Virtual ligand screening: strategies, perspectives and limitations

[1]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[2]  P. Goodford A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.

[3]  I. Kuntz,et al.  Docking flexible ligands to macromolecular receptors by molecular shape. , 1986, Journal of medicinal chemistry.

[4]  I. Kuntz,et al.  Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[5]  PatrickY.-S. Lam,et al.  Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. , 1994, Science.

[6]  A. Leach,et al.  Ligand docking to proteins with discrete side-chain flexibility. , 1994, Journal of molecular biology.

[7]  W. Guida,et al.  The art and practice of structure‐based drug design: A molecular modeling perspective , 1996, Medicinal research reviews.

[8]  Thomas Lengauer,et al.  A fast flexible docking method using an incremental construction algorithm. , 1996, Journal of molecular biology.

[9]  Christoph A. Sotriffer,et al.  Comparative docking studies on ligand binding to the multispecific antibodies IgE-La2 and IgE-Lb4 , 1996, J. Comput. Aided Mol. Des..

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

[11]  J. S. Dixon,et al.  Evaluation of the CASP2 docking section , 1997, Proteins.

[12]  I. Kuntz,et al.  Molecular docking to ensembles of protein structures. , 1997, Journal of molecular biology.

[13]  Elaine C. Meng,et al.  Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design. , 1997 .

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

[15]  Matthias Rarey,et al.  Feature trees: A new molecular similarity measure based on tree matching , 1998, J. Comput. Aided Mol. Des..

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

[17]  Lahana,et al.  How many leads from HTS? , 1999, Drug discovery today.

[18]  Robin Taylor,et al.  SuperStar: a knowledge-based approach for identifying interaction sites in proteins. , 1999, Journal of molecular biology.

[19]  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.

[20]  T Lengauer,et al.  The particle concept: placing discrete water molecules during protein‐ligand docking predictions , 1999, Proteins.

[21]  H. Bosshard,et al.  Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition , 1999, Journal of molecular recognition : JMR.

[22]  L. Kuhn,et al.  Virtual screening with solvation and ligand-induced complementarity , 2000 .

[23]  Ramesha,et al.  How many leads from HTS? - Comment. , 2000, Drug discovery today.

[24]  X Fradera,et al.  Similarity‐driven flexible ligand docking , 2000, Proteins.

[25]  J. Mccammon,et al.  Accommodating Protein Flexibility in Computational Drug Design 1 , 2 , 2000 .

[26]  Ruben Abagyan,et al.  Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR , 2000, J. Comput. Aided Mol. Des..

[27]  G. Klebe,et al.  Knowledge-based scoring function to predict protein-ligand interactions. , 2000, Journal of molecular biology.

[28]  Gerhard Klebe,et al.  Predicting binding modes, binding affinities and ‘hot spots’ for protein-ligand complexes using a knowledge-based scoring function , 2000 .

[29]  J A McCammon,et al.  Accommodating protein flexibility in computational drug design. , 2000, Molecular pharmacology.

[30]  Matthias Rarey,et al.  Small Molecule Docking and Scoring , 2001 .

[31]  Shaomeng Wang,et al.  How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment , 2001, J. Chem. Inf. Comput. Sci..

[32]  Y. Kurogi,et al.  Pharmacophore modeling and three-dimensional database searching for drug design using catalyst. , 2001, Current medicinal chemistry.

[33]  D. Vanderwall,et al.  Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis. , 2001, Biochimica et biophysica acta.

[34]  Thomas Lengauer,et al.  FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.

[35]  M Rarey,et al.  Detailed analysis of scoring functions for virtual screening. , 2001, Journal of medicinal chemistry.

[36]  R Abagyan,et al.  High-throughput docking for lead generation. , 2001, Current opinion in chemical biology.

[37]  G Klebe,et al.  Docking ligands onto binding site representations derived from proteins built by homology modelling. , 2001, Journal of molecular biology.

[38]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. , 2001, Advanced drug delivery reviews.

[39]  Paul D Lyne,et al.  Structure-based virtual screening: an overview. , 2002, Drug discovery today.

[40]  Gerhard Klebe,et al.  Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation. , 2002, Journal of medicinal chemistry.

[41]  G. Klebe,et al.  pH‐Dependent Binding Modes Observed in Trypsin Crystals: Lessons for Structure‐Based Drug Design , 2002 .

[42]  Thomas Lengauer,et al.  Flexible docking under pharmacophore type constraints , 2002, J. Comput. Aided Mol. Des..

[43]  B. Shoichet,et al.  Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. , 2002, Journal of medicinal chemistry.

[44]  J. Irwin,et al.  Lead discovery using molecular docking. , 2002, Current opinion in chemical biology.

[45]  Barbara M. Bolten,et al.  Trends in development cycles , 2002, Nature Reviews Drug Discovery.

[46]  A. Hopkins,et al.  The druggable genome , 2002, Nature Reviews Drug Discovery.

[47]  D. Goodsell,et al.  Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock , 2002, Proteins.

[48]  Gerhard Klebe,et al.  Docking into knowledge-based potential fields: a comparative evaluation of DrugScore. , 2002, Journal of medicinal chemistry.

