A chemogenomics view on protein-ligand spaces

BMC Bioinformatics

Volumn 10, Issue SUPPL. 6, 2009, Pages

  Strömbergsson, Helena ^a   Kleywegt, Gerard J ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL INFORMATION; MULTIDIMENSIONAL DATA; NEAREST NEIGHBOUR; PHYSICOCHEMICAL FEATURES; PRINCIPAL COMPONENTS; PROTEIN DATA BANK; PROTEIN FEATURES; PROTEIN-LIGAND INTERACTIONS;

PRINCIPAL COMPONENT ANALYSIS; PROTEINS;

LIGANDS;

ACAMPROSATE; GLUTAMATE RECEPTOR 5; LIGAND; PROTEIN;

AMINO ACID SEQUENCE; CHEMOGENOMICS; COMPLEX FORMATION; CONFERENCE PAPER; CONTROLLED STUDY; DRUG PROTEIN BINDING; DRUG RESEARCH; DRUG TARGETING; GENOMICS; LIGAND BINDING; MOLECULAR RECOGNITION; PHYSICAL CHEMISTRY; PROTEIN DATABASE; PROTEIN INTERACTION; PROTEIN STRUCTURE; STRUCTURAL BIOINFORMATICS; ARTICLE; BINDING SITE; BIOLOGY; CHEMISTRY; DRUG DEVELOPMENT; METHODOLOGY;

BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DRUG DISCOVERY; GENOMICS; LIGANDS; PROTEINS;

EID: 67649100477     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-S6-S13     Document Type: Conference Paper

References (55)

