Computational methods in drug discovery
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[1] R. Huddleston. Structure , 2018, Jane Austen's Style.
[2] Aboul Ella Hassanien,et al. PQSAR: The membrane quantitative structure-activity relationships in cheminformatics , 2016, Expert Syst. Appl..
[3] Kenji Mizuguchi,et al. Integration of Ligand and Structure Based Approaches for CSAR-2014 , 2016, J. Chem. Inf. Model..
[4] Yi Pan,et al. HybridDock: A Hybrid Protein-Ligand Docking Protocol Integrating Protein- and Ligand-Based Approaches , 2016, J. Chem. Inf. Model..
[5] Lei Liang,et al. Development of novel proteasome inhibitors based on phthalazinone scaffold. , 2016, Bioorganic & medicinal chemistry letters.
[6] Ben M. Webb,et al. Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.
[7] Pratyush Tiwary,et al. Prediction of Protein-Ligand Binding Poses via a Combination of Induced Fit Docking and Metadynamics Simulations. , 2016, Journal of chemical theory and computation.
[8] J. Edwards,et al. A Prospective Virtual Screening Study: Enriching Hit Rates and Designing Focus Libraries To Find Inhibitors of PI3Kδ and PI3Kγ. , 2016, Journal of medicinal chemistry.
[9] Yi Wang,et al. Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds , 2016, J. Chem. Inf. Model..
[10] Dong-Sheng Cao,et al. ADME Properties Evaluation in Drug Discovery: Prediction of Caco-2 Cell Permeability Using a Combination of NSGA-II and Boosting , 2016, J. Chem. Inf. Model..
[11] J. Irwin,et al. Docking Screens for Novel Ligands Conferring New Biology. , 2016, Journal of medicinal chemistry.
[12] R. Siva,et al. Virtual screening of the inhibitors targeting at the viral protein 40 of Ebola virus , 2016, Infectious Diseases of Poverty.
[13] Gustavo Henrique Goulart Trossini,et al. Use of machine learning approaches for novel drug discovery , 2016, Expert opinion on drug discovery.
[14] Jens Meiler,et al. Improving quantitative structure–activity relationship models using Artificial Neural Networks trained with dropout , 2016, Journal of Computer-Aided Molecular Design.
[15] Gang Fu,et al. PubChem Substance and Compound databases , 2015, Nucleic Acids Res..
[16] Pedro J Ballester,et al. Machine‐learning scoring functions to improve structure‐based binding affinity prediction and virtual screening , 2015, Wiley interdisciplinary reviews. Computational molecular science.
[17] Chung F. Wong,et al. Flexible receptor docking for drug discovery , 2015, Expert opinion on drug discovery.
[18] A. Mazar,et al. Virtual High-Throughput Screening To Identify Novel Activin Antagonists. , 2015, Journal of medicinal chemistry.
[19] J. Andrew McCammon,et al. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation , 2015, Journal of chemical theory and computation.
[20] Enrico Glaab,et al. Building a virtual ligand screening pipeline using free software: a survey , 2015, Briefings Bioinform..
[21] Michael J E Sternberg,et al. The Phyre2 web portal for protein modeling, prediction and analysis , 2015, Nature Protocols.
[22] Rafael C. Bernardi,et al. Enhanced sampling techniques in molecular dynamics simulations of biological systems. , 2015, Biochimica et biophysica acta.
[23] Dima Kozakov,et al. The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins , 2015, Nature Protocols.
[24] Pei Tang,et al. Ensemble-based virtual screening for cannabinoid-like potentiators of the human glycine receptor α1 for the treatment of pain. , 2015, Journal of medicinal chemistry.
[25] Sonya M. Hanson,et al. Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation , 2015, Biophysical journal.
[26] Antonio Lavecchia,et al. Machine-learning approaches in drug discovery: methods and applications. , 2015, Drug discovery today.
[27] Jie Zhu,et al. BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge , 2015, Journal of Computer-Aided Molecular Design.
[28] Jie Liu,et al. Classification of Current Scoring Functions , 2015, J. Chem. Inf. Model..
[29] Sally R. Ellingson,et al. Multi-conformer ensemble docking to difficult protein targets. , 2015, The journal of physical chemistry. B.
[30] Ly Le,et al. Identification of Novel Compounds against an R294K Substitution of Influenza A (H7N9) Virus Using Ensemble Based Drug Virtual Screening , 2015, International journal of medical sciences.
[31] G. Ciccotti,et al. Temperature‐accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain , 2014, Proteins.
[32] Christel A. S. Bergström,et al. Computational Prediction of Drug Solubility in Fasted Simulated and Aspirated Human Intestinal Fluid , 2014, Pharmaceutical Research.
