Bibliography
- Hawkins PCD, Skillman AG, Nicholls A. Comparison of shape matching and docking as virtual screening tools. J Med Chem 2007;7:74-82
- Kirchmair J, Distinto S, Markt P, How to optimize shape-based virtual screening: choosing the right query and including chemical information. J Chem Inf Model 2009;49:678-92
- Keiser MJ, Irwin JJ, Shoichet BK. The chemical basis of pharmacology. Biochemistry 2010;49:10267-76
- Azzaoui K, Hamon J, Faller B, Modeling promiscuity based on in vitro safety pharmacology profiling data. ChemMedChem 2007;2:874-80
- Merlot C. In silico methods for early toxicity assessment. Curr Opin Drug Discov Devel 2008;11:80-5
- Campillos M, Kuhn M, Gavin AC, Drug target identification using side-effect similarity. Science 2008;321:263-6
- Fedorov O, Marsden B, Pogacic V, A systematic interaction map of validated kinase inhibitors with Ser/Thr kinases. Proc Natl Acad Sci USA 2007;104:20523-8
- Trubetskoy OV, Finel M, Kurkela M, High throughput screening assay for UDP-glucuronosyltransferase 1A1 glucuronidation profiling. Assay Drug Dev Technol 2007;5:343-54
- Nobeli I, Favia AD, Thornton JM. Protein promiscuity and its implications for biotechnology. Nat Biotechnol 2009;2:157-67
- Chong CR, Sullivan DJ. New uses for old drugs. Nature 2007;448:645-6
- Sato H, Shewchuk LM, Tang J. Prediction of multiple binding modes of the CDK2 inhibitors, anilinopyrazoles, using the automated docking programs GOLD, FlexX, and LigandFit: an evaluation of performance. J Chem Inf Model 2006;46:2552-62
- Xu Y, Gurusiddappa S, Rich RL, Multiple binding sites in collagen type i for the integrins alpha1beta1 and alpha2beta1J. Biol Chem 2000;275:38981-9
- Williams S, Bledsoe RK, Collins JL, X-ray crystal structure of the Liver X Receptor beta ligand binding domain: regulation by a Histidine-Tryptophan Switch. J Biol Chem 2003;278:27138-43
- Rahimi N. VEGFR-1 and VEGFR-2: two non-identical twins with a unique physiognomy. Front Biosci 2006;11:818-29
- Taha MO, Qandil AM, Zaki DD, Aldaben MA. Ligand-based assessment of factor Xa binding site flexibility via elaborate pharmacophore exploration and genetic algorithm-based QSAR modeling. Eur J Med Chem 2005;40:701-27
- Hung-Ju H, Keng-Chang T, Yi-Kun S, Factor Xa active site substrate specificity with substrate phage display and computational molecular modeling. J Biol Chem 2008;283:12343-53
- Giannakis E, Male DA, Ormsby RJ, Multiple ligand binding sites on domain seven of human complement factor H. Int Immunopharmacol 2001;1:433-43
- Bourhis E, Tam C, Franke Y, Reconstitution of a Frizzled8·Wnt3a·LRP6 signaling complex reveals multiple Wnt and Dkk1 binding sites on LRP6. J Biol Chem 2010;285:9172-9
- Sok DE, Kim YB, Choi SJ, Multiple binding sites involved in the effect of choline esters on decarbamoylation of monomethylcarbamoyl- or dimethylcarbamoly-acetylcholinesterase. Biochem J 1994;301:713-20
- Zhao Q, Yang G, Mei X, Design of novel carbamate acetylcholinesterase inhibitors based on the multiple binding sites of acetylcholinesterase. J Pestic Sci 2008;33:371-5
- Lee YS, Chen Z, Kador PF. Molecular modeling studies of the binding modes of Aldose Reductase inhibitors at the active site of human Aldose Reductase. Bioorg Med Chem 1998;6:1811-19
- Steuber H, Zentgraf M, La Motta C, Evidence for a novel binding site conformer of Aldose Reductase in ligand-bound state. J Mol Biol 2007;369:186-97
- Pargellis C, Tong L, Churchill L, Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site. Nat Struct Biol 2002;9:268-72
- Barrow JC, Stauffer SR, Rittle KE, Discovery and X-ray crystallographic analysis of a spiropiperidine iminohydantoin inhibitor of beta-Secretase. J Med Chem 2008;51:6259-62
- Stachel SJ, Coburn CA, Steele TG, Conformationally biased P3 amide replacements of beta-secretase inhibitors. Bioorg Med Chem Lett 2006;16:641-4
- Caflisch A, Walchli R, Ehrhardt C. Computer-aided design of thrombin inhibitors. News Physiol Sci 1998;13:182-8
- Meh DA, Siebenlist KR, Mosesson MW. Identification and characterization of the thrombin binding sites on Fibrin. J Biol Chem 1996;271:23121-5