1. Rognan D Chemogenomic approaches to rational drug design Br J Pharmacol 2007, 152(1):38-52. 1978269 17533416
2. Lipinski CA Drug-like properties and the causes of poor solubility and poor permeability J Pharmacol Toxicol Methods 2000, 44(1):235-249. 11274893
3. Eyre TA Ducluzeau F Sneddon TP Povey S Bruford EA Lush MJ The HUGO Gene Nomenclature Database, 2006 updates Nucleic Acids Res 200634 (Database):D319-321. 1347509 16381876
4. O'Donovan C Apweiler R Bairoch A The human proteomics initiative (HPI) Trends Biotechnol 2001, 19:178-181. 11301130
5. Martin RE Green LG Guba W Kratochwil N Christ A Discovery of the first nonpeptidic, small-molecule, highly selective somatostatin receptor subtype 5 antagonists: A chemogenomics approach J Med Chem 2007, 50(25):6291-6294. 18020390
6. Guba W Green LG Martin RE Roche O Kratochwil N Mauser H Bissantz C Christ A Stahl M From astemizole to a novel hit series of small-molecule somatostatin 5 receptor antagonists via GPCR affinity profiling J Med Chem 2007 50, 25:6295-6298. 18020391
7. Lindström A Pettersson F Almquist F Berglund A Kihlberg J Linusson A Hierarchical PLS modeling for predicting the binding of a comprehensive set of structurally diverse protein-ligand complexes J Chem Inf Model 2006,46:1154-1167. 16711735
8. Bock JR Gough DA Virtual screen for ligands of orphan G protein-coupled receptors J Chem Inf Model 2005, 45(5):1402-1414. 16180917
9. Strömbergsson H Daniluk P Kryshtafovych A Fidelis K Wikberg JES Kleywegt GJ Hvidsten TR Interaction Model Based on Local Protein Substructures Generalizes to the Entire Structural Enzyme-Ligand Space J Chem Inf Mod 2008, 48(11):2278-2288.
10. Dobson CM Chemical space and biology Nature 2004, 432(7019):824-828. 15602547
11. Oprea TI Gottfries J Chemography: The art of navigating in chemical space J Comb Chem 2001, 3(2):157-166. 11300855
12. Bateman A Coin L Durbin R Finn RD Hollich V Griffiths-Jones S Khanna A Marshall M Moxon S Sonnhammer EL The Pfam protein families database Nucleic Acids Res 2004, 32(Database):D138-141. 308855 14681378
13. Murzin AG Brenner SE Hubbard T Chothia C SCOP: A structural classification of proteins database for the investigation of sequences and structures J Mol Biol 1995, 247(4):536-540. 7723011
14. Greene LH Lewis TE Addou S Cuff A Dallman T Dibley M Redfern O Pearl F Nambudiry R Reid A The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution Nucleic Acids Res 2007, 35(Database):D291-297. 1751535 17135200
15. Seiler KP George GA Happ MP Bodycombe NE Carrinski HA Norton S Brudz S Sullivan JP Muhlich J Serrano M ChemBank: A small-molecule screening and cheminformatics resource database Nucleic Acids Res 2008, 36(Database):D351-359. 2238881 17947324
16. Wishart DS Knox C Guo AC Cheng D Shrivastava S Tzur D Gautam B Hassanali M DrugBank: A knowledgebase for drugs, drug actions and drug targets Nucleic Acids Res 2008, 36:D901-906. 2238889 18048412
17. McInnes C Virtual screening strategies in drug discovery Curr Opin Chem Biol 2007, 11(5):494-502. 17936059
18. Nervall M Hanspers P Carlsson J Boukharta L Aqvist J Predicting binding modes from free energy calculations J Med Chem 2008, 51(9):2657-2567. 18410080
19. Park K Kim D Binding similarity network of ligand Proteins 2008, 71(2):960-971. 18004762
20. Campillos M Kuhn M Gavin AC Jensen LJ Bork P Drug target identification using side-effect similarity Science 2008, 321(5886):263-266. 18621671
21. Berman HM Westbrook J Feng Z Gilliland G Bhat TN Weissig H Shindyalov IN Bourne PE The Protein Data Bank Nucleic Acids Res 2000, 28(1):235-242. 102472 10592235
22. Dimitropoulos D Ionides J K H Using MSDchem to Search the PDB Ligand Dictionary Current Protocols in Bioinformatics Hoboken, N. J.: John Wiley & Sons AD B, Page RDM, Petsko GA, Stein LD, Stormo GD 2006:14.13.11-14.13.13.
23. Wang G Dunbrack RL Jr PISCES: A protein sequence culling server Bioinformatics 2003, 19(12):1589-1591. 12912846
24. Hvidsten TR Kryshtafovych A Fidelis K Local descriptors of protein structure: A systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions Proteins 2008. 19025980
25. Strömbergsson H Kryshtafovych A Prusis P Fidelis K Wikberg JES Komorowski J Hvidsten TR Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures Proteins 2006, 65(3):568-579. 16948162