[33] Felice C Lightstone,et al. A method to predict blood-brain barrier permeability of drug-like compounds using molecular dynamics simulations. , 2014, Biophysical journal.
[34] Haiyan Liu,et al. Case study on temperature-accelerated molecular dynamics simulation of ligand dissociation: inducer dissociation from the Lac repressor protein. , 2014, The journal of physical chemistry. A.
[35] Diane Joseph-McCarthy,et al. Ensemble-Based Docking Using Biased Molecular Dynamics , 2014, J. Chem. Inf. Model..
[36] J Andrew McCammon,et al. Taxodione and arenarone inhibit farnesyl diphosphate synthase by binding to the isopentenyl diphosphate site , 2014, Proceedings of the National Academy of Sciences.
[37] Zhihai Liu,et al. Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results , 2014, J. Chem. Inf. Model..
[38] Pierre Tufféry,et al. PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces , 2014, Nucleic Acids Res..
[39] P Reddanna,et al. Free energy calculations to estimate ligand-binding affinities in structure-based drug design. , 2014, Current pharmaceutical design.
[40] W. Kühlbrandt. The Resolution Revolution , 2014, Science.
[41] Anna Tramontano,et al. Critical assessment of methods of protein structure prediction (CASP) — round x , 2014, Proteins.
[42] J. Mccammon,et al. Exploring the role of receptor flexibility in structure-based drug discovery. , 2014, Biophysical chemistry.
[43] Krzysztof Fidelis,et al. CASP10 results compared to those of previous CASP experiments , 2014, Proteins.
[44] Edward W. Lowe,et al. Computational Methods in Drug Discovery , 2014, Pharmacological Reviews.
[45] Christoph Sommer,et al. Machine learning in cell biology – teaching computers to recognize phenotypes , 2013, Journal of Cell Science.
[46] J. Andrew McCammon,et al. Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units , 2013, Journal of chemical theory and computation.
[47] J. A. Gavira,et al. Conservation of protein structure over four billion years. , 2013, Structure.
[48] Robert J. Doerksen,et al. Docking Challenge: Protein Sampling and Molecular Docking Performance , 2013, J. Chem. Inf. Model..
[49] J Andrew McCammon,et al. AutoGrow 3.0: an improved algorithm for chemically tractable, semi-automated protein inhibitor design. , 2013, Journal of molecular graphics & modelling.
[50] Andrzej Kolinski,et al. CABS-fold: server for the de novo and consensus-based prediction of protein structure , 2013, Nucleic Acids Res..
[51] J Andrew McCammon,et al. Farnesyl Diphosphate Synthase Inhibitors from In Silico Screening , 2013, Chemical biology & drug design.
[52] Woody Sherman,et al. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments , 2013, Journal of Computer-Aided Molecular Design.
[53] J. Mccammon,et al. Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer‐Aided Drug Design , 2013, Chemical biology & drug design.
[54] William Sinko,et al. Antibacterial drug leads targeting isoprenoid biosynthesis , 2012, Proceedings of the National Academy of Sciences.
[55] Carol Friedman,et al. Drug-drug interaction through molecular structure similarity analysis , 2012, J. Am. Medical Informatics Assoc..
[56] J Andrew McCammon,et al. LigMerge: A Fast Algorithm to Generate Models of Novel Potential Ligands from Sets of Known Binders , 2012, Chemical biology & drug design.
[57] Jian Peng,et al. Template-based protein structure modeling using the RaptorX web server , 2012, Nature Protocols.
[58] Yang Zhang,et al. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge‐based force field , 2012, Proteins.
[59] Dima Kozakov,et al. FTMAP: extended protein mapping with user-selected probe molecules , 2012, Nucleic Acids Res..
[60] David Baker,et al. Accurate protein structure modeling using sparse NMR data and homologous structure information , 2012, Proceedings of the National Academy of Sciences.
[61] Ryan G. Coleman,et al. ZINC: A Free Tool to Discover Chemistry for Biology , 2012, J. Chem. Inf. Model..
[62] P. Stewart,et al. EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps. , 2012, Structure.
[63] Haruki Nakamura,et al. The Protein Data Bank at 40: reflecting on the past to prepare for the future. , 2012, Structure.
[64] Thomas A. Hopf,et al. Protein 3D Structure Computed from Evolutionary Sequence Variation , 2011, PloS one.
[65] J. Kästner. Umbrella sampling , 2011 .
[66] Jacob D. Durrant,et al. Molecular dynamics simulations and drug discovery , 2011, BMC Biology.
[67] Valery R. Polyakov,et al. Web services as applications' integration tool: QikProp case study , 2011, J. Comput. Chem..
