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| [[Image:2bza.gif|left|200px]] | | {{Seed}} |
| | [[Image:2bza.png|left|200px]] |
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| {{STRUCTURE_2bza| PDB=2bza | SCENE= }} | | {{STRUCTURE_2bza| PDB=2bza | SCENE= }} |
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| '''BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZYLAMINE'''
| | ===BOVINE PANCREAS BETA-TRYPSIN IN COMPLEX WITH BENZYLAMINE=== |
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| ==Overview==
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| The relative free energies of binding of trypsin to two amine inhibitors, benzamidine (BZD) and benzylamine (BZA), were calculated using non-Boltzmann thermodynamic integration (NBTI). Comparison of the simulations with the crystal structures of both complexes, trypsin-BZD and trypsin-BZA, shows that NBTI simulations better sample conformational space relative to thermodynamic integration (TI) simulations. The relative binding free energy calculated using NBTI was much closer to the experimentally determined value than that obtained using TI. The error in the TI simulation was found to be primarily due to incorrect sampling of BZA's conformation in the binding pocket. In contrast, NBTI produces a smooth mutation from BZD to BZA using a surrogate potential, resulting in a much closer agreement between the inhibitors' conformations and the omit electron density maps. This superior agreement between experiment and simulation, of both relative binding free energy differences and conformational sampling, demonstrates NBTI's usefulness for free energy calculations in macromolecular simulations. | | The line below this paragraph, {{ABSTRACT_PUBMED_10651279}}, adds the Publication Abstract to the page |
| | (as it appears on PubMed at http://www.pubmed.gov), where 10651279 is the PubMed ID number. |
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| | {{ABSTRACT_PUBMED_10651279}} |
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| ==About this Structure== | | ==About this Structure== |
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| [[Category: Shah, S S.]] | | [[Category: Shah, S S.]] |
| [[Category: Stroupe, C.]] | | [[Category: Stroupe, C.]] |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 21:00:26 2008'' | | |
| | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 04:48:13 2008'' |