{"id":"https://openalex.org/W2120781005","doi":"https://doi.org/10.1093/nar/gkm342","title":"MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape","display_name":"MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape","publication_year":2007,"publication_date":"2007-06-01","ids":{"openalex":"https://openalex.org/W2120781005","doi":"https://doi.org/10.1093/nar/gkm342","mag":"2120781005","pmid":"https://pubmed.ncbi.nlm.nih.gov/17545201"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkm342","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm342","pdf_url":"https://academic.oup.com/nar/article-pdf/35/suppl_2/W477/16747135/gkm342.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/35/suppl_2/W477/16747135/gkm342.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032096798","display_name":"Joel Franklin","orcid":"https://orcid.org/0000-0002-9073-5507"},"institutions":[{"id":"https://openalex.org/I55486353","display_name":"Reed College","ror":"https://ror.org/00a6ram87","country_code":"US","type":"education","lineage":["https://openalex.org/I55486353"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Joel Franklin","raw_affiliation_strings":["Department of Physics, Reed College, Portland, OR 97202, USA","Department of Physics, Reed College, Portland, OR 97202 USA"],"affiliations":[{"raw_affiliation_string":"Department of Physics, Reed College, Portland, OR 97202, USA","institution_ids":["https://openalex.org/I55486353"]},{"raw_affiliation_string":"Department of Physics, Reed College, Portland, OR 97202 USA","institution_ids":["https://openalex.org/I55486353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056170480","display_name":"Patrice Koehl","orcid":"https://orcid.org/0000-0002-0908-068X"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]},{"id":"https://openalex.org/I55486353","display_name":"Reed College","ror":"https://ror.org/00a6ram87","country_code":"US","type":"education","lineage":["https://openalex.org/I55486353"]},{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"Patrice Koehl","raw_affiliation_strings":["Department of Physics, Reed College, Portland, OR 97202, USA, 2Department of Computer Science and Genome Center, UC Davis, Davis, CA 95616, USA, 3Departments of Physics and Applied Physics, Stanford University, Stanford, CA 94305-4045, USA and 4Department of Structural Biology and Chemistry and URA 2185 du C.N.R.S., Institut Pasteur, Paris, France","Reed College, Portland, United States"],"affiliations":[{"raw_affiliation_string":"Department of Physics, Reed College, Portland, OR 97202, USA, 2Department of Computer Science and Genome Center, UC Davis, Davis, CA 95616, USA, 3Departments of Physics and Applied Physics, Stanford University, Stanford, CA 94305-4045, USA and 4Department of Structural Biology and Chemistry and URA 2185 du C.N.R.S., Institut Pasteur, Paris, France","institution_ids":["https://openalex.org/I55486353","https://openalex.org/I97018004","https://openalex.org/I84218800","https://openalex.org/I157536573"]},{"raw_affiliation_string":"Reed College, Portland, United States","institution_ids":["https://openalex.org/I55486353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039881572","display_name":"Sebastian Doniach","orcid":"https://orcid.org/0000-0001-5948-5821"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]},{"id":"https://openalex.org/I157536573","display_name":"Institut Pasteur","ror":"https://ror.org/0495fxg12","country_code":"FR","type":"funder","lineage":["https://openalex.org/I157536573"]},{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]},{"id":"https://openalex.org/I55486353","display_name":"Reed College","ror":"https://ror.org/00a6ram87","country_code":"US","type":"education","lineage":["https://openalex.org/I55486353"]}],"countries":["FR","US"],"is_corresponding":false,"raw_author_name":"Sebastian Doniach","raw_affiliation_strings":["Department of Physics, Reed College, Portland, OR 97202, USA, 2Department of Computer Science and Genome Center, UC Davis, Davis, CA 95616, USA, 3Departments of Physics and Applied Physics, Stanford University, Stanford, CA 94305-4045, USA and 4Department of Structural Biology and Chemistry and URA 2185 du C.N.R.S., Institut Pasteur, Paris, France","Reed College, Portland, United States"],"affiliations":[{"raw_affiliation_string":"Department of Physics, Reed College, Portland, OR 97202, USA, 2Department of Computer Science and Genome Center, UC Davis, Davis, CA 95616, USA, 3Departments of Physics and Applied Physics, Stanford University, Stanford, CA 94305-4045, USA and 4Department of Structural Biology and Chemistry and URA 2185 du C.N.R.S., Institut Pasteur, Paris, France","institution_ids":["https://openalex.org/I55486353","https://openalex.org/I97018004","https://openalex.org/I84218800","https://openalex.org/I157536573"]},{"raw_affiliation_string":"Reed College, Portland, United