[68] Grace W. Tang,et al. Comparative modeling: the state of the art and protein drug target structure prediction. , 2011, Combinatorial chemistry & high throughput screening.
[69] Roberto Sanchez,et al. Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures , 2011, Journal of Structural and Functional Genomics.
[70] Luhua Lai,et al. LigBuilder 2: A Practical de Novo Drug Design Approach , 2011, J. Chem. Inf. Model..
[71] Alexander D. MacKerell,et al. Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. , 2011, Current computer-aided drug design.
[72] J. Meiler,et al. RosettaEPR: an integrated tool for protein structure determination from sparse EPR data. , 2011, Journal of structural biology.
[73] Mark McGann,et al. FRED Pose Prediction and Virtual Screening Accuracy , 2011, J. Chem. Inf. Model..
[74] Jacob D. Durrant,et al. POVME: an algorithm for measuring binding-pocket volumes. , 2011, Journal of molecular graphics & modelling.
[75] Haruki Nakamura,et al. Prediction of ligand‐binding sites of proteins by molecular docking calculation for a random ligand library , 2011, Protein science : a publication of the Protein Society.
[76] Wei Chen,et al. Modeling Protein-Ligand Binding by Mining Minima. , 2010, Journal of chemical theory and computation.
[77] J. Bajorath,et al. Quo vadis, virtual screening? A comprehensive survey of prospective applications. , 2010, Journal of medicinal chemistry.
[78] Xiaoqin Zou,et al. Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. , 2010, Physical chemistry chemical physics : PCCP.
[79] Thomas E. Exner,et al. pKa based protonation states and microspecies for protein–ligand docking , 2010, J. Comput. Aided Mol. Des..
[80] Nicolas Foloppe,et al. Rigorous Free Energy Calculations in Structure‐Based Drug Design , 2010, Molecular informatics.
[81] Emilio Gallicchio,et al. The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. , 2010, Journal of chemical theory and computation.
[82] Sheng-Yong Yang,et al. Pharmacophore modeling and applications in drug discovery: challenges and recent advances. , 2010, Drug discovery today.
[83] E. Tajkhorshid,et al. Exploring transmembrane diffusion pathways with molecular dynamics. , 2010, Physiology.
[84] Mark Gerstein,et al. 3V: cavity, channel and cleft volume calculator and extractor , 2010, Nucleic Acids Res..
[85] G. Ullmann,et al. McVol - A program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm , 2010, Journal of molecular modeling.
[86] Jens Meiler,et al. Identification of Metabotropic Glutamate Receptor Subtype 5 Potentiators Using Virtual High-Throughput Screening , 2010, ACS chemical neuroscience.
[87] Jitender Verma,et al. 3D-QSAR in drug design--a review. , 2010, Current topics in medicinal chemistry.
[88] Chuan Wang,et al. DescFold: A web server for protein fold recognition , 2009, BMC Bioinformatics.
[89] Marianne A Grant,et al. Protein structure prediction in structure-based ligand design and virtual screening. , 2009, Combinatorial chemistry & high throughput screening.
[90] A. Elofsson,et al. Structure is three to ten times more conserved than sequence—A study of structural response in protein cores , 2009, Proteins.
[91] J. P. Grossman,et al. Millisecond-scale molecular dynamics simulations on Anton , 2009, Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis.
[92] M. Jacobson,et al. Automated site preparation in physics‐based rescoring of receptor ligand complexes , 2009, Proteins.
[93] P. Stewart,et al. EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. , 2009, Structure.
[94] Claudio N. Cavasotto,et al. Homology modeling in drug discovery: current trends and applications. , 2009, Drug discovery today.
[95] William L Jorgensen,et al. Efficient drug lead discovery and optimization. , 2009, Accounts of chemical research.
[96] 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..
[97] Yongbo Hu,et al. Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy , 2009, J. Chem. Inf. Model..
[98] Dario Ghersi,et al. SITEHOUND-web: a server for ligand binding site identification in protein structures , 2009, Nucleic Acids Res..
[99] L. Dawson,et al. A Method for the Measurement of Shielding Effectiveness of Planar Samples Requiring No Sample Edge Preparation or Contact , 2009, IEEE Transactions on Electromagnetic Compatibility.
[100] Samo Turk,et al. Design and synthesis of new hydroxyethylamines as inhibitors of D-alanyl-D-lactate ligase (VanA) and D-alanyl-D-alanine ligase (DdlB). , 2009, Bioorganic & medicinal chemistry letters.
[101] Thomas A. Halgren,et al. Identifying and Characterizing Binding Sites and Assessing Druggability , 2009, J. Chem. Inf. Model..