[49]  G. Klebe,et al.  DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. , 2002, Journal of medicinal chemistry.

[50]  G. Klebe,et al.  Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. , 2002, Angewandte Chemie.

[51]  Ruth Nussinov,et al.  Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.

[52]  Tudor I. Oprea Current trends in lead discovery: Are we looking for the appropriate properties? , 2002, J. Comput. Aided Mol. Des..

[53]  Irene Luque,et al.  Structural parameterization of the binding enthalpy of small ligands , 2002, Proteins.

[54]  G. Klebe,et al.  pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design. , 2002, Chembiochem : a European journal of chemical biology.

[55]  Jeremy L Jenkins,et al.  Virtual screening to enrich hit lists from high‐throughput screening: A case study on small‐molecule inhibitors of angiogenin , 2002, Proteins.

[56]  Gerhard Klebe,et al.  Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. , 2003, Journal of molecular biology.

[57]  Gerhard Klebe,et al.  Utilising structural knowledge in drug design strategies: applications using Relibase. , 2003, Journal of molecular biology.

[58]  E. Brown,et al.  High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. , 2003, Bioorganic & medicinal chemistry letters.

[59]  Didier Rognan,et al.  Protein‐based virtual screening of chemical databases. II. Are homology models of g‐protein coupled receptors suitable targets? , 2002, Proteins.

[60]  S. Teague Implications of protein flexibility for drug discovery , 2003, Nature Reviews Drug Discovery.

[61]  Martin Stahl,et al.  Binding site characteristics in structure-based virtual screening: evaluation of current docking tools , 2003, Journal of molecular modeling.

[62]  H. van de Waterbeemd,et al.  ADMET in silico modelling: towards prediction paradise? , 2003, Nature reviews. Drug discovery.

[63]  E. Bradley,et al.  Comparing performance of computational tools for combinatorial library design. , 2003, Journal of medicinal chemistry.

[64]  Renxiao Wang,et al.  Comparative evaluation of 11 scoring functions for molecular docking. , 2003, Journal of medicinal chemistry.

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

[66]  M. Congreve,et al.  A 'rule of three' for fragment-based lead discovery? , 2003, Drug discovery today.

[67]  G. Klebe,et al.  Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials. , 2003, Journal of molecular biology.

[68]  Gerhard Klebe,et al.  Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis. , 2003, Journal of medicinal chemistry.

[69]  Thierry Langer,et al.  Chemical feature-based pharmacophores and virtual library screening for discovery of new leads. , 2003, Current opinion in drug discovery & development.

[70]  B. Shoichet,et al.  Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. , 2003, Journal of medicinal chemistry.

[71]  Gerhard Klebe,et al.  ZZ made EZ: influence of inhibitor configuration on enzyme selectivity. , 2003, Journal of molecular biology.

[72]  Diane Joseph-McCarthy,et al.  Pharmacophore‐based molecular docking to account for ligand flexibility , 2003, Proteins.

[73]  Gerhard Klebe,et al.  Reconstructing the binding site of factor Xa in trypsin reveals ligand-induced structural plasticity. , 2003, Journal of molecular biology.

[74]  Christopher A Lipinski,et al.  Chris Lipinski discusses life and chemistry after the Rule of Five. , 2003, Drug discovery today.

[75]  Joanna Owens,et al.  Chris Lipinski discusses life and chemistry after the Rule of Five. , 2003 .

[76]  J. Alvarez High-throughput docking as a source of novel drug leads. , 2004, Current opinion in chemical biology.

[77]  R. Hilgenfeld,et al.  Utility of homology models in the drug discovery process , 2004, Drug Discovery Today.

[78]  Brian K Shoichet,et al.  Testing a flexible-receptor docking algorithm in a model binding site. , 2004, Journal of molecular biology.

[79]  D N Chin,et al.  Integration of virtual screening into the drug discovery process. , 2004, Mini reviews in medicinal chemistry.

[80]  Gerhard Klebe,et al.  Understanding protein-ligand interactions: the price of protein flexibility. , 2004, Journal of molecular biology.

[81]  M. Congreve,et al.  Fragment-based lead discovery , 2004, Nature Reviews Drug Discovery.

[82]  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.

[83]  Nicolas Foloppe,et al.  Drug-like Annotation and Duplicate Analysis of a 23-Supplier Chemical Database Totalling 2.7 Million Compounds , 2004, J. Chem. Inf. Model..

[84]  D. J. Price,et al.  Assessing scoring functions for protein-ligand interactions. , 2004, Journal of medicinal chemistry.

[85]  Brian K. Shoichet,et al.  Virtual screening of chemical libraries , 2004, Nature.

[86]  Paul Watson,et al.  Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment , 2004, J. Chem. Inf. Model..

[87]  J. Bajorath,et al.  Docking and scoring in virtual screening for drug discovery: methods and applications , 2004, Nature Reviews Drug Discovery.

[88]  Ajay N. Jain,et al.  Virtual screening in lead discovery and optimization. , 2004, Current opinion in drug discovery & development.

[89]  S. David Morley,et al.  Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock® , 2004, J. Comput. Aided Mol. Des..