- Guasch L, Sala E, Valls C, Structural insights for the design of new PPAR gamma partial agonists with high binding affinity and low transactivation activity. J Comput Aided Mol Des 2011;25:717-28
- Pochetti G, Godio C, Mitro N, Insights into the mechanism of partial Agonism. Crystal structures of the peroxisome proliferator-activated receptor ligand binding domain in the complex with two enantiomeric ligands. J Biol Chem 2007;282:17314-24
- Zoete V, Grosdidier A, Michielin O. Peroxisome proliferator-activated receptor structures: ligand specificity, molecular switch and interactions with regulators. Biochim Biophys Acta 2007;1771:915-25
- Davydov DR, Halpert JR. Allosteric P450 mechanisms: multiple binding sites, multiple conformers or both? Expert Opin Drug Metab Toxicol 2008;4:1523-35
- Lebbink RJ, Raynal N, de Ruiter T, Identification of multiple potent binding sites for human leukocyte associated Ig-like receptor LAIR on collagens II and III. Matrix Biol 2009;28:202-10
- Parsi MK, Adams JRJ, Whitelock J, Gibson MA. LTBP-2 has multiple heparin/heparan sulfate binding sites. Matrix Biol 2010;29:393-401
- Ekins S, Kortagere S, Iyer M, Challenges predicting ligand-receptor interactions of promiscuous proteins: the Nuclear Receptor PXR. PLoS Comput Biol 2009;5:e1000594
- Ung CY, Li H, Yap CW, Chen YZ. In Silico Prediction of Pregnane X receptor activators by machine learning approaches. Mol Pharmacol 2007;71:158-68
- Steuer C, Heinonen K, Kattner L, Klein CD. Optimization of assay conditions for Dengue virus protease: effect of various Polyols and Nonionic Detergents. J Biomol Screen 2009;14:1102-8
- Shelton CC, Zhu L, Chau D, Modulation of gamma-secretase specificity using small molecule allosteric inhibitors. PNAS 2009;106:20228-33
- Hammoudeh DI, Follis AV, Prochownik EV, Metallo SJ. Multiple independent binding sites for small-molecule inhibitors on the oncoprotein c-Myc. J Am Chem Soc 2009;131:7390-401
- Kellenberger E, Springael JY, Parmentier M, Identification of nonpeptide CCR5 receptor agonists by structure-based virtual screening. J Med Chem 2007;50:1294-303
- Perez-Nueno VI, Ritchie DW, Borrell JI, Teixido J. Clustering and classifying diverse HIV entry inhibitors using a novel consensus shape based virtual screening approach: further evidence for multiple binding sites within the CCR5 extracellular pocket. J Chem Inf Model 2008;48:2146-65
- Perez-Nueno VI, Ritchie DW, Rabal O, Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape-matching and ligand-receptor docking. J Chem Inf Model 2008;48:509-33
- Garcia-Perez J, Rueda P, Alcami J, Allosteric model of maraviroc binding to CC chemokine receptor 5 (CCR5). J Biol Chem 2011;286:33409-21
- Wong RSY, Bodart V, Metz M, Comparison of the potential multiple binding modes of Bicyclam, Monocylam, and Noncyclam Small-Molecule CXC chemokine receptor 4 inhibitors. Mol Pharmacol 2008;74:1485-95
- Pettersson S, Perez-Nueno VI, Mena MP, Novel Monocyclam Derivatives as HIV entry inhibitors: design, Synthesis, Anti-HIV evaluation, and their interaction with the CXCR4 Co-receptor. ChemMedChem 2010;5:1272-81
- Lam AR, Bhattacharya S, Patel K, Importance of receptor flexibility in binding of Cyclam compounds to the Chemokine Receptor CXCR4. J Chem Inf Model 2011;51:139-47
- Kawatkar SP, Yan M, Gevariya H, Computational analysis of the structural mechanism of inhibition of chemokine receptor CXCR4 by small molecule antagonists. Exp Biol Med 2011;236:844-50
- Neves MA, Simoes S, Sa e Melo ML. Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach. J Comput Aided Mol Des 2010;24:1023-103
- Xie L, Xie L, Bourne PE. Structure-based systems biology for analyzing off-target binding. Curr Opin Struct Biol 2011;21:1-11
- Li Y, Liu X, Jiang H, Feng Z. A rapid method of epitope mapping. Eur J Biochem 2005;176:153-60
- Han JF, Zhao TT, Liu HL, Identification of a new HLA-A*0201-restricted cytotoxic T lymphocyte epitope from CML28. Canc Immunol Immunother 2006;55:1575-83
- Feng BY, Simeonov A, Jadhav A, A high-throughput screen for aggregation-based inhibition in a large compound library. J Med Chem 2007;50:2385-90
- Koshland DE Jr. Correlation of structure and function in enzyme action. Science 1963;142:1533-41
