Complexity and simplicity of ligand-macromolecule interactions: The energy landscape perspective

Current Opinion in Structural Biology

Volumn 12, Issue 2, 2002, Pages 197-203

  Verkhivker, Gennady M ^a   Bouzida, Djamal ^a   Gehlhaar, Daniel K ^a   Rejto, Paul A ^a   Freer, Stephan T ^a   Rose, Peter W ^a  

^a AGOURON PHARMACEUTICALS INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

BINDING AFFINITY; BINDING SITE; CALCULATION; COMPLEX FORMATION; COMPUTER SIMULATION; LIGAND BINDING; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW;

EID: 0036535906     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(02)00310-X     Document Type: Review

References (79)

1. Theory of biomolecular recognition
2. Noncovalent interactions: A challenge for experiment and theory
3. Recent advances in structure-based rational drug design
4. Hydrogen bonding, hydrophobic interactions, and failure of the rigid receptor hypothesis
5. Intrinsically unstructured proteins: Reassessing the protein structure-function paradigm
6. Accommodating protein flexibility in computational drug design
7. The energy landscape in non-biological and biological molecules
8. The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios
9. Protein folding theory: From lattice to all-atom models
10. Unraveling principles of lead discovery: From unfrustrated energy landscapes to novel molecular anchors
11. Protein folding via binding and vice versa
12. Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions
13. Development and validation of a genetic algorithm for flexible docking
14. Evaluation of the FLEXx incremental construction algorithm for protein-ligand docking
15. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
16. Scoring functions: A view from the bench
17. Rapid empirical scoring functions in virtual screening applications
18. High-throughput docking for lead generation
19. Statistical potentials and scoring functions applied to protein-ligand binding
20. The 'dynamics' in the thermodynamics of binding
21. Conservation of polar residues as hot spots at protein interfaces
22. Protein functional epitopes: Hot spots, dynamics and combinatorial libraries
23. Structural stability of binding sites: Consequences for binding affinity and allosteric effects
24. Proteins with similar architecture exhibit similar large-scale dynamic behavior
25. Point mutations and sequence variability in proteins: Redistributions of preexisting populations
26. Convergent solutions to binding at a protein-protein interface
27. Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase
28. Folding funnels, binding funnels and protein function
29. Folding and binding cascades: Shifts in energy landscapes
30. Folding and binding cascades: Dynamic landscapes and population shifts
31. Protein-protein recognition: Exploring the energy funnels near the binding sites
32. A systematic study of low-resolution recognition in protein-protein complexes
33. How common is the funnel-like energy landscape in protein-protein interactions?
34. Free energy landscapes of encounter complexes in protein-protein association
35. Protein docking along smooth association pathways
36. Navigating ligand-protein binding free energy landscapes: Universality and diversity of protein folding and molecular recognition mechanisms
37. Speeding molecular recognition by using the folding funnel: The fly-casting mechanism
38. Monte Carlo simulations of ligand-protein binding energy landscapes with the weighted histogram analysis method
39. A mean field model of ligand-protein interactions; implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding
40. Structural consensus in ligand-protein docking identifies recognition peptide motifs that bind streptavidin
41. Examining ligand-protein interactions with binding energy landscapes
42. Discovering high-affinity ligands for proteins: SAR by NMR
43. Site-directed ligand discovery
44. Structure-based library design: Molecular modeling merges with combinatorial chemistry
45. A general and fast scoring function for protein-ligand interactions: A simplified potential approach
46. Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors
47. Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein
48. Knowledge-based scoring function to predict protein-ligand interactions
49. BLEEP-potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data
50. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
51. Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
52. Deciphering common failures in molecular docking of ligand-protein complexes
53. Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes. Structural analysis of the peptide complexes with SH2 domains
54. Hierarchy of simulation models in predicting structure and energetics of the Src SH2 domain binding to the tyrosyl phosphopeptides
55. Clustering of low-energy conformations near native structures of small proteins
56. Ab initio protein structure prediction: Progress and prospects
57. Similarity-driven flexible ligand docking
58. Exhaustive docking of molecular fragments with electrostatic solvation
59. Efficient electrostatic solvation model for protein-fragment docking
60. Ligand solvation in molecular docking
61. Inclusion of solvation in ligand binding free energy calculations using the generalized-Born model
62. A hierarchical method for generating low-energy conformers of a protein-ligand complex
63. Two-stage method for protein-ligand docking
64. Flexible ligand docking: A multistep strategy approach
65. FlexE: Efficient molecular docking considering protein structure variations
66. Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking
67. Predicting and harnessing protein flexibility in the design of species-specific inhibitors of thymidylate synthase(1,2)
68. Docking ligands onto binding site representations derived from proteins built by homology modeling
69. Monte Carlo simulations of HIV-1 protease binding dynamics and thermodynamics with ensembles of protein conformations: Incorporating protein flexibility in deciphering mechanisms of molecular recognition
70. Parallel simulated tempering dynamics of ligand-protein binding with ensembles of protein conformations
71. Rational discovery of novel nuclear hormone receptor antagonists
72. Efficacy and selectivity in flexible database docking
73. Design, docking, and evaluation of multiple libraries against multiple targets
74. Docking molecules by families to increase the diversity of hits in database screens: Computational strategy and experimental evaluation
75. Discovering high-affinity ligands from the computationally predicted structures and affinities of small molecules bound to a target: A virtual screening approach
76. Protein-based virtual screening of chemical databases. 1. Evaluations of different docking/scoring combinations
77. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
78. Detailed analysis of scoring functions for virtual screening
79. Protein structure prediction and structural genomics