[90]  Jürgen Bajorath,et al.  Virtual screening methods that complement HTS. , 2004, Combinatorial chemistry & high throughput screening.

[91]  Heather A Carlson,et al.  Incorporating protein flexibility in structure-based drug discovery: using HIV-1 protease as a test case. , 2004, Journal of the American Chemical Society.

[92]  W Patrick Walters,et al.  A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance , 2004, Proteins.

[93]  G. Klebe,et al.  Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model. , 2004, Journal of medicinal chemistry.

[94]  Gerhard Klebe,et al.  Probing flexibility and “induced‐fit” phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations , 2004, Proteins.

[95]  Gerhard Klebe,et al.  Crystallographic study of inhibitors of tRNA-guanine transglycosylase suggests a new structure-based pharmacophore for virtual screening. , 2004, Journal of molecular biology.

[96]  Tingjun Hou,et al.  Recent development and application of virtual screening in drug discovery: an overview. , 2004, Current pharmaceutical design.

[97]  X. Barril,et al.  Virtual screening in structure-based drug discovery. , 2004, Mini reviews in medicinal chemistry.

[98]  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.

[99]  Didier Rognan,et al.  Comparative evaluation of eight docking tools for docking and virtual screening accuracy , 2004, Proteins.

[100]  Eric J Martin,et al.  Target-biased scoring approaches and expert systems in structure-based virtual screening. , 2004, Current opinion in chemical biology.

[101]  Y. Martin,et al.  A bioavailability score. , 2005, Journal of medicinal chemistry.

[102]  T. Klabunde,et al.  Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor. , 2005, Journal of medicinal chemistry.

[103]  R. Glen,et al.  Screening for Dihydrofolate Reductase Inhibitors Using MOLPRINT 2D, a Fast Fragment-Based Method Employing the Naïve Bayesian Classifier: Limitations of the Descriptor and the Importance of Balanced Chemistry in Training and Test Sets , 2005, Journal of biomolecular screening.

[104]  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.

[105]  Brian K. Shoichet,et al.  ZINC - A Free Database of Commercially Available Compounds for Virtual Screening , 2005, J. Chem. Inf. Model..

[106]  Richard D. Taylor,et al.  Modeling water molecules in protein-ligand docking using GOLD. , 2005, Journal of medicinal chemistry.

[107]  Matthew P Jacobson,et al.  Virtual Ligand Screening against Escherichia coli Dihydrofolate Reductase: Improving Docking Enrichment Using Physics-Based Methods , 2005, Journal of biomolecular screening.

[108]  Mark C. Fishman,et al.  Pharmaceuticals: A new grammar for drug discovery , 2005, Nature.

[109]  Christian N Parker,et al.  McMaster University Data-Mining and Docking Competition , 2005, Journal of biomolecular screening.

[110]  H. Gohlke,et al.  Improving binding mode predictions by docking into protein-specifically adapted potential fields. , 2005, Journal of medicinal chemistry.

[111]  Arne Elofsson,et al.  All are not equal: A benchmark of different homology modeling programs , 2005, Protein science : a publication of the Protein Society.

[112]  K. Merz,et al.  Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes. , 2005, Journal of medicinal chemistry.

[113]  E. Jaeger,et al.  Comparison of automated docking programs as virtual screening tools. , 2005, Journal of Medicinal Chemistry.

[114]  P. Hajduk,et al.  Druggability indices for protein targets derived from NMR-based screening data. , 2005, Journal of medicinal chemistry.

[115]  John J Irwin,et al.  Here Be Dragons: Docking and Screening in an Uncharted Region of Chemical Space , 2005, Journal of biomolecular screening.

[116]  B. Shoichet,et al.  Decoys for docking. , 2005, Journal of medicinal chemistry.

[117]  Jean-Louis Reymond,et al.  Virtual exploration of the small-molecule chemical universe below 160 Daltons. , 2005, Angewandte Chemie.

[118]  X. Barril,et al.  Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. , 2005, Journal of medicinal chemistry.

[119]  E. Jaeger,et al.  Docking: successes and challenges. , 2005, Current pharmaceutical design.

[120]  Jürgen Bajorath,et al.  Evaluating the High-Throughput Screening Computations , 2005, Journal of biomolecular screening.

[121]  Nadine H. Elowe,et al.  Experimental Screening of Dihydrofolate Reductase Yields a “Test Set” of 50,000 Small Molecules for a Computational Data-Mining and Docking Competition , 2005, Journal of biomolecular screening.

[122]  Robin Taylor,et al.  Comparing protein–ligand docking programs is difficult , 2005, Proteins.

[123]  Hugo Kubinyi,et al.  Success Stories of Computer‐Aided Design , 2006 .

[124]  G. Klebe,et al.  Expect the unexpected or caveat for drug designers: multiple structure determinations using aldose reductase crystals treated under varying soaking and co-crystallisation conditions. , 2006, Journal of molecular biology.

[125]  Brian K. Shoichet,et al.  Molecular Docking and High-Throughput Screening for Novel Inhibitors of Protein Tyrosine Phosphatase-1 B , 2022 .