Non-sequential protein structure alignment by conformational space annealing and local refinement

Autor: InSuk Joung, Keehyoung Joo, Jong Yun Kim, Jooyoung Lee
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Models
Molecular
Protein Structure Comparison
Optimization
Protein Structure
Computer science
Bioinformatics
Science
0206 medical engineering
02 engineering and technology
Research and Analysis Methods
Biochemistry
03 medical and health sciences
Database and Informatics Methods
Protein structure
Search algorithm
Macromolecular Structure Analysis
Genetics
Databases
Protein
Molecular Biology
030304 developmental biology
0303 health sciences
Evolutionary Biology
Multidisciplinary
Population Biology
Applied Mathematics
Simulation and Modeling
Computational Biology
Biology and Life Sciences
Proteins
Gene Pool
Protein structure prediction
Protein Structure
Tertiary
Physical Sciences
Heuristic Alignment Procedure
Medicine
Structural Proteins
Algorithm
Sequence Analysis
Sequence Alignment
020602 bioinformatics
Algorithms
Software
Mathematics
Population Genetics
Research Article
Zdroj: PLoS ONE, Vol 14, Iss 1, p e0210177 (2019)
PLoS ONE
ISSN: 1932-6203
Popis: Protein structure alignment is an important tool for studying evolutionary biology and protein modeling. A tool which intensively searches for the globally optimal non-sequential alignments is rarely found. We propose ALIGN-CSA which shows improvement in scores, such as DALI-score, SP-score, SO-score and TM-score over the benchmark set including 286 cases. We performed benchmarking of existing popular alignment scoring functions, where the dependence of the search algorithm was effectively eliminated by using ALIGN-CSA. For the benchmarking, we set the minimum block size to 4 to prevent much fragmented alignments where the biological relevance of small alignment blocks is hard to interpret. With this condition, globally optimal alignments were searched by ALIGN-CSA using the four scoring functions listed above, and TM-score is found to be the most effective in generating alignments with longer match lengths and smaller RMSD values. However, DALI-score is the most effective in generating alignments similar to the manually curated reference alignments, which implies that DALI-score is more biologically relevant score. Due to the high demand on computational resources of ALIGN-CSA, we also propose a relatively fast local refinement method, which can control the minimum block size and whether to allow the reverse alignment. ALIGN-CSA can be used to obtain much improved alignment at the cost of relatively more extensive computation. For faster alignment, we propose a refinement protocol that improves the score of a given alignment obtained by various external tools. All programs are available from http://lee.kias.re.kr.
Databáze: OpenAIRE
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