CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

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CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction

MOTIVATION Protein homology detection, a fundamental problem in computational biology, is an indispensable step toward predicting protein structures and understanding protein functions. Despite the advances in recent decades on sequence alignment, threading and alignment-free methods, protein homology detection remains a challenging open problem. Recently, network methods that try to find trans...

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Naturally occurring proteins comprise a special subset of all plausible sequences and structures selected through evolution. Simulating protein evolution with simplified and all-atom models has shed light on the evolutionary dynamics of protein populations, the nature of evolved sequences and structures, and the extent to which today's proteins are shaped by selection pressures on folding, stru...

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Protein structure and evolutionary history determine sequence space topology.

Understanding the observed variability in the number of homologs of a gene is a very important unsolved problem that has broad implications for research into coevolution of structure and function, gene duplication, pseudogene formation, and possibly for emerging diseases. Here, we attempt to define and elucidate some possible causes behind the observed irregularity in sequence space. We present...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2016

ISSN: 1367-4803,1460-2059

DOI: 10.1093/bioinformatics/btw271