Computational modelling of inhibitor binding to human thrombin

European Journal of Pharmaceutical Sciences

Volumn 12, Issue 4, 2001, Pages 441-446

  Ljungberg, Kajsa B ^a   Marelius, John ^a   Musil, Djordje ^b   Svensson, Peder ^b   Norden, Bo ^b   Åqvist, Johan ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b ASTRAZENECA R AND D   (Sweden)

Author keywords

Binding free energy; Computer aided ligand design; Molecular dynamics; Serine proteases; Thrombin

Indexed keywords

THROMBIN; THROMBIN INHIBITOR;

ARTICLE; BINDING AFFINITY; BINDING SITE; CALCULATION; COMPUTER ANALYSIS; ENERGY; ENZYME SUBSTRATE COMPLEX; MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING;

ANTITHROMBINS; HUMANS; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; STEREOISOMERISM; STRUCTURE-ACTIVITY RELATIONSHIP; THROMBIN;

EID: 0035105526     PISSN: 09280987     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0928-0987(00)00185-8     Document Type: Article

References (22)

1. On the coagulation of platelet-rich plasma - physiological mechanism and pharmacological consequences
2. An overview of hemostasis
3. An approximate but efficient method to calculate free energy trends by computer simulation: application to dihydrofolate reductase-inhibitor complexes
4. Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations
5. Ligand binding affinity prediction by linear interaction energy methods
6. Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method
7. Free energy calculations: applications to chemical and biochemical phenomena
8. Estimation of the binding affinities of FKBP12 inhibitors using a linear response method
9. A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
10. Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases
11. Q: An MD program for free energy calculations and empirical valence bond simulations in biomolecular systems
12. Evolution of proteolytic enzymes
13. Receptor-based prediction of binding affinities
14. Structures of thrombin complexes with a designed and a natural exosite peptide inhibitor
15. The application of three approximate free energy calculation methods to structure based ligand design: trypsin and its complex with inhibitors
16. Cold adaption of enzymes - structural comparison between salmon and bovine trypsins
17. Scoring functions: a view from the bench
18. What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?
19. Ranking ligand binding affinities with avidin: a molecular dynamics-based interaction energy study
20. A new method for predicting binding affinity in computer-aided drug design
21. Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions