tag:blogger.com,1999:blog-82676854057667159922024-03-12T19:22:12.337-07:00Polymer InformaticsAdvancing the communication and design of macromolecular materialsAxel D.http://www.blogger.com/profile/06438831836545774008noreply@blogger.comBlogger1125tag:blogger.com,1999:blog-8267685405766715992.post-87050580925471150282015-03-31T18:45:00.000-07:002015-03-31T21:06:26.780-07:00What is polymer informatics?<div dir="ltr" style="text-align: left;" trbidi="on">
<b>Polymer informatics</b> combines <b>polymer chemistry</b>, <b>computer science</b> and <b>information science</b>. The idea of polymer informatics is to advance the design, analysis and understanding of polymer systems. A polymer informatician probes and employs insights from the systematic study of <b>computational methods</b>, <b>knowledge acquisition strategies</b> and <b>pattern recognition algorithms </b>to develop digitalized solutions for polymer research & engineering.<br />
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Like the related disciplines <b>cheminformatics</b> and <b>bioinformatics</b>, polymer informatics is an interdisciplinary field. It is an emerging discipline that should not be considered a subdiscipline of cheminformatics. Cheminformatics “deals” with small molecules, i.e. molecules with a confined structure whose
composition and atom connectivity can precisely be represented by a
molecular graph and an associated connection table. The subject of polymer informatics is the rational management of macromolecules—chain-like molecules consisting of one or more <b>structural repeat units</b> (<b>SRUs</b>). Regular single- and multi-strand polymers and copolymers are the key ingredients of polymer systems; for example blends and composites. Cheminformatics and polymer informatics are mostly design-oriented. In contrast, bioinformatics pays particular attention to the sequence patterns (typically nucleic acid and protein sequences) of biomacromolecules within the context of biological processes and gene-based drug discovery.<br />
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Critical for the unambiguous description, storage, search and modeling of polymer systems is the adoption of recommended, agreed-upon nomenclatures and structural representation systems. An IUPAC recommendation for organic polymers exists and provides a <b>structure-based nomenclature</b> for regular single-strand polymers [1]. The <b>chemical</b> <b>Sgroup</b> approach serves as a polymer
abstraction concept [2]. The <b>Polymer Markup Language</b> (<b>PLM</b>) utilizes XML technology to manage polymer information [3]. The user-friendly <b>CurlySMILES</b> language supports structural encoding of macromolecules as annotated SMILES notation [4,5], CurlySMILES is currently enhanced for the encoding of multi-stand polymers and copolymers. Further, CurlySMILES provides a syntax to represent complex systems such as polymer assemblies, polymer solutions, doped polymers and nanocomposites in a compact single line notation.<br />
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A recent thesis on automatic polymer data evaluation in combination with the <b>Polymer Informatics Knowledge System</b> (<b>PIKS</b>) constitutes an excellent source to familiarize oneself with solutions and challenges in computer-assisted polymer research [6].<br />
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The present <b><i>Polymer Informatics</i> blog</b> is intended as a platform to discuss diverse aspects of integrating polymer science with data management technologies and computational disciplines.<br />
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<b>References</b><br />
[1] J. Kahovec, R. B. Fox and K. Hatada: <b>Nomenclature of regular single-strand organic polymers</b>. <i>Pure Appl. Chem</i> <b>2002</b>, <i>74</i> (10), pp. 1921-1956.<br />
<b><span style="color: #444444;">PDF</span></b>: <a href="http://pac.iupac.org/publications/pac/pdf/2002/pdf/7410x1921.pdf">pac.iupac.org/publications/pac/pdf/2002/pdf/7410x1921.pdf</a>.<br />
[2] A. J. Gushurst, J. G. Nourse, W. D. Hounshell, B. A. Leland and D. G. Raich: <b>The substance module: the representation, storage, and searching of complex structures</b>. <i>J. Chem. Inf. Comput. Sci.</i> <b>1991</b>, <i>31</i> (4), pp. 447-454. <b><span style="color: #444444;">DOI</span></b>: <a href="http://dx.doi.org/10.1021/ci00004a003">10.1021/ci00004a003</a>.<br />
[3] N. Adams, J. Winter, P. Murray-Rust and H. S. Rzepa: <b>Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language</b>. <i>J. Chem. Inf. Model</i> <b>2008</b>, <i>48</i>, pp. 2118-2128. <b><span style="color: #444444;">DOI</span></b>: <a href="http://dx.doi.org/10.1021/ci8002123">10.1021/ci8002123</a>.<br />
[4] A. Drefahl: <b>CurlySMILES: a chemical language to customize and annotate encodings of molecular and nonodevice structures</b>. <i>J. Cheminform.</i> <b>2011</b>, 3:1. <b><span style="color: #444444;">DOI</span></b>; <a href="http://dx.doi.org/10.1186/1758-2946-3-1">10.1186/1758-2946-3-1</a>.<br />
[5] A. Drefahl: <b>CurlySMILES encoding of homopolymers</b>.<br />
<b><span style="color: #444444;">Internet</span></b>: <a href="http://www.axeleratio.com/csm/encoding/polymers/homopolymers.htm">www.axeleratio.com/csm/encoding/polymers/homopolymers.htm</a>. <br />
[6] N. W. England: <b>Automatic analysis and validation of open polymer data</b>. Dissertation submitted for the degree of Doctor of Philosophy. University of Cambridge, United Kingdom, <b>2011</b>. <b><span style="color: #444444;">Internet</span></b>: <a href="https://www.repository.cam.ac.uk/handle/1810/237228">https://www.repository.cam.ac.uk/handle/1810/237228</a>.<br />
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Axel D.http://www.blogger.com/profile/06438831836545774008noreply@blogger.com0