Side-chain conformations in 4-α-helical bundles
نویسندگان
چکیده
منابع مشابه
Steric interactions determine side-chain conformations in protein cores.
We investigate the role of steric interactions in defining side-chain conformations in protein cores. Previously, we explored the strengths and limitations of hard-sphere dipeptide models in defining sterically allowed side-chain conformations and recapitulating key features of the side-chain dihedral angle distributions observed in high-resolution protein structures. Here, we show that modelin...
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Using a new representation for interactions in protein sequences based on correlations between pairs of amino acids, we have examined α-helical segments from known protein structures for important interactions. Traditional techniques for representing protein sequences usually make an explicit assumption of conditional independence of residues in the sequences. Protein structure analyses, howeve...
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Despite recent improvements in computational methods for protein design, we still lack a quantitative, predictive understanding of the intrinsic probabilities for amino acids to adopt particular side-chain conformations. Surprisingly, this question has remained unsettled for many years, in part because of inconsistent results from different experimental approaches. To explicitly determine the r...
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Determination of side-chain conformations is an important step in protein structure prediction and protein design. Many such methods have been presented, although only a small number are in widespread use. SCWRL is one such method, and the SCWRL3 program (2003) has remained popular because of its speed, accuracy, and ease-of-use for the purpose of homology modeling. However, higher accuracy at ...
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We have developed a knowledge-based system which models the side chain conformations of residues in the variable domains of antibody Fv fragments. The system is written in Prolog and uses an object-oriented database of aligned antibody structures in conjunction with a side chain rotamer library. The antibody database provides 3-dimensional clusters of side chain conformations which can be copie...
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ژورنال
عنوان ژورنال: Protein Engineering, Design and Selection
سال: 2001
ISSN: 1741-0134,1741-0126
DOI: 10.1093/protein/14.5.321