Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.4.23.16 (HIV-1 protease)
 2,107 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A generalized numerical treatment of rapid-equilibrium enzyme kinetics is presented. This new approach relies on automatic computer derivation of the underlying mathematical model (a system of simultaneous nonlinear algebraic equations) from a symbolic representation of the reaction mechanism (a system of biochemical equations) provided by the researcher. The method allows experimental biochemists to analyze initial-rate enzyme kinetic data without having to use any mathematical equations. An illustrative example is based on the inhibition kinetics of 17beta-hydroxysteroid dehydrogenase type 5 by a class of natural compounds. A computer implementation of the new method, a newly modified software package DYNAFIT [Kuzmic, P., 1996. Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase. Anal. Biochem. 237, 260-273], is freely available to all academic researchers.
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PMID:A generalized numerical approach to rapid-equilibrium enzyme kinetics: application to 17beta-HSD. 1636 83

A deriving pharmacophore model from the three-dimensional structure of a target protein provides helpful information for analyzing protein-ligand interactions and further improvement of ligand binding affinity. A standalone program, Pocket v.2, has been developed based on the original Pocket module in the de novo drug design program LigBuilder. Pocket v.2 is able to derive a pharmacophore model directly from a given protein-ligand complex structure without human intervention. Key features in the pharmacophore model are automatically reduced to a reasonable number. Pocket v.2 has been applied to several case studies, including cyclin dependent kinase 2, HIV-1 protease, estrogen receptor, and 17beta-hydroxysteroid dehydrogenase. It well reproduced previously published pharmacophore models in all of these cases. One notable feature of Pocket v.2 is that it can tolerate minor conformational changes on the protein side upon binding of different ligands to give a consistent pharmacophore model. For different proteins accommodating the same ligand, Pocket v.2 gives similar pharmacophore models, which opens the possibility to classify proteins with their binding features.
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PMID:Pocket v.2: further developments on receptor-based pharmacophore modeling. 1712 8