Molecular Docking and Structure-Based Drug Design

[1]  Pierre Tufféry,et al.  MTiOpenScreen: a web server for structure-based virtual screening , 2015, Nucleic Acids Res..

[2]  Desmond J. Higham,et al.  An Algorithmic Introduction to Numerical Simulation of Stochastic Differential Equations , 2001, SIAM Rev..

[3]  Walter Filgueira de Azevedo,et al.  Molecular docking algorithms. , 2008, Current drug targets.

[4]  Paul Labute,et al.  Variability in docking success rates due to dataset preparation , 2012, Journal of Computer-Aided Molecular Design.

[5]  Leonardo L. G. Ferreira,et al.  Molecular Docking and Structure-Based Drug Design Strategies , 2015, Molecules.

[6]  Li Li,et al.  RDOCK: Refinement of rigid‐body protein docking predictions , 2003, Proteins.

[7]  Renxiao Wang,et al.  The PDBbind database: methodologies and updates. , 2005, Journal of medicinal chemistry.

[8]  Todd J. A. Ewing,et al.  DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases , 2001, J. Comput. Aided Mol. Des..

[9]  J. Drews Drug discovery: a historical perspective. , 2000, Science.

[10]  Thomas L. James,et al.  Docking to RNA via Root-Mean-Square-Deviation-Driven Energy Minimization with Flexible Ligands and Flexible Targets , 2008, J. Chem. Inf. Model..

[11]  Mamta Baunthiyal,et al.  In Silico Identification of Mimicking Molecules as Defense Inducers Triggering Jasmonic Acid Mediated Immunity against Alternaria Blight Disease in Brassica Species , 2017, Front. Plant Sci..

[12]  Rommie E. Amaro,et al.  Ensemble Docking in Drug Discovery. , 2018, Biophysical journal.

[13]  M. Rarey,et al.  FlexX‐Scan: Fast, structure‐based virtual screening , 2004, Proteins.

[14]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[15]  Lazaros Mavridis,et al.  HexServer: an FFT-based protein docking server powered by graphics processors , 2010, Nucleic Acids Res..

[16]  Richard D. Taylor,et al.  Improved protein–ligand docking using GOLD , 2003, Proteins.

[17]  Dev Bukhsh Singh,et al.  Structural insight into binding mode of inhibitor with SAHH of Plasmodium and human: interaction of curcumin with anti-malarial drug targets , 2016, Journal of chemical biology.

[18]  Sandor Vajda,et al.  CAPRI: A Critical Assessment of PRedicted Interactions , 2003, Proteins.

[19]  David C. Young,et al.  Computational Chemistry: A Practical Guide for Applying Techniques to Real World Problems , 2001 .

[20]  Natasja Brooijmans,et al.  Molecular recognition and docking algorithms. , 2003, Annual review of biophysics and biomolecular structure.

[21]  C. Aflalo,et al.  Hydrophobic docking: A proposed enhancement to molecular recognition techniques , 1994, Proteins.

[22]  Ayushi Gupta,et al.  Identification of new drug-like compounds from millets as Xanthine oxidoreductase inhibitors for treatment of Hyperuricemia: A molecular docking and simulation study , 2018, Comput. Biol. Chem..

[23]  C. Dominguez,et al.  HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. , 2003, Journal of the American Chemical Society.

[24]  John B. O. Mitchell,et al.  Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein-ligand complexes , 2003, Bioinform..

[25]  Janusz M. Bujnicki,et al.  DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking , 2011, BMC Bioinformatics.

[26]  Yuhai Zhao,et al.  An Efficient ABC_DE_Based Hybrid Algorithm for Protein–Ligand Docking , 2018, International journal of molecular sciences.

[27]  H. C. Andersen,et al.  Molecular dynamics study of melting and freezing of small Lennard-Jones clusters , 1987 .

[28]  Vladimir B Sulimov,et al.  Advances in Docking. , 2020, Current medicinal chemistry.

[29]  Eran Meshorer,et al.  BindDB: An Integrated Database and Webtool Platform for "Reverse-ChIP" Epigenomic Analysis. , 2015, Cell stem cell.

[30]  N. Zhang,et al.  Enriching screening libraries with bioactive fragment space. , 2016, Bioorganic & medicinal chemistry letters.

[31]  Alexander D. MacKerell,et al.  Molecular mechanics. , 2014, Current pharmaceutical design.

[32]  T. Hubbard,et al.  Critical assessment of methods of protein structure prediction (CASP): Round III , 1999 .

[33]  J. A. Grant,et al.  Gaussian docking functions. , 2003, Biopolymers.

[34]  William J. Allen,et al.  DOCK 6: Impact of new features and current docking performance , 2015, J. Comput. Chem..

