{"id":"https://openalex.org/W2077412035","doi":"https://doi.org/10.1073/pnas.0603553103","title":"Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction","display_name":"Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction","publication_year":2006,"publication_date":"2006-06-19","ids":{"openalex":"https://openalex.org/W2077412035","doi":"https://doi.org/10.1073/pnas.0603553103","mag":"2077412035","pmid":"https://pubmed.ncbi.nlm.nih.gov/16785435"},"language":"en","primary_location":{"id":"doi:10.1073/pnas.0603553103","is_oa":false,"landing_page_url":"https://doi.org/10.1073/pnas.0603553103","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1502548","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064335115","display_name":"Payel Das","orcid":"https://orcid.org/0000-0002-7288-0516"},"institutions":[{"id":"https://openalex.org/I4210110509","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795","https://openalex.org/I4210110509","https://openalex.org/I4210112577"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Payel Das","raw_affiliation_strings":["Departments of *Chemistry,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of *Chemistry,","institution_ids":["https://openalex.org/I4210110509"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061397940","display_name":"Mark Moll","orcid":"https://orcid.org/0000-0002-0451-2797"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mark Moll","raw_affiliation_strings":["Computer Science, and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science, and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046489872","display_name":"Hern\u00e1n Stamati","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hern\u00e1n Stamati","raw_affiliation_strings":["Computer Science, and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science, and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067205988","display_name":"Lydia E. Kavraki","orcid":"https://orcid.org/0000-0003-0699-8038"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lydia E. Kavraki","raw_affiliation_strings":["Bioengineering, Rice University, Houston, TX 77005; and","Computer Science, and","Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030","Bioengineering, Rice University, Houston, TX 77005; and; Computer Science, and; Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioengineering, Rice University, Houston, TX 77005; and","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Computer Science, and","institution_ids":[]},{"raw_affiliation_string":"Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Bioengineering, Rice University, Houston, TX 77005; and; Computer Science, and; Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030","institution_ids":["https://openalex.org/I181547552","https://openalex.org/I74775410"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061903235","display_name":"Cecilia Clementi","orcid":"https://orcid.org/0000-0001-9221-2358"},"institutions":[{"id":"https://openalex.org/I4210110509","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795","https://openalex.org/I4210110509","https://openalex.org/I4210112577"]},{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cecilia Clementi","raw_affiliation_strings":["Bioengineering, Rice University, Houston, TX 77005; and","Departments of *Chemistry,","Bioengineering, Rice University, Houston, TX 77005; and; Departments of *Chemistry,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioengineering, Rice University, Houston, TX 77005; and","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Departments of *Chemistry,","institution_ids":["https://openalex.org/I4210110509"]},{"raw_affiliation_string":"Bioengineering, Rice University, Houston, TX 77005; and; Departments of *Chemistry,","institution_ids":["https://openalex.org/I74775410"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":6.5386,"has_fulltext":false,"cited_by_count":344,"citation_normalized_percentile":{"value":0.97604365,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"103","issue":"26","first_page":"9885","last_page":"9890"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T11162","display_name":"Enzyme Structure and Function","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10591","display_name":"Theoretical and Computational Physics","score":0.9861000180244446,"subfield":{"id":"https://openalex.org/subfields/3104","display_name":"Condensed Matter Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/energy-landscape","display_name":"Energy landscape","score":0.8022974729537964},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.7015012502670288},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.6556844711303711},{"id":"https://openalex.org/keywords/folding","display_name":"Folding (DSP implementation)","score":0.6504522562026978},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6182588338851929},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.5328109264373779},{"id":"https://openalex.org/keywords/reaction-coordinate","display_name":"Reaction coordinate","score":0.49689605832099915},{"id":"https://openalex.org/keywords/downhill-folding","display_name":"Downhill