26. Henschel A Winter C Kim WK Schroeder M Using structural motif descriptors for sequence-based binding site prediction BMC Bioinformatics 2007, 8(Suppl 4):S5. 1892084 17570148
27. Li ZR Lin HH Han LY Jiang L Chen X Chen YZ PROFEAT: A web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence Nucleic Acids Res 2006, 34(Web Server):W32-37. 1538821 16845018
28. Sandberg M Eriksson L Jonsson J Sjostrom M Wold S New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids J Med Chem 1998, 41(14):2481-2491. 9651153
29. Wikberg JES Lapinsh M Prusis P Proteochemometrics: A tool for modeling the molecular interaction space Chemogenomics in drug discovery Darmstadt: Wiley-VCH Kubinyi H, Müller G 2004.
30. Dubchak I Muchnik I Holbrook SR Kim SH Prediction of protein folding class using global description of amino acid sequence PNAS 1995, 92(19):8700-8704. 41034 7568000
31. Terfloth L Calculation of structure descriptors Chemoinformatics Darmstadt: Wiley-VCH Gasteiger J, Engel T 2003:401-431.
32. Larsson J Gottfries J Muresan S Backlund A ChemGPS-NP: Tuned for navigation in biologically relevant chemical space J Nat Prod 2007, 70(5):789-794. 17439280
33. Hastie T Tibshirani R Friedman J Unsupervised learning The elements of statistical learning New York: Springer-verlag 2001:437-504.
34. Boothby LA Doering PL Acamprosate for the treatment of alcohol dependence Clinical Therapeutics 2005, 27(6):695-714. 16117977
35. Pieper U Eswar N Davis FP Braberg H Madhusudhan MS Rossi A Marti-Renom M Karchin R Webb BM Eramian D et al MODBASE: A database of annotated comparative protein structure models and associated resources Nucleic Acids Res 2006, 34(Database):D291-295. 1347422 16381869
36. Nayal M Honig B On the nature of cavities on protein surfaces: application to the identification of drug-binding sites Proteins 2006, 63(4):892-906. 16477622
37. Pastor M Cruciani G McLay I Pickett S Clementi S GRid-INdependent descriptors (GRIND): A novel class of alignment-independent three-dimensional molecular descriptors J Med Chem 2000, 43(17):3233-3243. 10966742
38. Haylett DG Direct measurement of drug binding to receptors Textbook of receptor pharmacology Boca Raton: CRC Press Foreman JC, Johansen T 2003:153-182.
39. Kitchen DB Decornez H Furr JR Bajorath J Docking and scoring in virtual screening for drug discovery: Methods and applications Nat Rev Drug Discov 2004, 3(11):935-949. 15520816
40. Golovin A Oldfield TJ Tate JG Velankar S Barton GJ Boutselakis H Dimitropoulos D Fillon J Hussain A Ionides JM et al E-MSD: An integrated data resource for bioinformatics Nucleic Acids Res 2004, 32(Database):D211-216. 308812 14681397
41. Kleywegt GJ Brunger AT Checking your imagination: Applications of the free R value Structure 1996, 4(8):897-904. 8805582
42. Laskowski RA PDBsum: Summaries and analyses of PDB structures Nucleic Acids Res 2001, 29(1):221-222. 29784 11125097
43. Needleman SB Wunsch CD A general method applicable to the search for similarities in the amino acid sequence of two proteins J Mol Biol 1970, 48(3):443-453. 5420325
44. Rice P Longden I Bleasby A EMBOSS: The European Molecular Biology Open Software Suite Trends Genet 2000, 16(6):276-277. 10827456
45. OCA, a browser-database for protein structure/function http://bip.weizmann.ac.il/oca
46. UniProt C The universal protein resource (UniProt) Nucleic Acids Res 2008 36(Database):D190-195. 2238893 18045787
47. Reference Manual for PROFEAT http://jing.cz3.nus.edu.sg/prof/ prof_manual.pdf
48. Dragon. Talete srl. Via V. Pisani 13, 20124 Milano, Italy http://www.talete.mi.it/main_exp.htm
49. Gasteiger J Rudolph C Sadowski J Automatic generation of 3D-atomic coordinates for organic molecules Tetrahedron Comp Method 1990, 3:537-547.
50. SIMCA-P+ 10.5 http://www.umetrics.com
51. Eriksson L Johansson E Kettaneh-Wold N Trygg J Wikström C Wold S PCA Multi- and megavariate data analysis Umeå: Umetrics 2006:39-61.
52. TOPCAT http://www.star.bris.ac.uk/~mbt/topcat/
53. PyMOL home page http://pymol.sourceforge.net/
54. Smith TF Waterman MS Identification of common molecular subsequences J Mol Biol 1981, 147(1):195-197. 7265238
55. Guha R Howard MT Hutchison GR Murray-Rust P Rzepa H Steinbeck C Wegner J Willighagen EL The Blue Obelisk-interoperability in chemical informatics J Chem Inf Model 2006, 46(3):991-998. 16711717