Scoring docked conformations generated by rigid-body protein-protein docking

Proteins: Structure, Function and Genetics

Volumn 40, Issue 3, 2000, Pages 525-537

  Camacho, Carlos J ^a   Gatchell, David W ^a   Kimura, S Roy ^a   Vajda, Sandor ^a  

^a Boston University   (United States)

Author keywords

Energy minimization; Fast Fourier transform; Free energy function; Implicit solvation; Protein modeling

Indexed keywords

DOCKING PROTEIN;

ALGORITHM; ARTICLE; CONFORMATIONAL TRANSITION; ENTHALPY; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; SOLVATION;

ALGORITHMS; APROTININ; ELECTROSTATICS; ENDOPEPTIDASES; FOURIER ANALYSIS; PROTEASE INHIBITORS; PROTEIN BINDING; PROTEIN CONFORMATION; SUPPORT, U.S. GOV'T, NON-P.H.S.; THERMODYNAMICS; TRYPSIN;

EID: 0034663658     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20000815)40:3<525::AID-PROT190>3.0.CO;2-F     Document Type: Article

References (56)

1. Predictive docking of protein-protein and protein-DNA complexes
2. Evaluation of the CASP2 docking section
3. Grid-search molecular accessible surface algorithm for solving the protein docking problem
4. PUZZLE: A new method for automated protein docking based on surface shape complementarity
5. Soft docking: Matching of molecular surface cubes
6. A geometry-based suite of molecular docking processes
7. Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
8. Simple method for locating possible ligand binding sites on protein surfaces
9. BIGGER: A new (soft) docking algorithm for predicting protein interactions
10. Hydrophobic docking: A proposed enhancement to molecular recognition techniques
11. The Fourier-Green's function and the rapid evaluation of molecular potentials
12. Surveying molecular interactions with DOT
13. Low-resolution docking: Prediction of complexes for undetermined structures
14. Protein docking combining symbolic descriptions of molecular surfaces and grid-based scoring functions
15. Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking
16. Fourier-filtered van der waals contact surfaces: Accurate ligand shapes from protein structures
17. Modeling protein docking using shape complementarity, electrostatics, and biochemical information
18. High resolution fast quantitative docking using fourier domain correlation techniques
19. Protein docking and complementarity
20. A continuum model for protein-protein interactions: Application to the docking problem
21. Prediction of complexes using empirical free energy functions
22. Docking by least-squares fitting of molecular surface patterns
23. Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
24. Use of pair potentials across protein interfaces in screening predicted docked complexes
25. Docking enzyme-inhibitor complexes using a preference-based free energy surface
26. Examination of shape complementarity in docking of unbound proteins
27. Definition of the interaction domain for cytochrome c on cytochrome c oxidase. III. Prediction of the docked complex by a complete, systematic search
28. Definition of the interaction domain for cytochrome c on cytochrome c oxidase. I. Biochemical, spectral, and kinetic characterization of surface mutants in subunit II of Rhodobacter sphaeroides cytochrome aa(3)
29. Protein-protein recognition analyzed by docking simulation
30. Rigid body docking with mutant constraints of influenza hemagglutinin with antibody HC19
31. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 Å accuracy
32. Energy functions that discriminate x-ray and near-native folds from well-constructed decoys
33. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
34. Evaluation of atomic level mean force potentials via inverse refinement of protein structures: Atomic burial position and pairwise non-bonded interactions
35. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent
36. Effect of conformational flexibility and solvation on receptor-ligand binding free energies
37. Determination of atomic desolvation energies from the structures of crystalized proteins
38. Peptide docking using dynamic programming
39. Empirical free energy as a target function in docking and design: Application to hiv-1 protease inhibitors
40. Entropy in protein folding and in protein-protein interactions
41. Empirical potentials and functions for protein folding and binding
42. On the attribution of binding energy in the antigen-antibody complexes McPC 603, D1.3 and HyHEL-5
43. Calculation of the free energy of association for protein complexes
44. Solvent accessibility as a predictive tool for the free energy of inhibitor binding to the HIV-1 protease
45. Computational methods to predict binding free energy in ligand-receptor complexes
46. A new class of models for computing receptor-ligand binding affinities
47. Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity
48. A preference-based free energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
49. Charmm: A program for macromolecular energy, minimization, and dynamics calculations
50. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
51. Affinity and specificity of serine endopeptidase-protein inhibitor interactions
52. Protein folding and association-insights from the interracial and thermodynamic properties of hydrocarbons
53. Free energy landscapes of encounter complexes in protein-protein association
54. Selecting near-native conformations in homology modeling: The role of molecular mechanics and solvation terms
55. A systematic study of low-resolution recognition in protein-protein complexes