AMMOS software: Method and application

Methods in Molecular Biology

Volumn 819, Issue , 2012, Pages 127-141

  Pencheva, T ^a   Lagorce, D ^b   Pajeva, I ^a   Villoutreix, B O ^b   Miteva, M A ^b  

^a INSTITUTE OF BIOPHYSICS AND BIOMEDICAL ENGINEERING   (Bulgaria)

^b UNIVERSITÉ PARIS DESCARTES   (France)

Author keywords

3D structure generation; AMMOS; AMMP; Open source free software; Structure refinement; Virtual screening

Indexed keywords

PROTEIN;

ARTICLE; AUTOMATION; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; DRUG SCREENING; METHODOLOGY;

AUTOMATION; COMPUTATIONAL BIOLOGY; DRUG EVALUATION, PRECLINICAL; MOLECULAR CONFORMATION; PROTEINS; SOFTWARE;

EID: 84855927725     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-465-0_9     Document Type: Article

References (47)

1. Shoichet BK (2004) Virtual screening of chemical libraries. Nature 432:862-86.
2. Villoutreix BO, Bastard K, et al (2008) In silicoin vitro screening of protein-protein interactions: towards the next generation of therapeutics. Curr Pharm Biotechnol 9:103-12.
3. Clark D (2008) What has virtual screening ever done for drug discovery? Expert Opin Drug Discov 3:841-85.
4. Vistoli G, Pedretti A and Testa B (2008) Assessing drug-likeness-what are we missing? Drug Discov Today 13:285-29.
5. Lagorce D, Sperandio O, et al (2008) FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects. BMC Bioinformatics 9:396
6. Downs GM and Willett P (1995) Similarity searching in databases of chemical structures In Reviews in Computational Chemistry (Lipkowitz KB, and Boyd DB, Eds.), pp 67-117, VCH Publishers NY
7. [http://www.eyesopen.com] ROCS software
8. Sperandio O, Andrieu O, et al (2007) MED-SuMoLig: A New Ligand-Based Screening Tool for Efficient Scaffold Hopping. J Chem Inf Model 47:1097-111.
9. Schwab CH (2010) Conformations and 3D pharmacophore searching. Drug Discovery Today: Technologies 7:e245-53.
10. Kuntz ID (1992) Structure-based strategies for drug design and discovery. Science 257:1078-108.
11. Leach AR, Shoichet BK and Peishoff CE (2006) Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J Med Chem 49:5851-585.
12. Bottegoni G, Kufareva I, et al (2009) Fourdimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. J Med Chem 52:397-40.
13. Sperandio O, Villoutreix BO and Miteva MA (2010) Structure-Based Virtual Screening, In In silico lead discovery (Miteva MA, Ed.), Bentham Science Publishers
14. Pencheva T, Soumana OS, et al (2010) Post-docking virtual screening of diverse binding pockets: comparative study using DOCK, AMMOS, X-Score and FRED scoring functions. Eur J Med Chem 45:2622-262.
15. Bologa CG, Olah MM and Oprea TI (2006) Chemical database preparation for compound acquisition or virtual screening. Methods Mol Biol 316:375-38.
16. Lagorce D, Sperandio O, et al (2010) Chemical libraries for virtual screening, In In silico lead discovery (Miteva MA, Ed.), Bentham Science Publishers
17. Huang N, Kalyanaraman C, et al (2006) Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys 8:5166-517.
18. Pencheva T, Lagorce D, et al (2008) AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening. BMC Bioinformatics 9:438
19. Lagorce D, Pencheva T, et al (2009) DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening. BMC Chem Biol 9:6
20. Weber IT and Harrison RW (1997) Molecular mechanics calculations on Rous sarcoma virus protease with peptide substrates. Protein Sci 6:2365-237.
21. Crippen GM and Havel TF (1988) Distance geometry and molecular conformations, Wiley, New York
22. Rappé AK, Casewit CJ, et al (1992) UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J Am Chem Soc 114: 10024-1003.
23. Bagossi P, Zahuczky G, et al (1999) Improved parameters for generating partial charges: correlation with observed dipole moments. J Mol Model 5:143-15.
24. Berman HM, Westbrook J, et al (2000) The Protein Data Bank. Nucleic Acids Res 28:235-24.
25. Sauton N, Lagorce D, et al (2008) MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. BMC Bioinformatics 9:184
26. Moustakas DT, Lang PT, et al (2006) Development and validation of a modular, extensible docking program: DOCK 5. J Comput Aided Mol Des 20:601-61.
27. Lagorce D, Villoutreix BO and Miteva MA (2011) Three-dimensional structure generators of drug-like compounds: DG-AMMOS, an open-source package. Expert Opinion on Drug Discovery 6:339-51
28. Miteva MA, Guyon F and Tuffery P (2010) Frog2: Efficient 3D conformation ensemble generator for small compounds. Nucleic Acids Res 38 Suppl:W622-62.
29. Leite TB, Gomes D, et al (2007) Frog: a FRee Online druG 3D conformation generator. Nucleic Acids Res 35:W568-57.
30. Vainio MJ and Johnson MS (2007) Generating conformer ensembles using a multiobjective genetic algorithm. J Chem Inf Model 47:2462-247.
31. Watts KS, Dalal P, et al (2010) ConfGen: a conformational search method for efficient generation of bioactive conformers. J Chem Inf Model 50:534-54.
32. Sperandio O, Souaille M, et al (2009) MED-3DMC: a new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space. Eur J Med Chem 44: 1405-140.
33. Verma J, Khedkar VM and Coutinho EC (2010) 3D-QSAR in drug design-a review. Curr Top Med Chem 10:95-11.
34. Renner S and Schneider G (2006) Scaffoldhopping potential of ligand-based similarity concepts. ChemMedChem 1:181-18.
35. Osterberg F, Morris GM, et al (2002) Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in Auto-Dock. Proteins 46:34-4.
36. Trott O and Olson AJ (2010) AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455-46.
37. Verdonk ML, Chessari G, et al (2005) Modeling water molecules in protein-ligand docking using GOLD. J Med Chem 48: 6504-651.
38. Venkatachalam CM, Jiang X, et al (2003) LigandFit: a novel method for the shapedirected rapid docking of ligands to protein active sites. J Mol Graph Model 21:289-30.
39. Montes M, Miteva MA and Villoutreix BO (2007) Structure-based virtual ligand screening with LigandFit: pose prediction and enrichment of compound collections. Proteins 68:712-72.
40. Cavasotto CN and Abagyan RA (2004) Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol 337:209-22.
41. Amaro RE, Minh DD, et al (2007) Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design. J Am Chem Soc 129:7764-776.
42. Miteva MA, Robert CH, et al (2010) Receptor flexibility in ligand docking and virtual screening, In In silico lead discovery (Miteva MA, Ed.), Bentham Science Publishers
43. Cavasotto CN, Kovacs JA and Abagyan RA (2005) Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 127:9632-964.
44. Sperandio O, Mouawad L, et al (2010) How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur Biophys J 39:1365-137.
45. Segers K, Sperandio O, et al (2007) Design of protein-membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V. Proc Natl Acad Sci USA 104:12697-1270.
46. Montes M, Braud E, et al (2008) Receptorbased virtual ligand screening for the identification of novel CDC25 phosphatase inhibitors. J Chem Inf Model 48:157-16.
47. Wells JA and McClendon CL (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450:1001-100.