ArticleNucleic acids research2011
iPBA: a tool for protein structure comparison using sequence alignment strategies.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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45 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction.International journal of molecular sciences · 2021Article
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- Benchmarking Methods of Protein Structure Alignment.Journal of molecular evolution · 2020Article
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- Discrete analysis of camelid variable domains: sequences, structures, and in-silico structure prediction.PeerJ · 2020Article
- HKT1;5 Transporter Gene Expression and Association of Amino Acid Substitutions With Salt Tolerance Across Rice Genotypes.Frontiers in plant science · 2019Article
- iPBAvizu: a PyMOL plugin for an efficient 3D protein structure superimposition approach.Source code for biology and medicine · 2019Article
Corrections and comments
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With the immense growth in the number of available protein structures, fast and accurate structure comparison has been essential. We propose an efficient method for structure comparison, based on a structural alphabet. Protein Blocks (PBs) is a widely used structural alphabet with 16 pentapeptide conformations that can fairly approximate a complete protein chain. Thus a 3D structure can be translated into a 1D sequence of PBs. With a simple Needleman-Wunsch approach and a raw PB substitution matrix, PB-based structural alignments were better than many popular methods. iPBA web server presents an improved alignment approach using (i) specialized PB Substitution Matrices (SM) and (ii) anchor-based alignment methodology. With these developments, the quality of ∼88% of alignments was improved. iPBA alignments were also better than DALI, MUSTANG and GANGSTA(+) in >80% of the cases. The webserver is designed to for both pairwise comparisons and database searches. Outputs are given as sequence alignment and superposed 3D structures displayed using PyMol and Jmol. A local alignment option for detecting subs-structural similarity is also embedded. As a fast and efficient 'sequence-based' structure comparison tool, we believe that it will be quite useful to the scientific community. iPBA can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/ipba/.
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