[102] E. V. Name,et al. High-Potency Olfactory Receptor Agonists Discovered by Virtual High-Throughput Screening: Molecular Probes for Receptor Structure and Olfactory Function , 2008, Neuron.
[103] A. Laio,et al. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science , 2008 .
[104] Colin W. G. Fishwick,et al. Synthesis of de novo designed small-molecule inhibitors of bacterial RNA polymerase , 2008 .
[105] J. Nosanchuk,et al. Biological Function and Molecular Mapping of M Antigen in Yeast Phase of Histoplasma capsulatum , 2008, PloS one.
[106] J. Essex,et al. Hit identification and binding mode predictions by rigorous free energy simulations. , 2008, Journal of medicinal chemistry.
[107] E. Carpenter,et al. Overcoming the challenges of membrane protein crystallography , 2008, Current opinion in structural biology.
[108] Olivier Sperandio,et al. FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects , 2008, BMC Bioinformatics.
[109] D. Hazuda,et al. Discovery of raltegravir, a potent, selective orally bioavailable HIV-integrase inhibitor for the treatment of HIV-AIDS infection. , 2008, Journal of medicinal chemistry.
[110] Sitao Wu,et al. MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information , 2008, Proteins.
[111] J. Meiler,et al. A model for the solution structure of the rod arrestin tetramer. , 2008, Structure.
[112] William L Jorgensen,et al. Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria. , 2008, Journal of chemical theory and computation.
[113] Mark Johnson,et al. NCBI BLAST: a better web interface , 2008, Nucleic Acids Res..
[114] Markus Ringnér,et al. What is principal component analysis? , 2008, Nature Biotechnology.
[115] Natalia Artemenko,et al. Distance Dependent Scoring Function for Describing Protein-Ligand Intermolecular Interactions , 2008, J. Chem. Inf. Model..
[116] Jens Meiler,et al. De novo high-resolution protein structure determination from sparse spin-labeling EPR data. , 2008, Structure.
[117] Reiji Teramoto,et al. Consensus Scoring with Feature Selection for Structure-Based Virtual Screening , 2008, J. Chem. Inf. Model..
[118] Yang Zhang,et al. I-TASSER server for protein 3D structure prediction , 2008, BMC Bioinformatics.
[119] Nikhil S. Ketkar,et al. High confidence predictions of drug-drug interactions: predicting affinities for cytochrome P450 2C9 with multiple computational methods. , 2008, Journal of medicinal chemistry.
[120] M. Parrinello,et al. Well-tempered metadynamics: a smoothly converging and tunable free-energy method. , 2008, Physical review letters.
[121] Rommie E. Amaro,et al. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design , 2008, J. Comput. Aided Mol. Des..
[122] Istvan J. Enyedy,et al. Can we use docking and scoring for hit-to-lead optimization? , 2008, J. Comput. Aided Mol. Des..
[123] D. Kern,et al. Dynamic personalities of proteins , 2007, Nature.
[124] William L Jorgensen,et al. From docking false-positive to active anti-HIV agent. , 2007, Journal of medicinal chemistry.
[125] A. Barabasi,et al. Drug—target network , 2007, Nature Biotechnology.
[126] Dietmar Schomburg,et al. Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines , 2007, Proteins.
[127] Wolfgang Wenzel,et al. Receptor‐specific scoring functions derived from quantum chemical models improve affinity estimates for in‐silico drug discovery , 2007, Proteins.
[128] Andrzej Kolinski,et al. Protein structure prediction: Combining de novo modeling with sparse experimental data , 2007, J. Comput. Chem..
[129] L. Jong,et al. Computer-aided rational drug design: a novel agent (SR13668) designed to mimic the unique anticancer mechanisms of dietary indole-3-carbinol to block Akt signaling. , 2007, Journal of medicinal chemistry.
[130] Richard A. Friesner,et al. Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets , 2007, J. Chem. Inf. Model..
[131] Sorin Draghici,et al. Machine Learning and Its Applications to Biology , 2007, PLoS Comput. Biol..
[132] Paola Gramatica,et al. Principles of QSAR models validation: internal and external , 2007 .
[133] T. Schwede,et al. Sulfonylureas and Glinides Exhibit Peroxisome Proliferator-Activated Receptor γ Activity: A Combined Virtual Screening and Biological Assay Approach , 2007, Molecular Pharmacology.
[134] Xin Wen,et al. BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities , 2006, Nucleic Acids Res..
[135] SHENG-YOU HUANG,et al. An iterative knowledge‐based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials , 2006, J. Comput. Chem..
[136] Jens Meiler,et al. ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility , 2006, Proteins.