[35]  Dan Li,et al.  Comprehensive evaluation of ten docking programs on a diverse set of protein-ligand complexes: the prediction accuracy of sampling power and scoring power. , 2016, Physical chemistry chemical physics : PCCP.

[36]  Robert J. Doerksen,et al.  Docking Challenge: Protein Sampling and Molecular Docking Performance , 2013, J. Chem. Inf. Model..

[37]  Renu Vyas,et al.  Pharmacophore and Docking Based Virtual Screening of Validated Mycobacterium tuberculosis Targets. , 2015, Combinatorial chemistry & high throughput screening.

[38]  Mamta Baunthiyal,et al.  Computer aided screening of natural compounds targeting the E6 protein of HPV using molecular docking , 2015, Bioinformation.

[39]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[40]  Michal Brylinski,et al.  Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets , 2015, Journal of Cheminformatics.

[41]  Victor Guallar,et al.  PELE:  Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique. , 2005, Journal of chemical theory and computation.

[42]  Jens Meiler,et al.  Solvent accessible surface area approximations for rapid and accurate protein structure prediction , 2009, Journal of molecular modeling.

[43]  A. Tramontano,et al.  Critical assessment of methods of protein structure prediction (CASP)—round IX , 2011, Proteins.

[44]  Ajay N. Jain Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search , 2007, J. Comput. Aided Mol. Des..

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

[46]  Dev Bukhsh Singh,et al.  Success, Limitation and Future of Computer Aided Drug Designing , 2014 .

[47]  L. Dardenne,et al.  Receptor–ligand molecular docking , 2013, Biophysical Reviews.

[48]  I. Kuntz,et al.  DOCK 6: combining techniques to model RNA-small molecule complexes. , 2009, RNA.

[49]  Gerhard Klebe,et al.  AffinDB: a freely accessible database of affinities for protein–ligand complexes from the PDB , 2005, Nucleic Acids Res..

[50]  Gerhard Klebe,et al.  DSX: A Knowledge-Based Scoring Function for the Assessment of Protein-Ligand Complexes , 2011, J. Chem. Inf. Model..

[51]  Hege S. Beard,et al.  Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. , 2004, Journal of medicinal chemistry.

[52]  J. Mesirov,et al.  Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[53]  S. Jois,et al.  Solution structure of a cyclic RGD peptide that inhibits platelet aggregation. , 1996, Journal of biomolecular structure & dynamics.

[54]  Ajay N. Jain Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities , 1996, J. Comput. Aided Mol. Des..

[55]  W. Goddard,et al.  UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations , 1992 .

[56]  T. Qidwai,et al.  QSAR modeling, docking and ADMET studies for exploration of potential anti-malarial compounds against Plasmodium falciparum , 2017, In Silico Pharmacology.

[57]  Andrew E. Torda,et al.  The GROMOS biomolecular simulation program package , 1999 .

[58]  Ruben Abagyan,et al.  Docking and scoring with ICM: the benchmarking results and strategies for improvement , 2012, Journal of Computer-Aided Molecular Design.

[59]  Aurélien Grosdidier,et al.  SwissDock, a protein-small molecule docking web service based on EADock DSS , 2011, Nucleic Acids Res..

[60]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[61]  Marcel E Dinger,et al.  The impact of genomics on the future of medicine and health , 2014, The Medical journal of Australia.

[62]  M. Mezei,et al.  Molecular docking: a powerful approach for structure-based drug discovery. , 2011, Current computer-aided drug design.

[63]  Zhiping Weng,et al.  ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers , 2014, Bioinform..

[64]  Luhua Lai,et al.  Further development and validation of empirical scoring functions for structure-based binding affinity prediction , 2002, J. Comput. Aided Mol. Des..

[65]  Janusz M. Bujnicki,et al.  NPDock: a web server for protein–nucleic acid docking , 2015, Nucleic Acids Res..

[66]  Yanli Wang,et al.  PubChem: a public information system for analyzing bioactivities of small molecules , 2009, Nucleic Acids Res..

[67]  Wei Zhao,et al.  Validation of Molecular Docking Programs for Virtual Screening against Dihydropteroate Synthase , 2009, J. Chem. Inf. Model..

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

[69]  Mamta Baunthiyal,et al.  In silico identification of mimicking molecule(s) triggering von Willebrand factor in human: a molecular drug target for regulating coagulation pathway , 2020, Journal of biomolecular structure & dynamics.

[70]  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.

[71]  Shaomeng Wang,et al.  MCDOCK: A Monte Carlo simulation approach to the molecular docking problem , 1999, J. Comput. Aided Mol. Des..

[72]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[73]  Thomas A. Halgren,et al.  Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94 , 1996, J. Comput. Chem..