 2012, Journal of Molecular Modeling.

[34]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.

[35]  Feroz Khan,et al.  QSAR and docking based semi-synthesis and in vitro evaluation of 18 β-glycyrrhetinic acid derivatives against human lung cancer cell line A-549. , 2013, Medicinal chemistry (Shariqah (United Arab Emirates)).

[36]  Marc Parham,et al.  Prediction of aqueous solubility based on large datasets using several QSPR models utilizing topological structure representation. , 2004, Chemistry & biodiversity.

[37]  Roger Crossley.  The design of screening libraries targeted at G-protein coupled receptors. , 2004, Current topics in medicinal chemistry.

[38]  A. Hagler,et al.  Chemoinformatics and Drug Discovery , 2002, Molecules : A Journal of Synthetic Chemistry and Natural Product Chemistry.

[39]  David S. Goodsell,et al.  Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998 .