[137] M. Jacobson,et al. Molecular mechanics methods for predicting protein-ligand binding. , 2006, Physical chemistry chemical physics : PCCP.
[138] C. E. Peishoff,et al. A critical assessment of docking programs and scoring functions. , 2006, Journal of medicinal chemistry.
[139] David M. Ferguson,et al. A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist , 2006, J. Comput. Aided Mol. Des..
[140] Ben M. Webb,et al. Comparative Protein Structure Modeling Using Modeller , 2006, Current protocols in bioinformatics.
[141] D. E. Clark. What has computer-aided molecular design ever done for drug discovery? , 2006, Expert opinion on drug discovery.
[142] Z. Xiang,et al. Advances in homology protein structure modeling. , 2006, Current protein & peptide science.
[143] Xueliang Fang,et al. Discovery of a nanomolar inhibitor of the human murine double minute 2 (MDM2)-p53 interaction through an integrated, virtual database screening strategy. , 2006, Journal of medicinal chemistry.
[144] Tudor I. Oprea,et al. Virtual and biomolecular screening converge on a selective agonist for GPR30 , 2006, Nature chemical biology.
[145] R. Friesner,et al. Novel procedure for modeling ligand/receptor induced fit effects. , 2006, Journal of medicinal chemistry.
[146] David S. Wishart,et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration , 2005, Nucleic Acids Res..
[147] Laxmikant V. Kalé,et al. Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..
[148] Hu Mei,et al. Support vector machine applied in QSAR modelling , 2005 .
[149] P. Bradley,et al. Toward High-Resolution de Novo Structure Prediction for Small Proteins , 2005, Science.
[150] G. Klebe,et al. DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. , 2005, Journal of medicinal chemistry.
[151] 刘金明,et al. IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW,Thompson RW,et al//Proc Natl Acad Sci U S A , 2005 .
[152] Johannes Söding,et al. The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..
[153] S. Gupta,et al. A quantitative structure–activity relationship study on some aromatic/heterocyclic sulfonamides and their charged derivatives acting as carbonic anhydrase inhibitors , 2005, Journal of enzyme inhibition and medicinal chemistry.
[154] M. Karplus,et al. Molecular dynamics and protein function. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[155] Richard M. Jackson,et al. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites , 2005, Bioinform..
[156] Christel A. S. Bergström,et al. In silico predictions of drug solubility and permeability: two rate-limiting barriers to oral drug absorption. , 2005, Basic & clinical pharmacology & toxicology.
[157] John B. O. Mitchell,et al. Predicting protein-ligand binding affinities: a low scoring game? , 2004, Organic & biomolecular chemistry.
[158] Didier Rognan,et al. Comparative evaluation of eight docking tools for docking and virtual screening accuracy , 2004, Proteins.
[159] J. Bajorath,et al. Docking and scoring in virtual screening for drug discovery: methods and applications , 2004, Nature Reviews Drug Discovery.
[160] Shaomeng Wang,et al. An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes , 2004, J. Chem. Inf. Model..
[161] Mark Embrey,et al. A naphthyridine carboxamide provides evidence for discordant resistance between mechanistically identical inhibitors of HIV-1 integrase. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[162] W Patrick Walters,et al. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance , 2004, Proteins.
[163] A. W. Schüttelkopf,et al. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. , 2004, Acta crystallographica. Section D, Biological crystallography.
[164] J. Mongan,et al. Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules. , 2004, The Journal of chemical physics.
[165] D. J. Price,et al. Assessing scoring functions for protein-ligand interactions. , 2004, Journal of medicinal chemistry.
[166] J Andrew McCammon,et al. Discovery of a novel binding trench in HIV integrase. , 2004, Journal of medicinal chemistry.
[167] W. L. Jorgensen. The Many Roles of Computation in Drug Discovery , 2004, Science.
[168] Daisuke Takaya,et al. Protein structure prediction in structure based drug design. , 2004, Current medicinal chemistry.
[169] 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.
[170] Kenji Mizuguchi,et al. Fold recognition for drug discovery , 2004 .
[171] Natasja Brooijmans,et al. Molecular recognition and docking algorithms. , 2003, Annual review of biophysics and biomolecular structure.
[172] J. Skolnick,et al. TOUCHSTONEX: Protein structure prediction with sparse NMR data , 2003, Proteins.
[173] M. Congreve,et al. A 'rule of three' for fragment-based lead discovery? , 2003, Drug discovery today.
[174] Jens Meiler,et al. Epothilones: Quantitative Structure Activity Relations Studied by Support Vector Machines and Artificial Neural Networks , 2003 .
