Development of new hydrogen-bond descriptors and their application to comparative molecular field analyses

Journal of Medicinal Chemistry

Volumn 45, Issue 8, 2002, Pages 1585-1597

  Böhm, Markus ^a   Klebe, Gerhard ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE; CARBONYL DERIVATIVE; ENZYME INHIBITOR; HYDROGEN; THERMOLYSIN;

ANALYSIS; ARTICLE; COMPARATIVE STUDY; CRYSTALLOGRAPHY; HYDROGEN BOND; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

DATABASES, FACTUAL; HYDROGEN BONDING; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; THERMOLYSIN;

EID: 0037061650     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm011039x     Document Type: Article

References (56)

1. What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs?
2. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
3. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure
4. Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds
5. Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds
6. Functionality maps of binding sites: A multiple copy simultaneous search method
7. Multiple copy simultaneous search and construction of ligands in binding sites: Application to inhibitors of HIV-1 aspartic proteinase
8. Design of dimerization inhibitors of HIV-1 aspartic proteinase: A computer-based combinatorial approach
9. Experimental and computational mapping of the binding surface of a crystalline protein
10. Automated site-directed drug design: A general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces
11. Automated site-directed drug design: The prediction and observation of ligand point positions at hydrogen-bonding regions on protein surfaces
12. Characterising non-covalent interactions with the Cambridge Structural Database
13. Three-dimensional hydrogen-bond geometry and probability information from a crystal survey
14. An automated method for predicting the positions of hydrogen-bonding atoms in binding sites
15. A novel method for the modelling of peptide ligands to their receptors
16. X-SITE: Use of empirically derived atomic packing preferences to identify favourable interaction regions in the binding sites of proteins
17. Molecular recognition by proteins: Protein-ligand interactions from a structural perspective
18. The protein databank: A computer-based archival file for macromolecular structures
19. The protein data bank
20. Minireceptors and pseudoreceptors
21. Pseudo-receptor modeling: A new concept for the three-dimensional construction of receptor binding sites
22. Structure-activity relationships of cannabinoids: A joint CoMFA and pseudoreceptor modelling study
23. Development of a binding site model for histamine H3-receptor agonists
24. Pseudoreceptor model for ryanodine derivatives at calcium release channels
25. Docking ligands onto binding site representations derived from proteins built by homology modelling
26. Progress in predicting human ADME parameters in silico
27. Drug-like properties and the causes of poor solubility and poor permeability
28. ADME/PK as part of a rational approach to drug discovery
29. Screening for human ADME/Tox drug properties in drug discovery
30. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
31. Comparative molecular similarity indices analysis: CoMSIA
32. Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries
33. The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands
34. A fast and efficient method to generate biologically relevant conformations
35. IsoStar: A library of information about nonbonded interactions
36. SuperStar: A knowledge-based approach for identifying interaction sites in proteins
37. SuperStar: Improved knowledge-based interaction fields for protein binding sites
38. A general and fast scoring function for protein-ligand interactions: A simplified potential approach
39. Knowledge-based scoring function to predict protein-ligand interactions
40. Predicting binding modes, binding affinities and "Hot Spots" for protein-ligand complexes using a knowledge-based scoring function
41. 3D-QSAR of angiotensin-converting enzyme and thermolysin inhibitors: A comparison of CoMFA models based on deduced and experimentally determined active site geometries
42. AM1: A new general purpose quantum mechanical molecular model
43. MOPAC: A semiempirical molecular orbital program
44. Sample-distance partial least squares: PLS optimized for many variables, with application to CoMFA
45. Recommendations for CoMFA studies and 3D QSAR publications
46. Practical problems in PLS analyses
47. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
48. The Developing Practice of Comparative Molecular Field Analysis
49. CoMFA: Scope and limitations
50. Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa
51. Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation
52. Molecular similarity based on electrostatic potential and electric field