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            <title xml:lang="en">Improvement of protein structure comparison using a structural alphabet.</title>
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                <forename type="first">Agnel Praveen</forename>
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                <forename>Alexandre G.</forename>
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            <funder>These works were supported by grants from the French Ministry of Research, University of Paris Diderot - Paris 7, French National Institute for Blood Transfusion (INTS), French Institute for Health and Medical Research (INSERM) and Department of Biotechnology, India.</funder>
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              <date type="whenSubmitted">2011-11-29 15:01:22</date>
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            <idno type="halRefHtml">&lt;i&gt;Biochimie&lt;/i&gt;, 2011, 93 (9), pp.1434-45. &lt;a target="_blank" href="https://dx.doi.org/10.1016/j.biochi.2011.04.010"&gt;&amp;#x27E8;10.1016/j.biochi.2011.04.010&amp;#x27E9;&lt;/a&gt;</idno>
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                <title xml:lang="en">Improvement of protein structure comparison using a structural alphabet.</title>
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                    <surname>Joseph</surname>
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                <title level="j">Biochimie</title>
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                  <publisher>Elsevier</publisher>
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                  <biblScope unit="issue">9</biblScope>
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                  <date type="datePub">2011-09</date>
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                <term xml:lang="en">Protein Data Bank</term>
                <term xml:lang="en">protein structure mining</term>
                <term xml:lang="en">structural comparison</term>
                <term xml:lang="en">protein folds</term>
                <term xml:lang="en">anchorbased alignment</term>
                <term xml:lang="en">semi-global alignment</term>
                <term xml:lang="en">Protein Blocks</term>
                <term xml:lang="en">structural alphabet</term>
                <term xml:lang="en">amino acid</term>
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              <classCode scheme="mesh">Algorithms</classCode>
              <classCode scheme="mesh">Databases, Protein</classCode>
              <classCode scheme="mesh">Models, Molecular</classCode>
              <classCode scheme="mesh">Protein Conformation</classCode>
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              <p>The three dimensional structure of a protein provides major insights into its function. Protein structure comparison has implications in functional and evolutionary studies. A structural alphabet (SA) is a library of local protein structure prototypes that can abstract every part of protein main chain conformation. Protein Blocks (PBs) is a widely used SA, composed of 16 prototypes, each representing a pentapeptide backbone conformation defined in terms of dihedral angles. Through this description, the 3D structural information can be translated into a 1D sequence of PBs. In a previous study, we have used this approach to compare protein structures encoded in terms of PBs. A classical sequence alignment procedure based on dynamic programming was used, with a dedicated PB Substitution Matrix (SM). PB-based pairwise structural alignment method gave an excellent performance, when compared to other established methods for mining. In this study, we have (i) refined the SMs and (ii) improved the Protein Block Alignment methodology (named as iPBA). The SM was normalized in regards to sequence and structural similarity. Alignment of protein structures often involves similar structural regions separated by dissimilar stretches. A dynamic programming algorithm that weighs these local similar stretches has been designed. Amino acid substitutions scores were also coupled linearly with the PB substitutions. iPBA improves (i) the mining efficiency rate by 6.8% and (ii) more than 82% of the alignments have a better quality. A higher efficiency in aligning multi-domain proteins could be also demonstrated. The quality of alignment is better than DALI and MUSTANG in 81.3% of the cases. Thus our study has resulted in an impressive improvement in the quality of protein structural alignment.</p>
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