ATTRACT: Protein-protein docking in CAPRI using a reduced protein model

Proteins: Structure, Function and Genetics

Volumn 60, Issue 2, 2005, Pages 252-256

  Zacharias, Martin ^a  

^a JACOBS UNIVERSITY BREMEN   (Germany)

Author keywords

Biomolecular modeling; Docking minimization; Flexible docking; Mean field optimization; Protein protein interaction

Indexed keywords

AMINO ACID;

ATOM; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; ENERGY; EXPERIMENT; MOLECULAR DYNAMICS; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

ALGORITHMS; ANIMALS; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; DIMERIZATION; HUMANS; INTERNET; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; MUTATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 21644435306     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20566     Document Type: Conference Paper

References (18)

1. Janin J. Welcome to CAPRI; a critical assessment of predicted interactions. Proteins 2002;47:257.
2. Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003;12: 1271-1282.
3. Koehl P, Delarue M. Mean-field minimization methods for biological macromolecules. Curr Opin Struct Biol 1996;6:222-226.
4. Stetefeld J, Mayer U, Timpl R, Huber R. Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin y1 chain harboring the nidogen binding site. J Mol Biol 1996;257:644-657.
5. Poschl E, Mayer U, Stetefeld J, Baumgartner R, Holak TA, Huber R, Timpl R. Site-directed mutagenesis and structural interpretation of the nidogen binding site of laminin y1 chain. EMBO J 1996;15:5154-5159.
6. Takagi J, Yang Y, Liu J, Wang J, Springer TA. Complex between nidogen and laminin fragments reveals a paradigmatic b-propeller interface. Nature 2003;424:969-974.
7. Terrak M, Kerff F, Langsetmo K, Tao T, Dominguez R. Structural basis of protein phosphatase 1 regulation. Nature 2004;429:780-784.
8. Eghiaian F, Grosclaude J, Lesceu S, Debey P, Doublet B, Treguer E, Rezaei H, Knossow M. Insight into the PrPC→PrPSc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants. Proc Natl Acad Sci USA 2004;101:10254-10259.
9. von Tilbeurgh H, Le Coq D, Declerck N. Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator. EMBO J 2001;20:3789-3799.
10. Graille M, Zhou C-Z, Receveur-Bréchot V, Collinet B, Declerck N, van Tilbeurgh H. Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes. J Biol Chem 2005;280:14780-14789.
11. Goldberg J, Huang HB, Kwon YG, Greengard P, Nairn AC, Kuriyan J. The three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1. Nature 1995; 376:745-753.
12. Cohen PTW. Protein phosphatase 1-targeted in many directions. J. Cell Sci 2002;115:241-256.
13. Krengel U, Dijkstra BW. Three-dimensional structure of endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum. J Mol Biol 1996;263:70-78.
14. Sansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcours JA, Rabijns A. Structural basis for inhibition of Aspergillus niger xylanase by Triticum aestivum xylanase inhibitor-I. J Biol Chem 2004;279:36022-36028.
15. Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998;33:417-429.
16. Zacharias M, Sklenar H. Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: application to a DNA minor groove ligand complex. J Comput Chem 1999;20:287-300.
17. Zacharias M. Rapid Protein-ligand docking including soft degrees of freedom from molecular dynamics simulations to account for protein flexibility: FK506 binding to FKBP binding protein as an example. Proteins 2004;54:759-767.
18. Lopez-Garcia F, Zahn R, Riek R, Wuthrich K. NMR structure of the bovine prion protein. Proc Natl Acad Sci USA 2000;97:8334-8339.