Docking ligands onto binding site representations derived from proteins built by homology modelling

Journal of Molecular Biology

Volumn 307, Issue 1, 2001, Pages 407-427

  Schafferhans, Andrea ^a   Klebe, Gerhard ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

Docking; Drug design; Homology modelling; Ligand alignment; QSAR

Indexed keywords

LIGAND; PROTEIN; SERINE PROTEINASE; THROMBIN; THROMBIN INHIBITOR;

ACCURACY; ALGORITHM; ANALYTIC METHOD; ARTICLE; BINDING SITE; CALCULATION; CRYSTAL STRUCTURE; DRUG DESIGN; MOLECULAR MODEL; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; THEORY;

RUMEX;

EID: 0035896038     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2000.4453     Document Type: Article

References (42)

1. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
2. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
3. Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries
4. A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors
5. Practical evaluation of comparative modelling and threading methods
6. 1 receptor: Molecular modeling and site-directed mutagenesis as tools to identify agonist and antagonist recognition sites
7. 3 adenosine antagonists: Structural homology and receptor docking
8. 1 receptor
9. 2-adrenergic receptor that exploits the domain structure of G-protein-coupled receptors
10. Three-dimensional models of estrogen receptor ligand binding domain complexes, based on related crystal structures and mutational and structure-activity relationship data
11. Homology model for the ligand-binding domain of the human estrogen receptor
12. Ligand-ligand and ligand-receptor approaches to modeling the cannabinoid CB1 and CB2 receptors: Achievements and challenges
13. Pseudo-receptor modeling: A new concept for the three-dimensional construction of receptor binding sites
14. Quasi-atomistic receptor modeling. A bridge between 3D QSAR and receptor fitting
15. Structure-activity relationships of cannabinoids: A joint CoMFA and pseudoreceptor modelling study
16. Computational methods for biomolecular docking
17. Computational approaches to structure-based ligand design
18. An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap
19. Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics, thrombin and thermolysin inhibitors
20. Methodological developments and strategies for a fast flexible superposition of drug-size molecules
21. Ligsite: Automatic and efficient detection of potential small molecule-binding sites in proteins
22. The computer program LUDI: A new method for the de novo design of enzyme inhibitors
23. LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
24. An all atom force field for simulations of proteins and nucleic acids
25. Iterative partial equalization of orbital electronegativity - A rapid access to atomic charges
26. A brief review and table of semiempirical parameters used in the Hueckel molecular orbital method
27. Atomic physicochemical parameters for three-dimensional structure-directed quantitative structure-activity relationships. I. Partition coefficients as a measure of hydrophobicity
28. Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics
29. Prediction of hydrophobic (lipophilic) properties of small organic molecules using fragmental methods: An analysis of alogp and clogp methods
30. The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands
31. IsoStar: A library of information about nonbonded interactions
32. Comparative protein modelling by satisfaction of spatial restraints
33. A fast and efficient method to generate biologically relevant conformations
34. The structural alignment between two proteins: Is there a unique answer?
35. Databases for protein-ligand complexes
36. Factorising ligand affinity: A combined thermodynamic and crystallographic study of trypsin and thrombin inhibitors
37. Mapping the protein universe
38. Alignment of three-dimensional protein structures: Network server for database searching
39. Molecular recognition at the thrombin active site: Structure-based design and synthesis of potent and selective thrombin inhibitors and X-ray crystal structures of two thrombin-inhibitor complexes
40. 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