folding","score":0.4853338301181793},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.4838787317276001},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4548812508583069},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45396101474761963},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4477701485157013},{"id":"https://openalex.org/keywords/statistical-physics","display_name":"Statistical physics","score":0.4301038682460785},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.31319573521614075},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2921604514122009},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2872309982776642},{"id":"https://openalex.org/keywords/phi-value-analysis","display_name":"Phi value analysis","score":0.25962120294570923},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15878704190254211},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.09277647733688354},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09013080596923828},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.07990095019340515}],"concepts":[{"id":"https://openalex.org/C119621388","wikidata":"https://www.wikidata.org/wiki/Q5377166","display_name":"Energy landscape","level":2,"score":0.8022974729537964},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.7015012502670288},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.6556844711303711},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6504522562026978},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6182588338851929},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.5328109264373779},{"id":"https://openalex.org/C18553476","wikidata":"https://www.wikidata.org/wiki/Q1076414","display_name":"Reaction coordinate","level":2,"score":0.49689605832099915},{"id":"https://openalex.org/C46449900","wikidata":"https://www.wikidata.org/wiki/Q5303170","display_name":"Downhill folding","level":4,"score":0.4853338301181793},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.4838787317276001},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4548812508583069},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45396101474761963},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4477701485157013},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.4301038682460785},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.31319573521614075},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2921604514122009},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2872309982776642},{"id":"https://openalex.org/C162203774","wikidata":"https://www.wikidata.org/wiki/Q7181581","display_name":"Phi value analysis","level":3,"score":0.25962120294570923},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15878704190254211},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.09277647733688354},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09013080596923828},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.07990095019340515},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C46141821","wikidata":"https://www.wikidata.org/wiki/Q209402","display_name":"Nuclear magnetic resonance","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"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":"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":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018909","descriptor_name":"src Homology Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018909","descriptor_name":"src Homology Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018909","descriptor_name":"src Homology Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1073/pnas.0603553103","is_oa":false,"landing_page_url":"https://doi.org/10.1073/pnas.0603553103","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},{"id":"pmid:16785435","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16785435","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":"Proceedings of the National Academy of Sciences of the United States of America","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:475938","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1502548","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1502548","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1502548","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Proc Natl Acad Sci U S A","raw_type":"Text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.434.6264","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.434.6264","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.kavrakilab.org/sites/default/files/das2006low-dim-land-folding-dim-reduction.pdf","raw_type":"text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:1502548","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1502548","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Proc Natl Acad Sci U S A","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.6600000262260437,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2809669130","display_name":"CRI:  Acquisition of Rice Physical and Biological Computing (PBC) Cluster","funder_award_id":"0454333","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3677753297","display_name":"CAREER: Holistic Approach to the Study of Protein Mechanisms","funder_award_id":"0349303","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7588286486","display_name":"ITR: Representations and Algorithms for Deformable Objects","funder_award_id":"0205671","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G920019786","display_name":"MRI:  Acquisition of CITI Terascale Cluster (CTC)","funder_award_id":"0216467","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W101236918","https://openalex.org/W1506342804","https://openalex.org/W1506690472","https://openalex.org/W1554174647","https://openalex.org/W1598956036","https://openalex.org/W1599657075","https://openalex.org/W1829737394","https://openalex.org/W1964286936","https://openalex.org/W1964556356","https://openalex.org/W1968408173","https://openalex.org/W1970440715","https://openalex.org/W1972317081","https://openalex.org/W1991591212","https://openalex.org/W1993321394","https://openalex.org/W1996636262","https://openalex.org/W2001141328","https://openalex.org/W2001773296","https://openalex.org/W2012429795","https://openalex.org/W2027384625","https://openalex.org/W2028660585","https://openalex.org/W2030148200","https://openalex.org/W2030457014","https://openalex.org/W2040169601","https://openalex.org/W2049277949","https://openalex.org/W2049558868","https://openalex.org/W2051039246","https://openalex.org/W2051116535","https://openalex.org/W2053186076","https://openalex.org/W2054543766","https://openalex.org/W2057022167","https://openalex.org/W2065065181","https://openalex.org/W2065864578","https://openalex.org/W2071075252","https://openalex.org/W2073623394","https://openalex.org/W2078455576","https://openalex.org/W2091983181","https://openalex.org/W2092181851","https://openalex.org/W2095411560","https://openalex.org/W2097308346","https://openalex.org/W2098693229","https://openalex.org/W2131578092","https://openalex.org/W2133753659","https://openalex.org/W2135463994","https://openalex.org/W2138451337","https://openalex.org/W2140565568","https://openalex.org/W2140721561","https://openalex.org/W2145326890","https://openalex.org/W2146332813","https://openalex.org/W2146598193","https://openalex.org/W2146967264","https://openalex.org/W2147396853","https://openalex.org/W2156287497","https://openalex.org/W2158476854","https://openalex.org/W2161859154","https://openalex.org/W2162251926","https://openalex.org/W2168546474","https://openalex.org/W2178063079","https://openalex.org/W2999905431","https://openalex.org/W3145128584","https://openalex.org/W4292023222"],"related_works":["https://openalex.org/W1994742030","https://openalex.org/W2476476683","https://openalex.org/W1974862140","https://openalex.org/W1649895068","https://openalex.org/W2049509393","https://openalex.org/W2057022167","https://openalex.org/W2021938401","https://openalex.org/W2163814597","https://openalex.org/W1641469383","https://openalex.org/W2136249024"],"abstract_inverted_index":{"The":[0,82,106],"definition":[1],"of":[2,8,58,72,103,114,137],"reaction":[3,11],"coordinates":[4,48,91],"for":[5,19],"the":[6,20,30,56,63,88,94,100,104,112,115,119,128],"characterization":[7],"a":[9,15,37,45,68,134,138],"protein-folding":[10],"has":[12],"long":[13],"been":[14],"controversial":[16],"issue,":[17],"even":[18],"\"simple\"":[21],"case":[22],"in":[23],"which":[24],"one":[25],"single":[26],"free-energy":[27,84],"barrier":[28],"separates":[29],"folded":[31],"and":[32],"unfolded":[33],"ensemble.":[34],"We":[35,54],"propose":[36],"general":[38],"approach":[39],"to":[40,43],"this":[41,59],"problem":[42],"obtain":[44],"few":[46,89],"collective":[47],"by":[49,61,78],"using":[50],"nonlinear":[51],"dimensionality":[52,95],"reduction.":[53],"validate":[55],"usefulness":[57],"method":[60,130],"characterizing":[62],"folding":[64,83,116,121],"landscape":[65,85],"associated":[66],"with":[67],"coarse-grained":[69],"protein":[70,143],"model":[71],"src":[73],"homology":[74],"3":[75],"as":[76,142],"sampled":[77],"molecular":[79],"dynamics":[80],"simulations.":[81],"projected":[86],"on":[87],"relevant":[90],"emerging":[92],"from":[93],"reduction":[96],"can":[97,131],"correctly":[98],"identify":[99],"transition-state":[101],"ensemble":[102],"reaction.":[105],"first":[107],"embedding":[108],"dimension":[109],"efficiently":[110,132],"captures":[111],"evolution":[113],"process":[117,140],"along":[118],"main":[120],"route.":[122],"These":[123],"results":[124],"clearly":[125],"show":[126],"that":[127],"proposed":[129],"find":[133],"low-dimensional":[135],"representation":[136],"complex":[139],"such":[141],"folding.":[144]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":21},{"year":2021,"cited_by_count":19},{"year":2020,"cited_by_count":19},{"year":2019,"cited_by_count":27},{"year":2018,"cited_by_count":24},{"year":2017,"cited_by_count":20},{"year":2016,"cited_by_count":15},{"year":2015,"cited_by_count":23},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":18},{"year":2012,"cited_by_count":19}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
