Crossref journal-article
Elsevier BV
Journal of Molecular Biology (78)
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Gray, J. J., Moughon, S., Wang, C., Schueler-Furman, O., Kuhlman, B., Rohl, C. A., & Baker, D. (2003). Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations. Journal of Molecular Biology, 331(1), 281–299.

Authors 7
  1. Jeffrey J. Gray (first)
  2. Stewart Moughon (additional)
  3. Chu Wang (additional)
  4. Ora Schueler-Furman (additional)
  5. Brian Kuhlman (additional)
  6. Carol A. Rohl (additional)
  7. David Baker (additional)
References 60 Referenced 993
  1. 10.1016/S0959-440X(02)00285-3 / Curr. Opin. Struct. Biol. / Prediction of protein–protein interactions by docking methods by Smith (2002)
  2. 10.1016/S0959-440X(02)00286-5 / Curr. Opin. Struct. Biol. / Protein–protein association kinetics and protein docking by Camacho (2002)
  3. 10.1002/prot.10115 / Proteins: Struct. Funct. Genet. / Principles of docking: an overview of search algorithms and a guide to scoring functions by Halperin (2002)
  4. 10.1016/0022-2836(91)80222-G / J. Mol. Biol. / Protein docking and complementarity by Shoichet (1991)
  5. 10.1073/pnas.89.6.2195 / Proc. Natl Acad. Sci. USA / Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques by Katchalski-Katzir (1992)
  6. 10.1006/jmbi.1997.1203 / J. Mol. Biol. / Modelling protein docking using shape complementarity, electrostatics and biochemical information by Gabb (1997)
  7. 10.1002/1097-0134(20000815)40:3<525::AID-PROT190>3.0.CO;2-F / Proteins: Struct. Funct. Genet. / Scoring docked conformations generated by rigid-body protein–protein docking by Camacho (2000)
  8. 10.1002/(SICI)1097-0134(20000601)39:4<372::AID-PROT100>3.0.CO;2-Q / Proteins: Struct. Funct. Genet. / BiGGER: a new (soft) docking algorithm for predicting protein interactions by Palma (2000)
  9. 10.1093/protein/14.2.105 / Protein Eng. / Protein docking using continuum electrostatics and geometric fit by Mandell (2001)
  10. 10.1110/ps.12901 / Protein Sci. / Electrostatic contributions to protein–protein interactions: fast energetic filters for docking and their physical basis by Norel (2001)
  11. 10.1110/ps.26002 / Protein Sci. / Electrostatics in protein–protein docking by Heifetz (2002)
  12. 10.1073/pnas.96.15.8477 / Proc. Natl Acad. Sci. USA / A systematic study of low-resolution recognition in protein–protein complexes by Vakser (1999)
  13. 10.1093/protein/15.4.257 / Protein Eng. / SOFTDOCK: understanding of molecular recognition through a systematic docking study by Jiang (2002)
  14. 10.1002/prot.10092 / Proteins: Struct. Funct. Genet. / Docking unbound proteins using shape complementarity, desolvation, and electrostatics by Chen (2002)
  15. 10.1006/jmbi.1997.1519 / J. Mol. Biol. / Rapid refinement of protein interfaces incorporating solvation: application to the docking problem by Jackson (1998)
  16. 10.1110/ps.2830102 / Protein Sci. / Protein–protein docking with multiple residue conformations and residue substitutions by Lorber (2002)
  17. 10.1110/ps.19202 / Protein Sci. / Soft protein–protein docking in internal coordinates by Fernandez-Recio (2002)
  18. 10.1002/prot.10054 / Proteins: Struct. Funct. Genet. / Critical assessment of methods of protein structure prediction (CASP): round IV by Moult (2001)
  19. 10.1002/prot.1170 / Proteins: Struct. Funct. Genet. / Rosetta in CASP4: progress in ab initio protein structure prediction by Bonneau (2001)
  20. 10.1006/jmbi.1997.0959 / J. Mol. Biol. / Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions by Simons (1997)
  21. 10.1002/(SICI)1097-0134(19990101)34:1<82::AID-PROT7>3.0.CO;2-A / Proteins: Struct. Funct. Genet. / Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins by Simons (1999)
  22. Tsai, J., Bonneau, R., Morozov, A.V., Kuhlman, B., Rohl, C.A., & Baker, D. (2003). An improved protein decoy set for testing energy functions for protein structure prediction. Proteins: Struct. Funct. Genet..
