MCCE2: Improving protein pKacalculations with extensive side chain rotamer sampling
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چکیده
منابع مشابه
MCCE2: Improving protein pKa calculations with extensive side chain rotamer sampling
Multiconformation continuum electrostatics (MCCE) explores different conformational degrees of freedom in Monte Carlo calculations of protein residue and ligand pK(a)s. Explicit changes in side chain conformations throughout a titration create a position dependent, heterogeneous dielectric response giving a more accurate picture of coupled ionization and position changes. The MCCE2 methods for ...
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MOTIVATION The protein side-chain conformation problem is a central problem in proteomics with wide applications in protein structure prediction and design. Computational complexity results show that the problem is hard to solve. Yet, instances from realistic applications are large and demand fast and reliable algorithms. RESULTS We propose a new global optimization algorithm, which for the f...
متن کاملA Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data
A major bottleneck in protein structure determination via nuclear magnetic resonance (NMR) is the lengthy and laborious process of assigning resonances and nuclear Overhauser effect (NOE) cross peaks. Recent studies have shown that accurate backbone folds can be determined using sparse NMR data, such as residual dipolar couplings (RDCs) or backbone chemical shifts. This opens a question of whet...
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Appendix 1 briefly reviews the high-resolution protein backbone determination from residual dipolar coupling data. Appendix 2 derives the Hausdorff-based measure for evaluating the matching score between a back-computed NOE pattern and experimental spectra. Appendix 3 briefly reviews the DEE and A* search algorithms. Appendix 4 describes the NMR experimental procedures. Appendix 5 describes the...
متن کاملImproved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation
MOTIVATION Side-chain modeling has seen wide applications in computational structure biology. Most of the popular side-chain modeling programs explore the conformation space using discrete rigid rotamers for speed and efficiency. However, in the tightly packed environments of protein interiors, these methods will inherently lead to atomic clashes and hinder the prediction accuracy. RESULTS We...
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ژورنال
عنوان ژورنال: Journal of Computational Chemistry
سال: 2009
ISSN: 0192-8651,1096-987X
DOI: 10.1002/jcc.21222