{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:12:43Z","timestamp":1773274363820,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation:\u2003Atomistic or coarse grained (CG) potentials derived from statistical distributions of internal variables have recently become popular due to the need of simplified interactions for reaching larger scales in simulations or more efficient conformational space sampling. However, the process of parameterization of accurate and predictive statistics-based force fields requires a huge amount of work and is prone to the introduction of bias and errors.<\/jats:p><jats:p>Results:\u2003This article introduces SecStAnT, a software for the creation and analysis of protein structural datasets with user-defined primary\/secondary structure composition, with a particular focus on the CG representation. In addition, the possibility of managing different resolutions and the primary\/secondary structure selectivity allow addressing the mapping-backmapping of atomistic to CG representation and study the secondary to primary structure relations. Sample datasets and distributions are reported, including interpretation of structural features.<\/jats:p><jats:p>Availability and implementation:\u2003SecStAnT is available free of charge at secstant.sourceforge.net\/. Source code is freely available on request, implemented in Java and supported on Linux, MS Windows and OSX.<\/jats:p><jats:p>Contact:\u2003giuseppe.maccari@iit.it<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt586","type":"journal-article","created":{"date-parts":[[2013,10,16]],"date-time":"2013-10-16T04:00:10Z","timestamp":1381896010000},"page":"668-674","source":"Crossref","is-referenced-by-count":7,"title":["SecStAnT: secondary structure analysis tool for data selection, statistics and models building"],"prefix":"10.1093","volume":"30","author":[{"given":"Giuseppe","family":"Maccari","sequence":"first","affiliation":[{"name":"1 Center for Nanotechnology and Innovation @NEST, Istituto Italiano di Tecnologia, 2NEST, Istituto Nanoscienze \u2013 CNR and Scuola Normale Superiore, Piazza San Silvestro 12-56127 Pisa and 3Dipartimento di Fisica \u2018E. Fermi\u2019, Universit\u00e0 di Pisa Largo B. Pontecorvo 3-56127 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giulia L.B.","family":"Spampinato","sequence":"additional","affiliation":[{"name":"1 Center for Nanotechnology and Innovation @NEST, Istituto Italiano di Tecnologia, 2NEST, Istituto Nanoscienze \u2013 CNR and Scuola Normale Superiore, Piazza San Silvestro 12-56127 Pisa and 3Dipartimento di Fisica \u2018E. Fermi\u2019, Universit\u00e0 di Pisa Largo B. Pontecorvo 3-56127 Pisa, Italy"},{"name":"1 Center for Nanotechnology and Innovation @NEST, Istituto Italiano di Tecnologia, 2NEST, Istituto Nanoscienze \u2013 CNR and Scuola Normale Superiore, Piazza San Silvestro 12-56127 Pisa and 3Dipartimento di Fisica \u2018E. Fermi\u2019, Universit\u00e0 di Pisa Largo B. Pontecorvo 3-56127 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valentina","family":"Tozzini","sequence":"additional","affiliation":[{"name":"1 Center for Nanotechnology and Innovation @NEST, Istituto Italiano di Tecnologia, 2NEST, Istituto Nanoscienze \u2013 CNR and Scuola Normale Superiore, Piazza San Silvestro 12-56127 Pisa and 3Dipartimento di Fisica \u2018E. Fermi\u2019, Universit\u00e0 di Pisa Largo B. Pontecorvo 3-56127 Pisa, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2013,10,15]]},"reference":[{"key":"2023012710430031200_btt586-B1","doi-asserted-by":"crossref","first-page":"1589","DOI":"10.1021\/cr040426m","article-title":"Molecular dynamics: survey of methods for simulating the activity of proteins","volume":"106","author":"Adcock","year":"2006","journal-title":"Chem. Rev."},{"key":"2023012710430031200_btt586-B2","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/S0969-2126(02)00700-1","article-title":"Continuum secondary structure captures protein flexibility","volume":"10","author":"Andersen","year":"2002","journal-title":"Structure"},{"key":"2023012710430031200_btt586-B3","first-page":"980","article-title":"Announcing the worldwide Protein Data Bank","volume":"10","author":"Berman","year":"2003","journal-title":"Na. Struct. Biol."