[175] Jens Sadowski,et al. Comparison of Support Vector Machine and Artificial Neural Network Systems for Drug/Nondrug Classification , 2003, J. Chem. Inf. Comput. Sci..
[176] A. Anderson. The process of structure-based drug design. , 2003, Chemistry & biology.
[177] Richard D. Taylor,et al. Improved protein–ligand docking using GOLD , 2003, Proteins.
[178] Dawen Gao,et al. A Study on Prediction of the Bio‐toxicity of Substituted Benzene Based on Artificial Neural Network , 2003, Journal of environmental science and health. Part. B, Pesticides, food contaminants, and agricultural wastes.
[179] Manuel C. Peitsch,et al. SWISS-MODEL: an automated protein homology-modeling server , 2003, Nucleic Acids Res..
[180] Satya P. Gupta. Quantitative structure-activity relationships of renin inhibitors. , 2003, Mini reviews in medicinal chemistry.
[181] D. Fabbro,et al. Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking. , 2003, Journal of medicinal chemistry.
[182] Thierry Langer,et al. Chemical feature-based pharmacophores and virtual library screening for discovery of new leads. , 2003, Current opinion in drug discovery & development.
[183] C. Kontogiorgis,et al. Quantitative structure -- activity relationships (QSARs) of thrombin inhibitors: review, evaluation and comparative analysis. , 2003, Current medicinal chemistry.
[184] P. Leeson,et al. A comparison of physiochemical property profiles of development and marketed oral drugs. , 2003, Journal of medicinal chemistry.
[185] H. van de Waterbeemd,et al. ADMET in silico modelling: towards prediction paradise? , 2003, Nature reviews. Drug discovery.
[186] Martin Stahl,et al. Binding site characteristics in structure-based virtual screening: evaluation of current docking tools , 2003, Journal of molecular modeling.
[187] G. Klebe,et al. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. , 2002, Angewandte Chemie.
[188] Andrew R. Leach,et al. A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP , 2002, J. Comput. Aided Mol. Des..
[189] Ruth Nussinov,et al. Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.
[190] M. Hashida,et al. Prediction of Caco-2 cell permeability using a combination of MO-calculation and neural network. , 2002, International journal of pharmaceutics.
[191] Z. Luthey-Schulten,et al. Ab initio protein structure prediction. , 2002, Current opinion in structural biology.
[192] Bernard F. Buxton,et al. Drug Design by Machine Learning: Support Vector Machines for Pharmaceutical Data Analysis , 2001, Comput. Chem..
[193] F. Jørgensen,et al. A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities. , 2001, Journal of medicinal chemistry.
[194] A. Good,et al. 3-D pharmacophores in drug discovery. , 2001, Current pharmaceutical design.
[195] 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..
[196] D. Baker,et al. Prospects for ab initio protein structural genomics. , 2001, Journal of molecular biology.
[197] M Rarey,et al. Detailed analysis of scoring functions for virtual screening. , 2001, Journal of medicinal chemistry.
[198] D. Baker,et al. De novo protein structure determination using sparse NMR data , 2000, Journal of biomolecular NMR.
[199] M Pastor,et al. VolSurf: a new tool for the pharmacokinetic optimization of lead compounds. , 2000, European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences.
[200] Luhua Lai,et al. LigBuilder: A Multi-Purpose Program for Structure-Based Drug Design , 2000 .
[201] Uko Maran,et al. Non-Linear QSAR Treatment of Genotoxicity , 2000 .
[202] Shu-Kun Lin. Pharmacophore Perception, Development and Use in Drug Design. Edited by Osman F. Güner , 2000 .
[203] S. Ekins,et al. Progress in predicting human ADME parameters in silico. , 2000, Journal of pharmacological and toxicological methods.
[204] G. Klebe,et al. Knowledge-based scoring function to predict protein-ligand interactions. , 2000, Journal of molecular biology.
[205] Thomas Lengauer,et al. Protein Structure Prediction Methods for Drug Design , 2000, Briefings Bioinform..
[206] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[207] M. Murcko,et al. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. , 1999, Journal of medicinal chemistry.
[208] Thomas Lengauer,et al. Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking , 1999, Proteins.
[209] Janet M. Thornton,et al. BLEEP—potential of mean force describing protein–ligand interactions: I. Generating potential , 1999 .
[210] Andrew E. Torda,et al. The GROMOS biomolecular simulation program package , 1999 .
[211] David C. Jones,et al. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. , 1999, Journal of molecular biology.
[212] Y. Martin,et al. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. , 1999, Journal of medicinal chemistry.
[213] Dale J. Kempf,et al. ABT-378, a Highly Potent Inhibitor of the Human Immunodeficiency Virus Protease , 1998, Antimicrobial Agents and Chemotherapy.
