Abstract
Predicting 3D structure of proteins from the amino acid sequences is one of the most important unsolved problems in computational biology and biophysics. This review article attempts to introduce the most recent effort and progress on this problem. After a brief introduction of the background and basic concepts involved in protein structure prediction, we went through the specific steps that have been taken by most typical structural modeling approaches, including fold recognition, model initialization, conformational search, model selection, and atomic-level structure refinement. Several representative structure prediction methods were introduced in detail, including those from both template-based modeling and ab initio folding approaches. Finally, we overview the results shown in the community-wide Critical Assessment of protein Structure Prediction (CASP) experiments that have been developed for benchmarking the state of the art of the field.
Highlights
Since the latter half of 20th century, a growing number of researchers from diverse academic backgrounds are devoted to bio-related researches
It has been found in CASP12 that some free modeling (FM) targets with a larger size can be successfully folded with the assistance of the coevolution based contact map prediction
This review gives a brief introduction of protein structure prediction, including the background, general steps, representative methods and the critical assessment of protein structure prediction (CASP) experiments
Summary
Since the latter half of 20th century, a growing number of researchers from diverse academic backgrounds are devoted to bio-related researches. The various advanced experimental techniques to determine protein sequence and structure have been developed in the last several decades. The basic premise for threading to work is that protein structure is highly conservative in evolution and the number of unique structural folds are limited in nature.[9,10]. Both homology modeling (based on sequence comparison) and threading methods (based on fold-recognition) can be called template-based structure prediction methods.[11] Unlike homology modeling and threading methods, ab initio method aims to build structure from the first principles of physics which does not rely on any previously solved structure. We will present a short overview of the critical assessment of protein structure prediction (CASP) experiments[13,14] and some discussions about the current difficulties and future directions of protein structure prediction
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