},{"key":"2023012710430031200_btt586-B4","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.jmb.2004.06.091","article-title":"Local propensities and statistical potentials of backbone dihedral angles in proteins","volume":"342","author":"Betancourt","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023012710430031200_btt586-B5","doi-asserted-by":"crossref","first-page":"094112","DOI":"10.1063\/1.3557038","article-title":"Coarse-graining errors and numerical optimization using a relative entropy framework","volume":"134","author":"Chaimovich","year":"2011","journal-title":"J. Chem. Phys."},{"key":"2023012710430031200_btt586-B6","first-page":"1","article-title":"Further refinements of next-generation force fields \u2014 Nonempirical localization of off-centered points in molecules","author":"Chaudret","year":"2013","journal-title":"Can. J. Chem."},{"key":"2023012710430031200_btt586-B7","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/s00214-005-0026-8","article-title":"Protein folding simulations: combining coarse-grained models and all-atom molecular dynamics","volume":"116","author":"Colombo","year":"2005","journal-title":"Theor. Chem. Acc."},{"key":"2023012710430031200_btt586-B8","doi-asserted-by":"crossref","first-page":"L75","DOI":"10.1529\/biophysj.108.131565","article-title":"Ten-microsecond molecular dynamics simulation of a fast-folding WW domain","volume":"94","author":"Freddolino","year":"2008","journal-title":"Biophys. J."},{"key":"2023012710430031200_btt586-B9","doi-asserted-by":"crossref","first-page":"669","DOI":"10.2174\/092986607781483912","article-title":"Ramachandran plot on the web (2.0)","volume":"14","author":"Gopalakrishnan","year":"2007","journal-title":"Protein Pept. Lett."},{"key":"2023012710430031200_btt586-B10","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1016\/S0959-440X(96)80075-3","article-title":"Structure-derived potentials and protein simulations","volume":"6","author":"Jernigan","year":"1996","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023012710430031200_btt586-B11","doi-asserted-by":"crossref","first-page":"11225","DOI":"10.1021\/ja9621760","article-title":"Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids","volume":"118","author":"Jorgensen","year":"1996","journal-title":"J. Am. Chem. Soc."},{"key":"2023012710430031200_btt586-B12","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1002\/prot.20100","article-title":"Relationships between amino acid sequence and backbone torsion angle preferences","volume":"55","author":"Keskin","year":"2004","journal-title":"Proteins"},{"key":"2023012710430031200_btt586-B13","doi-asserted-by":"crossref","first-page":"e32131","DOI":"10.1371\/journal.pone.0032131","article-title":"Systematic validation of protein force fields against experimental data","volume":"7","author":"Lindorff-Larsen","year":"2012","journal-title":"PLoS One"},{"key":"2023012710430031200_btt586-B14","first-page":"3730","article-title":"Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach","volume":"52","author":"Lyubartsev","year":"1995","journal-title":"Phys. Rev. E Stat. Phy. Plasmas Fluids Relat. Interdiscip. Topics"},{"key":"2023012710430031200_btt586-B15","doi-asserted-by":"crossref","first-page":"7812","DOI":"10.1021\/jp071097f","article-title":"The MARTINI force field: coarse grained model for biomolecular simulations","volume":"111","author":"Marrink","year":"2007","journal-title":"J. Phys Chem. B"},{"key":"2023012710430031200_btt586-B16","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1016\/j.sbi.2006.06.013","article-title":"Knowledge-based potentials in protein design","volume":"16","author":"Poole","year":"2006","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023012710430031200_btt586-B17","doi-asserted-by":"crossref","first-page":"1624","DOI":"10.1002\/jcc.10307","article-title":"Deriving effective mesoscale potentials from atomistic simulations","volume":"24","author":"Reith","year":"2003","journal-title":"J. Comput. Chem."