States","institution_ids":["https://openalex.org/I55486353"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009891943","display_name":"Marc Delarue","orcid":"https://orcid.org/0000-0003-0723-8102"},"institutions":[{"id":"https://openalex.org/I55486353","display_name":"Reed College","ror":"https://ror.org/00a6ram87","country_code":"US","type":"education","lineage":["https://openalex.org/I55486353"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marc Delarue","raw_affiliation_strings":["Reed College, Portland, United States"],"affiliations":[{"raw_affiliation_string":"Reed College, Portland, United States","institution_ids":["https://openalex.org/I55486353"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5032096798"],"corresponding_institution_ids":["https://openalex.org/I55486353"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":2.0165,"has_fulltext":false,"cited_by_count":88,"citation_normalized_percentile":{"value":0.86328666,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"35","issue":"suppl_2","first_page":"W477","last_page":"W482"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.991599977016449,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10303","display_name":"Photosynthetic Processes and Mechanisms","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cartesian-coordinate-system","display_name":"Cartesian coordinate system","score":0.574687123298645},{"id":"https://openalex.org/keywords/crossover","display_name":"Crossover","score":0.5030142664909363},{"id":"https://openalex.org/keywords/hessian-matrix","display_name":"Hessian matrix","score":0.46122318506240845},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.45045122504234314},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.44382548332214355},{"id":"https://openalex.org/keywords/morphing","display_name":"Morphing","score":0.44030284881591797},{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.4326920807361603},{"id":"https://openalex.org/keywords/minification","display_name":"Minification","score":0.4155433177947998},{"id":"https://openalex.org/keywords/energy-minimization","display_name":"Energy minimization","score":0.4100886881351471},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.3754924237728119},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3113920986652374},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.23378819227218628},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.2254987359046936},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.144725501537323},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.11050701141357422}],"concepts":[{"id":"https://openalex.org/C16038011","wikidata":"https://www.wikidata.org/wiki/Q62912","display_name":"Cartesian coordinate system","level":2,"score":0.574687123298645},{"id":"https://openalex.org/C122507166","wikidata":"https://www.wikidata.org/wiki/Q628906","display_name":"Crossover","level":2,"score":0.5030142664909363},{"id":"https://openalex.org/C203616005","wikidata":"https://www.wikidata.org/wiki/Q620495","display_name":"Hessian matrix","level":2,"score":0.46122318506240845},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.45045122504234314},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.44382548332214355},{"id":"https://openalex.org/C50637493","wikidata":"https://www.wikidata.org/wiki/Q1136781","display_name":"Morphing","level":2,"score":0.44030284881591797},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.4326920807361603},{"id":"https://openalex.org/C147764199","wikidata":"https://www.wikidata.org/wiki/Q6865248","display_name":"Minification","level":2,"score":0.4155433177947998},{"id":"https://openalex.org/C14961307","wikidata":"https://www.wikidata.org/wiki/Q5377176","display_name":"Energy minimization","level":2,"score":0.4100886881351471},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.3754924237728119},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3113920986652374},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.23378819227218628},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.2254987359046936},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.144725501537323},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.11050701141357422},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004735","descriptor_name":"Energy Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017434","descriptor_name":"Protein Structure, Tertiary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1093/nar/gkm342","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm342","pdf_url":"https://academic.oup.com/nar/article-pdf/35/suppl_2/W477/16747135/gkm342.