[214] Luhua Lai,et al. SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex , 1998 .
[215] David S. Goodsell,et al. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function , 1998, J. Comput. Chem..
[216] A. Sali,et al. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[217] J. Skolnick,et al. Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model , 1998, Proteins.
[218] D. Fischer,et al. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. , 1997, Proceedings of the National Academy of Sciences of the United States of America.
[219] T. Kennedy. Managing the drug discovery/development interface , 1997 .
[220] J. Stürzebecher,et al. Synthesis and structure-activity relationships of potent thrombin inhibitors: piperazides of 3-amidinophenylalanine. , 1997, Journal of medicinal chemistry.
[221] G. V. Paolini,et al. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes , 1997, J. Comput. Aided Mol. Des..
[222] C Kooperberg,et al. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.
[223] F. Lombardo,et al. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings , 1997 .
[224] M. Swindells,et al. Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.
[225] Thomas Lengauer,et al. A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.
[226] M. Wolff,et al. BURGER'S MEDICINAL CHEMISTRY AND DRUG DISCOVERY , 1996 .
[227] S. Wodak,et al. Protein structure prediction by threading methods: Evaluation of current techniques , 1995, Proteins.
[228] R. Glen,et al. Computer-aided design and synthesis of 5-substituted tryptamines and their pharmacology at the 5-HT1D receptor: discovery of compounds with potential anti-migraine properties. , 1995, Journal of medicinal chemistry.
[229] A. N. Jain,et al. Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark. , 1994, Journal of medicinal chemistry.
[230] Hans-Joachim Böhm,et al. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..
[231] Peter A. Kollman,et al. FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .
[232] H. Villar,et al. Strategies for Indirect Computer-Aided Drug Design , 1993, Pharmaceutical Research.
[233] D. Wortham,et al. Terfenadine-ketoconazole interaction. Pharmacokinetic and electrocardiographic consequences. , 1993, JAMA.
[234] D. T. Jones,et al. A new approach to protein fold recognition , 1992, Nature.
[235] Gilles Klopmand,et al. Concepts and applications of molecular similarity, by Mark A. Johnson and Gerald M. Maggiora, eds., John Wiley & Sons, New York, 1990, 393 pp. Price: $65.00 , 1992 .
[236] J S Mills,et al. Antiviral properties of Ro 31-8959, an inhibitor of human immunodeficiency virus (HIV) proteinase. , 1991, Antiviral research.
[237] P. Timmermans,et al. The discovery of potent nonpeptide angiotensin II receptor antagonists: a new class of potent antihypertensives. , 1990, Journal of medicinal chemistry.
[238] John P. Overington,et al. Knowledge‐based protein modelling and design , 1988 .
[239] R Langridge,et al. A quantitative structure-activity relationship and molecular graphics study of carbonic anhydrase inhibitors. , 1985, Molecular pharmacology.
[240] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[241] J M Blaney,et al. A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.
[242] Peter A. Kollman,et al. AMBER: Assisted model building with energy refinement. A general program for modeling molecules and their interactions , 1981 .
[243] H. Koga,et al. Structure-activity relationships of antibacterial 6,7- and 7,8-disubstituted 1-alkyl-1,4-dihydro-4-oxoquinoline-3-carboxylic acids. , 1980, Journal of medicinal chemistry.
[244] A. Lesk,et al. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. , 1980, Journal of molecular biology.
[245] G J Williams,et al. The Protein Data Bank: a computer-based archival file for macromolecular structures. , 1978, Archives of biochemistry and biophysics.
[246] G. Torrie,et al. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .
[247] C. Hansch,et al. p-σ-π Analysis. A Method for the Correlation of Biological Activity and Chemical Structure , 1964 .
[248] R. Zwanzig. High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .
[249] W. Snodgrass. Physiology , 1897, Nature.
[250] Wilfrido Moreno,et al. Introduction to Artificial Neural Network (ANN) as a Predictive Tool for Drug Design, Discovery, Delivery, and Disposition , 2016 .
[251] S. Singh,et al. Application of Artificial Neural Networks in Modern Drug Discovery Chapter – 6 published in Artificial Neural Network for Drug Design, Delivery and Disposition , 2015 .
[252] Alexander D. MacKerell,et al. Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design. , 2015, Methods in molecular biology.
[253] Steffen Lindert,et al. In silico screening for Plasmodium falciparum enoyl-ACP reductase inhibitors , 2014, Journal of Computer-Aided Molecular Design.
[254] Christophe Chipot,et al. Frontiers in free‐energy calculations of biological systems , 2014 .
[255] Santiago Vilar,et al. Application of Monte Carlo-based receptor ensemble docking to virtual screening for GPCR ligands. , 2013, Methods in enzymology.