},{"key":"2023012710430031200_btt586-B18","doi-asserted-by":"crossref","first-page":"D475","DOI":"10.1093\/nar\/gks1200","article-title":"The RCSB Protein Data Bank: new resources for research and education","volume":"41","author":"Rose","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023012710430031200_btt586-B19","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1145\/1364782.1364802","article-title":"Anton, a special-purpose machine for molecular dynamics simulation","volume":"51","author":"Shaw","year":"2008","journal-title":"Commun. ACM"},{"key":"2023012710430031200_btt586-B20","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1007\/s11837-011-0102-6","article-title":"The potential of atomistic simulations and the knowledgebase of interatomic models","volume":"63","author":"Tadmor","year":"2011","journal-title":"JOM"},{"key":"2023012710430031200_btt586-B21","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.sbi.2005.02.005","article-title":"Coarse-grained models for proteins","volume":"15","author":"Tozzini","year":"2005","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2023012710430031200_btt586-B22","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1016\/j.jsb.2006.08.005","article-title":"Flap opening dynamics in HIV-1 protease explored with a coarse-grained model","volume":"157","author":"Tozzini","year":"2007","journal-title":"J. Struct. Biol."},{"key":"2023012710430031200_btt586-B23","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1021\/ct050294k","article-title":"Mapping all-atom models onto one-bead Coarse Grained Models: general properties and applications to a minimal polypeptide model","volume":"2","author":"Tozzini","year":"2006","journal-title":"J. Chem. Theory Comput."},{"key":"2023012710430031200_btt586-B24","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1017\/S0033583510000132","article-title":"Minimalist models for proteins: a comparative analysis","volume":"43","author":"Tozzini","year":"2010","journal-title":"Q. Rev. Biophys."},{"key":"2023012710430031200_btt586-B25","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1021\/ar9001476","article-title":"Multiscale modeling of proteins","volume":"43","author":"Tozzini","year":"2010","journal-title":"Acc. Chem. Res."},{"key":"2023012710430031200_btt586-B26","first-page":"187","article-title":"Minimalist models for biopolymers: Open problems, latest advances and perspectives","volume-title":"AIP Conference Proceedings","author":"Trovato","year":"2012"},{"key":"2023012710430031200_btt586-B27","volume-title":"Biomolecular Simulation: The GROMOS96 Manual und User Guide vdf","author":"van Gunsteren","year":"1996"},{"key":"2023012710430031200_btt586-B28","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1002\/jcc.21367","article-title":"CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields","volume":"31","author":"Vanommeslaeghe","year":"2010","journal-title":"J. Comput. Chem."},{"key":"2023012710430031200_btt586-B29","first-page":"13","article-title":"Elusive unfoldability: learning a contact potential to fold crambin","volume":"3","author":"Vendruscolo","year":"1998","journal-title":"Fold. Des."},{"key":"2023012710430031200_btt586-B30","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","article-title":"Development and testing of a general amber force field","volume":"25","author":"Wang","year":"2004","journal-title":"J. Comput. Chem."},{"key":"2023012710430031200_btt586-B31","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1021\/ct9006647","article-title":"Development of a polarizable force field using multiple fluctuating charges per atom","volume":"6","author":"Zhao","year":"2010","journal-title":"J. Chem. Theory Comput."},{"key":"2023012710430031200_btt586-B32","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1110\/ps.0217002","article-title":"Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction","volume":"11","author":"ZhouA","year":"2002","journal-title":"Protein Sci."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/5\/668\/48917730\/bioinformatics_30_5_668.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/5\/668\/48917730\/bioinformatics_30_5_668.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,18]],"date-time":"2024-05-18T18:23:34Z","timestamp":1716056614000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/5\/668\/246595"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,10,15]]},"references-count":32,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2014,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt586","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2014,3,1]]},"published":{"date-parts":[[2013,10,15]]}}}