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:17545201","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17545201","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:ark:/13030/qt2nj6x0t0","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:HAL:pasteur-02175143v1","is_oa":false,"landing_page_url":"https://pasteur.hal.science/pasteur-02175143","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Research, 2007, 35 (suppl_2), pp.W477-W482. &#x27E8;10.1093/nar/gkm342&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt2nj6x0t0","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/2nj6x0t0","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic acids research, vol 35, iss Web Server issue","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1933200","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1933200","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkm342","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm342","pdf_url":"https://academic.oup.com/nar/article-pdf/35/suppl_2/W477/16747135/gkm342.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.800000011920929}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2120781005.pdf","grobid_xml":"https://content.openalex.org/works/W2120781005.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1968407616","https://openalex.org/W1970414487","https://openalex.org/W1998367993","https://openalex.org/W2004067483","https://openalex.org/W2008852962","https://openalex.org/W2018748094","https://openalex.org/W2031320386","https://openalex.org/W2031340110","https://openalex.org/W2059998901","https://openalex.org/W2067204014","https://openalex.org/W2069777230","https://openalex.org/W2072572157","https://openalex.org/W2082028745","https://openalex.org/W2083144176","https://openalex.org/W2085162785","https://openalex.org/W2085266415","https://openalex.org/W2097504123","https://openalex.org/W2103873225","https://openalex.org/W2107268733","https://openalex.org/W2113971181","https://openalex.org/W2122326469","https://openalex.org/W2134528197","https://openalex.org/W2140889378","https://openalex.org/W2144646547","https://openalex.org/W2145745861","https://openalex.org/W2149744037","https://openalex.org/W2152655599","https://openalex.org/W2163216107","https://openalex.org/W2164548935","https://openalex.org/W2178631187","https://openalex.org/W2609912642","https://openalex.org/W3008921266"],"related_works":["https://openalex.org/W1679315481","https://openalex.org/W3151495635","https://openalex.org/W4236870338","https://openalex.org/W2016917053","https://openalex.org/W51472912","https://openalex.org/W4361020386","https://openalex.org/W4362722828","https://openalex.org/W2375652671","https://openalex.org/W4205835231","https://openalex.org/W4386770917"],"abstract_inverted_index":{"The":[0,22,111,154],"non-linear":[1,138,150],"problem":[2,23,139],"of":[3,12,38,82,105,131,143],"simulating":[4],"the":[5,40,43,47,69,83,85,96,99,106,121,132,136,157,173,180],"structural":[6,20],"transition":[7,181],"between":[8,46,156],"two":[9,158],"known":[10],"forms":[11],"a":[13,17,59,64,141,149],"macromolecule":[14],"still":[15],"remains":[16],"challenge":[18],"in":[19,27],"biology.":[21],"is":[24,74,92,117,165],"usually":[25],"addressed":[26],"an":[28,80,169],"approximate":[29],"way":[30],"using":[31,120,168],"'morphing'":[32],"techniques,":[33],"which":[34],"are":[35,108],"linear":[36,144],"interpolations":[37],"either":[39],"Cartesian":[41],"or":[42],"internal":[44],"coordinates":[45],"initial":[48,97],"and":[49,98,123,177,183],"end":[50],"states,":[51],"followed":[52],"by":[53,140,148],"energy":[54,160],"minimization.":[55],"Here":[56],"we":[57],"describe":[58],"web":[60],"tool":[61],"that":[62,73],"implements":[63],"new":[65],"method":[66],"to":[67],"calculate":[68],"most":[70,174],"probable":[71,175],"trajectory":[72,176],"exact":[75],"for":[76,95],"harmonic":[77],"potentials;":[78],"as":[79],"illustration":[81],"method,":[84],"classical":[86],"Calpha-based":[87],"Elastic":[88],"Network":[89],"Model":[90],"(ENM)":[91],"used":[93],"both":[94],"final":[100],"states":[101],"but":[102],"other":[103],"variants":[104],"ENM":[107],"also":[109],"possible.":[110],"Langevin":[112],"equation":[113],"under":[114],"this":[115],"potential":[116],"solved":[118],"analytically":[119],"Onsager":[122],"Machlup":[124],"action":[125],"minimization":[126],"formalism":[127],"on":[128],"each":[129,163],"side":[130],"transition,":[133],"thus":[134],"replacing":[135],"original":[137],"pair":[142],"differential":[145],"equations":[146],"joined":[147],"boundary":[151],"matching":[152],"condition.":[153],"crossover":[155],"multidimensional":[159],"curves":[161],"around":[162],"state":[164,182],"found":[166],"numerically":[167],"iterative":[170],"approach,":[171],"producing":[172],"fully":[178],"characterizing":[179],"its":[184],"energy.":[185],"Jobs":[186],"calculating":[187],"such":[188],"trajectories":[189],"can":[190],"be":[191],"submitted":[192],"on-line":[193],"at:":[194],"http://lorentz.dynstr.pasteur.fr/joel/index.php.":[195]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":6}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