[256] Riccardo Baron,et al. Computational Drug Discovery and Design , 2012, Methods in Molecular Biology.
[257] Jin Wang,et al. Pocket-Based Drug Design: Exploring Pocket Space , 2012, The AAPS Journal.
[258] J Andrew McCammon,et al. A molecular dynamics ensemble-based approach for the mapping of druggable binding sites. , 2012, Methods in molecular biology.
[259] J Andrew McCammon,et al. Accelerated molecular dynamics in computational drug design. , 2012, Methods in molecular biology.
[260] V. Vyas,et al. Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives , 2012, Indian journal of pharmaceutical sciences.
[261] Rizi Ai,et al. Homology modeling of cannabinoid receptors: discovery of cannabinoid analogues for therapeutic use. , 2012, Methods in molecular biology.
[262] Matthias Rarey,et al. A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function , 2012, Journal of Computer-Aided Molecular Design.
[263] Jürgen Bajorath,et al. Chemoinformatics and Computational Chemical Biology , 2011, Methods in Molecular Biology.
[264] Klaus Schulten,et al. Implementation of Accelerated Molecular Dynamics in NAMD. , 2011, Computational science & discovery.
[265] Jinbo Xu,et al. Raptorx: Exploiting structure information for protein alignment by statistical inference , 2011, Proteins.
[266] Santosh A. Khedkar,et al. Successful applications of computer aided drug discovery: moving drugs from concept to the clinic. , 2010, Current topics in medicinal chemistry.
[267] David L. Mobley,et al. Drug Design: Free-energy calculations in structure-based drug design , 2010 .
[268] Rommie E. Amaro,et al. Emerging methods for ensemble-based virtual screening. , 2010, Current topics in medicinal chemistry.
[269] Kenneth M. Merz,et al. Drug Design : Structure-and Ligand-Based Approaches , 2017 .
[270] Daniel J. Rigden,et al. From Protein Structure to Function with Bioinformatics , 2009 .
[271] Sitao Wu,et al. Ab Initio Protein Structure Prediction , 2009 .
[272] Corwin Hansch,et al. Camptothecins: a SAR/QSAR study. , 2009, Chemical reviews.
[273] M. Sternberg,et al. Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.
[274] T. Schwede,et al. Protein structure homology modeling using SWISS-MODEL workspace , 2008, Nature Protocols.
[275] J. Leroux,et al. Predicting the Solubility of the Anti-Cancer Agent Docetaxel in Small Molecule Excipients using Computational Methods , 2007, Pharmaceutical Research.
[276] Jin Li,et al. On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors , 2006, J. Chem. Inf. Model..
[277] David C Fry,et al. Protein-protein interactions as targets for small molecule drug discovery. , 2006, Biopolymers.
[278] GuanHua Chen,et al. A neural networks-based drug discovery approach and its application for designing aldose reductase inhibitors. , 2006, Journal of molecular graphics & modelling.
[279] I. Tetko,et al. In silico approaches to prediction of aqueous and DMSO solubility of drug-like compounds: trends, problems and solutions. , 2006, Current medicinal chemistry.
[280] Shuichi Hirono,et al. Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein-Ligand Complexes , 2006, J. Chem. Inf. Model..
[281] Brian K. Shoichet,et al. ZINC - A Free Database of Commercially Available Compounds for Virtual Screening , 2005, J. Chem. Inf. Model..
[282] ScienceDirect. Drug discovery today. Targets , 2004 .
[283] BMC Biology , 2004 .
[284] Beat Ernst,et al. Drug discovery today. , 2003, Current topics in medicinal chemistry.
[285] 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.
[286] Jens Meiler,et al. Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation , 2003, Proteins.
[287] Jung-Hsin Lin,et al. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. , 2003, Biopolymers.
[288] Luhua Lai,et al. Further development and validation of empirical scoring functions for structure-based binding affinity prediction , 2002, J. Comput. Aided Mol. Des..
[289] M J Sternberg,et al. Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM , 2001, Proteins.
[290] S. Ekins,et al. Application of in silico approaches to predicting drug--drug interactions. , 2001, Journal of pharmacological and toxicological methods.
[291] Gary D Bader,et al. BIND--The Biomolecular Interaction Network Database. , 2001, Nucleic acids research.
[292] M. Murcko,et al. Crystal Structure of HIV-1 Protease in Complex with Vx-478, a Potent and Orally Bioavailable Inhibitor of the Enzyme , 1995 .
[293] T L Blundell,et al. Protein structure--based drug design. , 1994, Annual review of biophysics and biomolecular structure.
[294] D. Goodsell,et al. Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.