Ligand-induced changes in the binding sites of proteins

Bioinformatics

Volumn 18, Issue 7, 2002, Pages 939-948

  Fradera, Xavier ^a   De La Cruz, Xavier ^a   Silva, Carlos H T P ^a   Gelpí, Jose Luis ^a   Luque, F J ^a   Orozco, Modesto ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CHYMOTRYPSIN; CYTOCHROME P450; LIGAND; LYSOZYME; PAPAIN; PROTEIN; THYMIDINE KINASE; TRYPSIN; XYLOSE ISOMERASE;

ANALYTIC METHOD; ARTICLE; BINDING SITE; CONTROLLED STUDY; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 0036323965     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.7.939     Document Type: Article

References (58)

1. Mechanistic implications and family from the structure of dethiobiotin synthetase
2. Docking small ligands in flexible binding sites
3. The protein data bank
4. A good ligand is hard to find: Automatic docking methods
5. Structure of chymotrypsin-trifluoromethyl ketone inhibitor complexes: Comparison of slowly and rapidly equilibrating inhibitors
6. An overview of structural genomics
7. Strutural genomics: Beyond the human genome project
8. Method for including the dynamic fluctuations of a protein in computer-aided drug design
9. X-ray analysis of D-xylose isomerase at 1.9 angstroms: Native enzyme in complex with substrate and with a mechanism-designed inactivator
10. Modes of binding substrates and their analogues to the enzyme D-xylose isomerase
11. Refined crystal structure of gamma-chymotrypsin at 1.9 A resolution. Comparison with other pancreatic serine proteases
12. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
13. Critical evaluation of search algorithm for flexible docking
14. New approaches to rational drug design
15. Similarity-driven flexible ligand docking
16. Use of classical molecular interaction potentials in molecular dynamics simulations of proteins
17. Calculation of the total electrostatic energy of a macromolecular system. Solvation energies, binding energies and conformational analysis
18. Calculating the electrostatic potential of molecules in solution
19. Automated docking of substrates to proteins by simulated annealing
20. Knowledge-based scoring functions to predict protein-ligand interactions
21. Molecular docking towards drug discovery
22. Evaluation of docking/scoring approaches: A comparatice study based on MMP3 inhibitors
23. Protein data bank 1bb5
24. Mechanism of an ATP-dependent carboxylase, dethiobiotin synthetase, based on studies of complexes with substrates and a intermediate
25. Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme-MgADP-ALF3-diaminopelargonic acid and enzyme-MgADP-dethiobiotin-phosphate; implications for catalysis
26. Episelection: Novel Ki ∼nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface
27. Crystal structure of papain-E64-c complex. Binding diversity of E64-c to papain S2 and S3 subsites
28. Binding affinities and non-bonded interaction energies
29. Molecular docking to ensembles of protein structures
30. Three-dimensional structure of chymotrypsin inactivated with (2S)-N-acetyl-L-alanyl-L-phenylalanyl alpha-chloroethane: Implications for the mechanism of inactivation of serine proteases by chloroketones
31. Structure-based strategies for drug design and discovery
32. Structure-based molecular design
33. SURFNET: A program for visualizing molecular surfaces, cavities and intermolecular interactions
34. MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
35. Computational methods for biomolecular docking
36. Orientational sampling and rigid-body minimization in molecular docking
37. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
38. Origin of carbohydrate recognition specificity human lysozyme revealed by affinity labeling
39. Theoretical methods for the description of the solvent effect in biomolecular systems
40. Crystal structure of substrate-free Pseudomonas putida cytochrome P450
41. Crystal structures of metyrapone- and phenylimidazole-inhibited complexes of cytochrome P450cam
42. High-resolution crystal structure of cytochrome P450cam
43. Crystal structure of the carbon monoxy-substrate-cytochrome P450/cam ternary complex
44. The structural basis for substrate-induced changes in redox potential and spin equilibrium in cytochrome P-450(cam)
45. Crystal structures of cytochrome P-450/cam complexed with camphane, thiocamphor, and adamantane: Factors controlling P-450 substrate hydroxylation
46. Formation, crystal structure, and rearrangement of a cytochrome P450cam-iron-phenyl complex
47. Inhibitor-induced conformational change in cytochrome P450cam
48. A fast flexible docking method using an incremental construction algorithm
49. Structure of dethiobiotin synthetase at 0.97 A resolution
50. X-ray crystallographic structure of a papainleupeptin complex
51. Structural genomics and its importance for gene function analysis
52. Structural changes of the active site cleft and different saccharide binding modes in lysozyme co-crystallized with hexa-n-acetylchitohexaose at pH 4.0
53. Structure and activity of two photoreversible cinnamates bound to chymotrypsin
54. Inhibition mechanism of cathepsin 1-specific inhibitors based on the crystal structure of papain-CLIK148 complex
55. Understanding the role of the essential Asp251 in cytochrome P450cam using site-directed mutagenesis, crystallography, and kinetic solvent isotope effect
56. Virtual screening an overview
57. Refined x-ray structure of papain(dot)E-64-c complex at 2.1-Angstroms resolution
58. Crystal structure of papain-succinyl-Gln-Val-Val-Ala-Ala-p-nitroanilide complex at 1.7 Angstroms resolution: Noncovalent binding mode of a common sequence of endogenous thiol protease inhibitors