Polymer informatics combines polymer chemistry, computer science and information science. 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 computational methods, knowledge acquisition strategies and pattern recognition algorithms to develop digitalized solutions for polymer research & engineering.
Like the related disciplines cheminformatics and bioinformatics, 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 structural repeat units (SRUs). 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.
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 structure-based nomenclature for regular single-strand polymers [1]. The chemical Sgroup approach serves as a polymer abstraction concept [2]. The Polymer Markup Language (PLM) utilizes XML technology to manage polymer information [3]. The user-friendly CurlySMILES 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.
A recent thesis on automatic polymer data evaluation in combination with the Polymer Informatics Knowledge System (PIKS) constitutes an excellent source to familiarize oneself with solutions and challenges in computer-assisted polymer research [6].
The present Polymer Informatics blog is intended as a platform to discuss diverse aspects of integrating polymer science with data management technologies and computational disciplines.
References
[1] J. Kahovec, R. B. Fox and K. Hatada: Nomenclature of regular single-strand organic polymers. Pure Appl. Chem 2002, 74 (10), pp. 1921-1956.
PDF: pac.iupac.org/publications/pac/pdf/2002/pdf/7410x1921.pdf.
[2] A. J. Gushurst, J. G. Nourse, W. D. Hounshell, B. A. Leland and D. G. Raich: The substance module: the representation, storage, and searching of complex structures. J. Chem. Inf. Comput. Sci. 1991, 31 (4), pp. 447-454. DOI: 10.1021/ci00004a003.
[3] N. Adams, J. Winter, P. Murray-Rust and H. S. Rzepa: Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language. J. Chem. Inf. Model 2008, 48, pp. 2118-2128. DOI: 10.1021/ci8002123.
[4] A. Drefahl: CurlySMILES: a chemical language to customize and annotate encodings of molecular and nonodevice structures. J. Cheminform. 2011, 3:1. DOI; 10.1186/1758-2946-3-1.
[5] A. Drefahl: CurlySMILES encoding of homopolymers.
Internet: www.axeleratio.com/csm/encoding/polymers/homopolymers.htm.
[6] N. W. England: Automatic analysis and validation of open polymer data. Dissertation submitted for the degree of Doctor of Philosophy. University of Cambridge, United Kingdom, 2011. Internet: https://www.repository.cam.ac.uk/handle/1810/237228.
Like the related disciplines cheminformatics and bioinformatics, 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 structural repeat units (SRUs). 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.
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 structure-based nomenclature for regular single-strand polymers [1]. The chemical Sgroup approach serves as a polymer abstraction concept [2]. The Polymer Markup Language (PLM) utilizes XML technology to manage polymer information [3]. The user-friendly CurlySMILES 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.
A recent thesis on automatic polymer data evaluation in combination with the Polymer Informatics Knowledge System (PIKS) constitutes an excellent source to familiarize oneself with solutions and challenges in computer-assisted polymer research [6].
The present Polymer Informatics blog is intended as a platform to discuss diverse aspects of integrating polymer science with data management technologies and computational disciplines.
References
[1] J. Kahovec, R. B. Fox and K. Hatada: Nomenclature of regular single-strand organic polymers. Pure Appl. Chem 2002, 74 (10), pp. 1921-1956.
PDF: pac.iupac.org/publications/pac/pdf/2002/pdf/7410x1921.pdf.
[2] A. J. Gushurst, J. G. Nourse, W. D. Hounshell, B. A. Leland and D. G. Raich: The substance module: the representation, storage, and searching of complex structures. J. Chem. Inf. Comput. Sci. 1991, 31 (4), pp. 447-454. DOI: 10.1021/ci00004a003.
[3] N. Adams, J. Winter, P. Murray-Rust and H. S. Rzepa: Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language. J. Chem. Inf. Model 2008, 48, pp. 2118-2128. DOI: 10.1021/ci8002123.
[4] A. Drefahl: CurlySMILES: a chemical language to customize and annotate encodings of molecular and nonodevice structures. J. Cheminform. 2011, 3:1. DOI; 10.1186/1758-2946-3-1.
[5] A. Drefahl: CurlySMILES encoding of homopolymers.
Internet: www.axeleratio.com/csm/encoding/polymers/homopolymers.htm.
[6] N. W. England: Automatic analysis and validation of open polymer data. Dissertation submitted for the degree of Doctor of Philosophy. University of Cambridge, United Kingdom, 2011. Internet: https://www.repository.cam.ac.uk/handle/1810/237228.