- Spiller B, Gershenson A, Arnold FH, Stevens RC. A structural view of evolutionary divergence. Proc Natl Acad Sci USA 1999;96:12305-10
- Bashton M, Chothia C. The generation of new protein functions by the combina- tion of domains. Structure 2007;15:85-99
- Parkison C, Ashizawa K, McPhie P, The monomer of pyruvate kinase, subtype M1, is both a kinase and a cytosolic thyroid hormone bind- ing protein. Biochem Biophys Res Commun 1991;179:668-74
- Guillet V, Lapthorn A, Hartley RW, Mauguen Y. Recognition between a bacte- rial ribonuclease, barnase, and its natural inhibitor, barstar. Structure 1993;1:165-76
- Mariuzza RA. Multiple paths to multispecificity. Immunity 2006;24:359-61
- Feng BY, Shelat A, Doman TN, High- throughput assays for promiscuous inhibitors. Nat Chem Biol 2005;1:146-8
- Roche O, Schneider P, Zuegge J, Development of a virtual screening method for identification of “Frequent Hitters” in compound libraries. J Med Chem 2002;45:137-42
- Borodina YV, Filimonov DA, Poroikov VV. Computer-aided prediction of prodrug activity using the PASS system. Phamaceutical Chem J 1996;30:760-3
- Li H, Gao Z, Kang L, TarFisDock: a web server for identifying drug targetsn with docking approach. Nucleic Acids Res 2006;34:W219-24
- Nigsch F, Bender A, Jenkins JL, Mitchell JBO. Ligand-target prediction using winnow and naive bayesian algorithms and the implications of overall performance statistics. J Chem Inf Model 2008;48:2313-25
- Niijima S, Yabuuchi H, Okuno Y. Cross-target view to feature selection: identification of molecular interaction features in ligand−target space. J Chem Inf Model 2011;51:15-24
- Paolini GV, Shapland RHB, van Hoorn WP, Global mapping of pharmacological space. Nat Biotechnol 2006;24:805-15
- Weskamp N, Hullermeier E, Klebe G. Merging chemical and biological space: Structural mapping of enzyme binding pocket space. Proteins 2009;76:317-30
- Keiser MJ, Setola V, Irwin JJ, Predicting new molecular targets for known drugs. Nature 2009;462:175-81
- Milletti F, Vulpetti A. Predicting polypharmacology by binding site similarity: from Kinases to the protein Universe. J Chem Inf Model 2010;50:1418-143
- Perez-Nueno VI, Venkatraman V, Mavridis L, Ritchie DW. Predicting drug polypharmacology using a novel surface property similarity-based approach. J Chemoinformatics 2011;3(Suppl 1):O19
- Altschul SA, Gish W, Miller W, Basic local alignment search tool. J Mol Biol 1990;215:403-10
- Altschul SA, Madden TL, Schaffer AA, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-402
- Pearson WR. Rapid and sensitive sequence comparison with fastp and fasta. Methods Enzymol 1990;183:63-98
- Arnold R, Rattei T, Tischler P, Simap-the similarity matrix of proteins. Bioinformatics 2005;21:ii42-6
- Liu X, Ouyang S, Yu B, PharmMapper server: a web server for potential drug target identification using pharmacophore mapping approach. Nucleic Acids Res 2010;38:W609-14
- Johnson MA, Maggiora GM. Concepts and applications of molecular similarity. Wiley & Sons; New York: 1990
- Keiser MJ, Roth BL, Armbruster BN, Relating protein pharmacology by ligand chemistry. Nat Biotechnol 2007;25:197-206
- Hert J, Keiser MJ, Irwin JJ, Quantifying the relationships among drug classes. J Chem Inf Model 2008;48:755-65
- Vidal D, Mestres J. In silico receptorome screening of antipsychotic drugs. Mol Infect 2010;29:543-51
- Mestres J, Gregori-Puigjane E, Valverde S, Sole RV. The topology of drug-target interaction networks: implicit dependence on drug properties and target families. Mol BioSyst 2009;5:1051-7
- Cleves AE, Jain AN. Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery. J Comput Aided Mol Des 2008;22:147-59
- Cleves AE, Jain AN. Robust ligand-based modeling of the biological targets of known drugs. J Med Chem 2006;49:2921-38
- Kinnings SL, Jackson RM. ReverseScreen3D: a structure-based ligand matching method to identify protein targets. J Chem Inf Model 2011;51:624-34
- Henrich S, Salo-Ahen OMH, Huang B, Computational approaches to identifying and characterizing protein binding sites for ligand design. J Mol Recognit 2010;23:209-19