  23. 10.1093/nar/28.1.235 / Nucl. Acids. Res. / The Protein Data Bank by Berman (2000)
  24. 10.1002/prot.10381 / Proteins: Struct. Funct. Genet. / CAPRI: a critical assessment of predicted interactions by Janin (2003)
  25. 10.1002/prot.10393 / Proteins: Struct. Funct. Genet. / Assessment of blind predictions of protein–protein interactions: current status of docking methods by Méndez (2003)
  26. 10.1002/prot.10384 / Proteins: Struct. Funct. Genet. / Protein–protein docking predictions for the CAPRI experiment by Gray (2003)
  27. 10.1073/pnas.97.19.10383 / Proc. Natl Acad. Sci. USA / Native protein sequences are close to optimal for their structures by Kuhlman (2000)
  28. 10.1002/pro.5560060807 / Protein Sci. / Bayesian statistical analysis of protein side-chain rotamer preferences by Dunbrack (1997)
  29. {'year': '1992', 'series-title': 'Numerical Recipes in FORTRAN: The Art of Scientific Computing', 'author': 'Press', 'key': '10.1016/S0022-2836(03)00670-3_BIB29'} / Numerical Recipes in FORTRAN: The Art of Scientific Computing by Press (1992)
  30. {'year': '1989', 'series-title': 'Computer Simulation of Liquids', 'author': 'Allen', 'key': '10.1016/S0022-2836(03)00670-3_BIB30'} / Computer Simulation of Liquids by Allen (1989)
  31. 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO;2-N / Proteins: Struct. Funct. Genet. / Effective energy function for proteins in solution by Lazaridis (1999)
  32. 10.1016/S0022-2836(03)00021-4 / J. Mol. Biol. / An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein–protein complexes by Kortemme (2003)
  33. 10.1002/prot.340200307 / Proteins: Struct. Funct. Genet. / Polar and nonpolar atomic environments in the protein core: implications for folding and binding by Koehl (1994)
  34. 10.1080/10618600.1996.10474713 / J. Comput. Graph. Stat. / R: a language for data analysis and graphics by Ihaka (1996)
  35. 10.1002/prot.10390 / Proteins: Struct. Funct. Genet. / A protein–protein docking benchmark by Chen (2003)
  36. 10.1073/pnas.181147798 / Proc. Natl Acad. Sci. USA / Protein docking along smooth association pathways by Camacho (2001)
  37. 10.1002/(SICI)1097-0134(19990515)35:3<364::AID-PROT11>3.0.CO;2-4 / Proteins: Struct. Funct. Genet. / Use of pair potentials across protein interfaces in screening predicted docked complexes by Moont (1999)
  38. 10.1002/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H / Proteins: Struct. Funct. Genet. / Residue frequencies and pairing preferences at protein–protein interfaces by Glaser (2001)
  39. 10.1016/S0022-2836(02)01038-0 / J. Mol. Biol. / Co-evolutionary analysis reveals insights into protein–protein interactions by Goh (2002)
  40. 10.1073/pnas.061411798 / Proc. Natl Acad. Sci. USA / Identification of protein oligomerization states by analysis of interface conservation by Elcock (2001)
  41. 10.1063/1.472061 / J. Chem. Phys. / Simulation of activation free energies in molecular systems by Neria (1996)
  42. 10.1002/jcc.540140309 / J. Comput. Chem. / Rapid approximation to molecular-surface area via the use of boolean logic and look-up tables by Legrand (1993)
  43. 10.1038/319199a0 / Nature / Solvation energy in protein folding and binding by Eisenberg (1986)
  44. 10.1073/pnas.202485799 / Proc. Natl Acad. Sci. USA / A simple physical model for binding energy hot spots in protein–protein complexes by Kortemme (2002)
  45. 10.3109/14756368809040723 / J. Enzyme Inhib. / Binding of the recombinant proteinase inhibitor eglin c from leech Hirudo medicinalis to human leukocyte elastase, bovine alpha-chymotrypsin and subtilisin Carlsberg: thermodynamic study by Ascenzi (1988)
