Predicting Protein Interactions by Brownian Dynamics Simulations.
We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations...
| Publicado en: | Journal of Biomedicine & Biotechnology Vol. 2012; pp. 1 - 12 |
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| Autores principales: | , , , , |
| Formato: | algorithm pictorial research tables/charts Journal Article |
| Publicado: |
Wiley-Blackwell
2012
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=ccm&AN=104298181&site=ehost-live header: @attributes: shortDbName: ccm uiTerm: 104298181 longDbName: CINAHL Complete uiTag: AN controlInfo: bkinfo: dissinfo: jinfo: jid: 11107243 137K jtl: Journal of Biomedicine & Biotechnology issn: 11107243 maglogo: N pubinfo: dt: 2012 vid: 2012 pid: 480 pub: Wiley-Blackwell place: Malden, Massachusetts artinfo: ui: 104298181 104298181 2011907103 NLM22500075 PMC3303761 104298181 ppf: 1 ppct: 11 formats: fmt: @attributes: type: P tig: atl: Predicting Protein Interactions by Brownian Dynamics Simulations. aug: au: Xuan-Yu Meng Yu Xu Hong-Xing Zhang Mezei, Mihaly Meng Cui affil: Department of Physiology and Biophysics, Virginia Commonwealth University, 1220 East Broad Street, P.O. Box 980551, Richmond, VA 23298, USA; State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China sug: subj: Computer Simulation Methods Metabolism Evaluation Biochemical Phenomena Evaluation Molecular Probe Techniques Methods Proteins Physiology Algorithms Physics Electricity Models, Statistical Data Analysis Software Descriptive Statistics Cluster Analysis Funding Source ab: We present a newly adapted Brownian-Dynamics (BD)-based protein docking method for predicting native protein complexes. The approach includes global BD conformational sampling, compact complex selection, and local energy minimization. In order to reduce the computational costs for energy evaluations, a shell-based grid force field was developed to represent the receptor protein and solvation effects. The performance of this BD protein docking approach has been evaluated on a test set of 24 crystal protein complexes. Reproduction of experimental structures in the test set indicates the adequate conformational sampling and accurate scoring of this BD protein docking approach. Furthermore, we have developed an approach to account for the flexibility of proteins, which has been successfully applied to reproduce the experimental complex structure from the structure of two unbounded proteins. These results indicate that this adapted BD protein docking approach can be useful for the prediction of protein-protein interactions. pubtype: Academic Journal doctype: algorithm pictorial research tables/charts Journal Article ougenre: Article language: English refInfo: holdings: @attributes: islocal: N |
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