- Sciabola S, Stanton RV, Mills JE, High-Throughput virtual screening of proteins using GRID molecular interaction fields. J Chem Inf Model 2010;50:155-69
- Schmitt S, Kuhn D, Klebe GA. New method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 2002;323:387-406
- Shulman-Peleg A, Nussinov R, Wolfson HJ. SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res 2005;33:W337-41
- Jambon M, Imberty A, Delage G, Geourjon C. A new bioinformatic approach to detect common 3D sites in protein structures. Proteins Struct Funct Genet 2003;52:137-45
- Kinnings SL, Jackson RM. Binding site similarity analysis for the functional classification of the protein kinase family. J Chem Inf Model 2009;49:318-29
- Najmanovich R, Kurbatova N, Thornton J. Detection of 3D atomic similarities and their use in the discrimination of small-molecule protein-binding sites. Bioinformatics 2008;24:i105-11
- Belongie S, Malik J, Puzicha J. Shape matching and object recognition using shape contexts. IEEE Trans Pattern Anal Mach Intell 2002;24:509-22
- Richmond NJ, Willett P, Clark RD. Alignment of three- dimensional molecules using an image recognition algorithm. J Mol Graph Model 2004;23:199-209
- Takigawa I, Tsuda K, Mamitsuka H. Mining significant substructure pairs for interpreting polypharmacology in drug-target network. PLoS One 2011;6:e16999
- Perez-Nueno VI, Venkatraman V, Mavridis L, Ritchie DW. Predicting drug promiscuity using spherical harmonic (SH) shape-based similarity comparisons. The Open Conference Proceedings Journal 2011; In Press
- Lin J, Clark T. An Analytical, Variable Resolution, Complete Description of Static Molecules and Their Intermolecular Binding Properties. J Chem Inf Model 2005;45:1010-16
- Ritchie DW, Kemp GJL. Protein docking using spherical polar fourier correlations. Proteins Struct Func Genet 2000;39:178-94
- CEPOS InSilico Ltd.: Erlangen, Germany, 2009. Available from: http://www.ceposinsilico.de/ [Last accessed 6 July 2011]
- Kortagere S, Krasowski MD, Ekins S. The importance of discerning shape in molecular pharmacology. Trends Pharmacol Sci 2009;30:138-47
- Yera ER, Cleves AE, Jain AN. Chemical structural novelty: on-targets and off-targets. J Med Chem 2011;54:6771-85
- Schwaha R, Ecker GF. Use of shape similarities for the classification of P-glycoprotein substrates and nonsubstrates. Future Med Chem 2011;3:1117-28
- Lewis PJ, de Jonge M, Daeyaert F, On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data. J Comput Aided Mol Des 2003;17:129-34
- Perez-Nueno VI, Ritchie DW. Using consensus-shape clustering to identify promiscuous ligands and protein targets and to choose the right query for shape-based virtual screening. J Chem Inf Model 2011;51:1233-48
- Shou M, Dai R, Cui D, A kinetic model for the metabolic interaction of two substrates at the active site of cytochrome P450 3A4. J Biol Chem 2001;276:2256-
- Stjernschantz E, Oostenbrink C. Improved ligand-protein binding affinity predictions using multiple binding modes. Biophys J 2010;98:2682-91
- Poulos TL, Howard AJ. Crystal structures of metyrapone- and phenylimidazole-inhibited complexes of cytochrome P-450cam. Biochemistry 1987;26:8165-74
- Badger J, Minor I, Kremer MJ, Structural analysis of a series of antiviral agents complexed with human rhinovirus 14. Proc Natl Acad Sci USA 1998;85:3304-8
- Uytterhoeven K, Sponer J, Van Meervelt L. Two 1:1 binding modes for distamycin in the minor groove of d(GGCCAATTGG). Eur J Biochem 2002;269:2868-77
- Wojtczak A, Cody V, Luft J, Pangborn W. Multiple binding modes. 2002. Available from: http://www.ndsu.nodak.edu/instruct/balaz/bioinf/002.htm [Last accessed 11 July 2002]
- Dohnalek J, Hasek J, Duskova J, A distinct binding mode of a hydroxyethylamine isostere inhibitor of HIV-1 protease. Acta Crystallogr 2001;D57:472-6
- Berger JP, Petro AE, Macnaul KL, Distinct properties and advantages of a novel peroxisome proliferator-activated protein gamma selective modulator. Mol Endocrinol 2003;17:662-76
- Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem 2006;49:6789-801
- Perez-Nueno VI, Venkatraman V, Mavridis L, Using spherical harmonic surface property representations for ligand-based virtual screening. Mol Infect 2011;30:151-9