Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir |
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Authors: | Tie Yunfeng Kovalevsky Andrey Y Boross Peter Wang Yuan-Fang Ghosh Arun K Tozser Jozsef Harrison Robert W Weber Irene T |
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Institution: | Program on Bioinformatics and Computational Biology, Iowa State University, Ames, Iowa 50011, USA. |
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Abstract: | Due to the limited distance data available from the experiments, the structures determined by NMR Spectroscopy may not always be as accurate as desired. Further refinement of the structures is often required and sometimes critical. With the increase of high quality protein structures determined and deposited in PDB Data Bank, commonly shared protein conformational properties can be extracted based on the statistical distributions of the properties in the structural database and used to improve the outcomes of the NMR-determined structures. Here we examine the distributions of protein interatomic distances in known protein structures. We show that based on these distributions, a set of mean-force potentials can be defined for proteins and employed to refine the NMR-determined structures. We report the test results on 70 NMR-determined structures and compare the potential energy, the Ramachandran plot, and the ensemble RMSD of the structures refined with and without using the derived mean-force potentials. |
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Keywords: | AIDS protease inhibitor darunavir drug resistance |
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