  46. 10.1021/cr960387h / Chem. Rev. / Protein–protein interactions: interface structure, binding thermodynamics, and mutational analysis by Stites (1997)
  47. 10.1074/jbc.270.34.19694 / J. Biol. Chem. / Fasciculin 2 binds to the peripheral site on acetylcholinesterase and inhibits substrate hydrolysis by slowing a step involving proton transfer during enzyme acylation by Eastman (1995)
  48. 10.1016/0022-2836(87)90463-3 / J. Mol. Biol. / Binding of the bovine pancreatic secretory trypsin inhibitor (Kazal) to bovine serine (pro)enzymes by Menegatti (1987)
  49. 10.1016/S0021-9258(18)53178-1 / J. Biol. Chem. / Bovine stefin C, a new member of the stefin family by Turk (1993)
  50. 10.1006/jmbi.1995.0591 / J. Mol. Biol. / Thermodynamic investigation of hirudin binding to the slow and fast forms of thrombin: evidence for folding transitions in the inhibitor and protease coupled to binding by Ayala (1995)
  51. 10.1006/jmbi.1997.1512 / J. Mol. Biol. / The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF.G9 complex by Huang (1998)
  52. 10.1038/341544a0 / Nature / Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli by Ward (1989)
  53. 10.1002/j.1460-2075.1995.tb00183.x / EMBO J. / A single amino acid in the SH3 domain of Hck determines its high affinity and specificity in binding to HIV-1 Nef protein by Lee (1995)
  54. 10.1016/0005-2728(93)90028-E / Biochim. Biophys. Acta / Binding constants for a physiologic electron-transfer protein complex between methylamine dehydrogenase and amicyanin. Effects of ionic strength and bound copper on binding by Davidson (1993)
  55. 10.1111/j.1432-1033.1980.tb04437.x / Eur. J. Biochem. / The interaction of bovine pancreatic deoxyribonuclease I and skeletal muscle actin by Mannherz (1980)
  56. 10.1021/bi971634u / Biochemistry / Cation-promoted association of Escherichia coli phosphocarrier protein IIAGlc with regulatory target protein glycerol kinase: substitutions of a Zinc(II) ligand and implications for inducer exclusion by Pettigrew (1998)
  57. 10.1016/S0021-9258(18)67515-5 / J. Biol. Chem. / A physicochemical study of protein G, a molecule with unique immunoglobulin G-binding properties by Akerstrom (1986)
  58. 10.1021/bi962349y / Biochemistry / Interactions of cyclins with cyclin-dependent kinases: a common interactive mechanism by Heitz (1997)
  59. 10.1016/S0021-9258(18)88952-9 / J. Biol. Chem. / Kinetics and thermodynamics of the interaction of elongation factor Tu with elongation factor Ts, guanine nucleotides, and aminoacyl-tRNA by Romero (1985)
  60. 10.1677/jme.0.0230347 / J. Mol. Endocrinol. / Analysis of binding properties between 20kDa human growth hormone (hGH) and hGH receptor (hGHR): the binding affinity for hGHR extracellular domain and mode of receptor dimerization by Uchida (1999)
Dates
Type When
Created 22 years, 1 month ago (July 22, 2003, 6:14 p.m.)
Deposited 8 months, 2 weeks ago (Dec. 13, 2024, 2:37 a.m.)
Indexed 3 days, 8 hours ago (Aug. 29, 2025, 5:45 a.m.)
Issued 22 years, 1 month ago (Aug. 1, 2003)
Published 22 years, 1 month ago (Aug. 1, 2003)
Published Print 22 years, 1 month ago (Aug. 1, 2003)
Funders 0

None

@article{Gray_2003, title={Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations}, volume={331}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/s0022-2836(03)00670-3}, DOI={10.1016/s0022-2836(03)00670-3}, number={1}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Gray, Jeffrey J. and Moughon, Stewart and Wang, Chu and Schueler-Furman, Ora and Kuhlman, Brian and Rohl, Carol A. and Baker, David}, year={2003}, month=aug, pages={281–299} }