publication . Other literature type . Article . 2018

SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation.

Jonas Schaub; Achim Zielesny;
Open Access
  • Published: 09 Aug 2018
  • Publisher: Springer Science and Business Media LLC
Abstract
Abstract Simplified Particle Input ConnEction Specification (SPICES) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like Dissipative Particle Dynamics by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box. An open Java library for SPICES structure handling and meso...
Subjects
free text keywords: Molecular structure representation, Line notation, Mesoscopic simulation, Dissipative Particle Dynamics, DPD, Information technology, T58.5-58.64, Chemistry, QD1-999, Software, Physical and Theoretical Chemistry, Library and Information Sciences, Computer Graphics and Computer-Aided Design, Computer Science Applications
Related Organizations
32 references, page 1 of 3

1.Text file (2018) PositionsBonds1.txt. https://github.com/zielesny/Jdpd/tree/master/src/de/gnwi/jdpd/tests/test_DMPC. Accessed 16 June 2018

Engel, T, Gasteiger, J. Chemoinformatics: basic concepts and methods. 2018

Engel, T, Gasteiger, J. Applied chemoinformatics: achievements and future opportunities. 2018

Siani, MA, Weininger, D, Blaney, JM. CHUCKLES: a method for representing and searching peptide and peptoid sequences on both monomer and atomic levels. J Chem Inf Comput Sci. 1994; 34 (3): 588-593 [OpenAIRE] [PubMed] [DOI]

Siani, MA, Weininger, D, James, CA, Blaney, JM. CHORTLES: a method for representing oligomeric and template-based mixtures. J Chem Inf Comput Sci. 1995; 35 (6): 1026-1033 [OpenAIRE] [PubMed] [DOI]

Drefahl, A. CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures. J Cheminf. 2011; 3: 1 [OpenAIRE] [DOI]

Zhang, T, Li, H, Xi, H, Stanton, RV, Rotstein, SH. HELM: a hierarchical notation language for complex biomolecule structure representation. J Chem Inf Model. 2012; 52 (10): 2796-2806 [OpenAIRE] [PubMed] [DOI]

Dufresne, Y, Noé, L, Leclère, V, Pupin, M. Smiles2Monomers: a link between chemical and biological structures for polymers. J Cheminf.. 2015; 7: 62 [OpenAIRE] [DOI]

Truszkowski, A, Daniel, M, Kuhn, H, Neumann, S, Steinbeck, C, Zielesny, A, Epple, M. A molecular fragment cheminformatics roadmap for mesoscopic simulation. J Cheminf. 2014; 6: 45 [OpenAIRE] [DOI]

Hoogerbrugge, PJ, Koelman, JMVA. Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhys Lett. 1992; 19 (3): 155-160 [OpenAIRE] [DOI]

Koelman, JMVA, Hoogerbrugge, PJ. Dynamic simulations of hard-sphere suspensions under steady shear. Europhys Lett. 1993; 21 (3): 363-368 [OpenAIRE] [DOI]

Espanol, P, Warren, P. Statistical mechanics of dissipative particle dynamics. Europhys Lett. 1995; 30 (4): 191-196 [OpenAIRE] [DOI]

Espanol, P. Hydrodynamics from dissipative particle dynamics. Phys Rev E. 1995; 52 (2): 1734-1742 [OpenAIRE] [DOI]

Groot, RD, Warren, P. Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulation. J Chem Phys.. 1997; 107 (11): 4423-4435 [OpenAIRE] [DOI]

Groot, RD, Madden, TJ. Dynamic simulation of diblock copolymer microphase separation. J Chem Phys. 1998; 105 (20): 8713-8724 [OpenAIRE] [DOI]

32 references, page 1 of 3
Abstract
Abstract Simplified Particle Input ConnEction Specification (SPICES) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like Dissipative Particle Dynamics by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box. An open Java library for SPICES structure handling and meso...
Subjects
free text keywords: Molecular structure representation, Line notation, Mesoscopic simulation, Dissipative Particle Dynamics, DPD, Information technology, T58.5-58.64, Chemistry, QD1-999, Software, Physical and Theoretical Chemistry, Library and Information Sciences, Computer Graphics and Computer-Aided Design, Computer Science Applications
Related Organizations
32 references, page 1 of 3

1.Text file (2018) PositionsBonds1.txt. https://github.com/zielesny/Jdpd/tree/master/src/de/gnwi/jdpd/tests/test_DMPC. Accessed 16 June 2018

Engel, T, Gasteiger, J. Chemoinformatics: basic concepts and methods. 2018

Engel, T, Gasteiger, J. Applied chemoinformatics: achievements and future opportunities. 2018

Siani, MA, Weininger, D, Blaney, JM. CHUCKLES: a method for representing and searching peptide and peptoid sequences on both monomer and atomic levels. J Chem Inf Comput Sci. 1994; 34 (3): 588-593 [OpenAIRE] [PubMed] [DOI]

Siani, MA, Weininger, D, James, CA, Blaney, JM. CHORTLES: a method for representing oligomeric and template-based mixtures. J Chem Inf Comput Sci. 1995; 35 (6): 1026-1033 [OpenAIRE] [PubMed] [DOI]

Drefahl, A. CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures. J Cheminf. 2011; 3: 1 [OpenAIRE] [DOI]

Zhang, T, Li, H, Xi, H, Stanton, RV, Rotstein, SH. HELM: a hierarchical notation language for complex biomolecule structure representation. J Chem Inf Model. 2012; 52 (10): 2796-2806 [OpenAIRE] [PubMed] [DOI]

Dufresne, Y, Noé, L, Leclère, V, Pupin, M. Smiles2Monomers: a link between chemical and biological structures for polymers. J Cheminf.. 2015; 7: 62 [OpenAIRE] [DOI]

Truszkowski, A, Daniel, M, Kuhn, H, Neumann, S, Steinbeck, C, Zielesny, A, Epple, M. A molecular fragment cheminformatics roadmap for mesoscopic simulation. J Cheminf. 2014; 6: 45 [OpenAIRE] [DOI]

Hoogerbrugge, PJ, Koelman, JMVA. Simulating microscopic hydrodynamic phenomena with dissipative particle dynamics. Europhys Lett. 1992; 19 (3): 155-160 [OpenAIRE] [DOI]

Koelman, JMVA, Hoogerbrugge, PJ. Dynamic simulations of hard-sphere suspensions under steady shear. Europhys Lett. 1993; 21 (3): 363-368 [OpenAIRE] [DOI]

Espanol, P, Warren, P. Statistical mechanics of dissipative particle dynamics. Europhys Lett. 1995; 30 (4): 191-196 [OpenAIRE] [DOI]

Espanol, P. Hydrodynamics from dissipative particle dynamics. Phys Rev E. 1995; 52 (2): 1734-1742 [OpenAIRE] [DOI]

Groot, RD, Warren, P. Dissipative particle dynamics: bridging the gap between atomistic and mesoscopic simulation. J Chem Phys.. 1997; 107 (11): 4423-4435 [OpenAIRE] [DOI]

Groot, RD, Madden, TJ. Dynamic simulation of diblock copolymer microphase separation. J Chem Phys. 1998; 105 (20): 8713-8724 [OpenAIRE] [DOI]

32 references, page 1 of 3
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