{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T13:08:37Z","timestamp":1788872917772,"version":"build-2803163510"},"reference-count":56,"publisher":"American Chemical Society (ACS)","issue":"17","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100000165","name":"Division of Chemistry","doi-asserted-by":"publisher","award":["CHE-2154834"],"award-info":[{"award-number":["CHE-2154834"]}],"id":[{"id":"10.13039\/100000165","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM148622"],"award-info":[{"award-number":["R01GM148622"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Understanding protein conformational dynamics is essential for elucidating biological function but remains challenging due to the wide range of time scales and the complexity of collective motions. Enhanced sampling methods overcome time scale limitations of conventional molecular dynamics, yet their effectiveness depends on the choice of collective variables (CVs), which are often difficult to define and may lack physical interpretability. In particular, collective variables derived from machine learning or collective vibrational modes can efficiently capture slow dynamics but are not easily mapped onto intuitive structural descriptors. Here, we present a fully automated framework that transforms enhanced sampling trajectories into human-readable representations of protein dynamics. Our approach combines enhanced sampling along CVs derived from frequency-selective anharmonic mode analysis with a post hoc analysis of biased trajectories using weighted dynamic cross-correlation matrices. From these, we identify residue pairs and domains exhibiting correlated and anticorrelated motions, yielding simple domain\u2013domain distances that serve as physically interpretable CVs. We apply this method to five proteins, including KRAS and HIV-1 protease, and show that it consistently identifies biologically relevant domains and motions without prior system-specific knowledge. Projection onto these distances produces free energy surfaces that reproduce known conformational states with low statistical uncertainty while maximizing independent dynamical information. This workflow enables systematic recasting of complex CVs into simple geometric descriptors without loss of essential dynamics. Its generality and automation make it broadly applicable for interpreting enhanced sampling simulations and generating interpretable conformational ensembles for integration with emerging machine learning approaches.<\/jats:p>","DOI":"10.1021\/acs.jctc.6c00914","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T11:36:23Z","timestamp":1788262583000},"page":"9145-9153","source":"Crossref","is-referenced-by-count":0,"title":["From Enhanced Sampling\nto Human-Readable Representations\nof Protein Dynamics"],"prefix":"10.1021","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5225-6233","authenticated-orcid":true,"given":"Souvik","family":"Mondal","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael A.","family":"Sauer","sequence":"additional","affiliation":[{"name":"Arizona State University , , , ,","place":["Tempe, Arizona, United States, 85287"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7956-5287","authenticated-orcid":true,"given":"Matthias","family":"Heyden","sequence":"additional","affiliation":[{"name":"Arizona State University , , , ,","place":["Tempe, Arizona, United States, 85287"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,26]]},"reference":[{"key":"2026090808095876900_cit1","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1038\/nature06522","article-title":"Dynamic personalities of proteins","volume":"450","author":"Henzler-Wildman","year":"2007","journal-title":"Nature"},{"key":"2026090808095876900_cit2","doi-asserted-by":"publisher","first-page":"14637","DOI":"10.1021\/bi020574b","article-title":"Proline cis- trans\nisomerization\nand protein folding","volume":"41","author":"Wedemeyer","year":"2002","journal-title":"Biochemistry"},{"key":"2026090808095876900_cit3","doi-asserted-by":"publisher","first-page":"3055","DOI":"10.1021\/cr050312q","article-title":"An NMR perspective on enzyme dynamics","volume":"106","author":"Boehr","year":"2006","journal-title":"Chem. Rev."},{"key":"2026090808095876900_cit4","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1038\/nsb0902-646","article-title":"Molecular dynamics\nsimulations of biomolecules","volume":"9","author":"Karplus","year":"2002","journal-title":"Nat. Struct. Biol."},{"key":"2026090808095876900_cit5","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1146\/annurev-biophys-042910-155245","article-title":"Biomolecular\nsimulation: A computational microscope for molecular biology","volume":"41","author":"Dror","year":"2012","journal-title":"Annu. Rev. Biophys."},{"key":"2026090808095876900_cit6","doi-asserted-by":"crossref","unstructured":"Shaw, D. E.; Adams, P. J.; Azaria, A.; Bank, J. A.; Batson, B.; Bell, A.; Bergdorf, M.; Bhatt, J.; Butts, J. A.; Correia, T.; et al.; Anton 3: Twenty microseconds of molecular\ndynamics simulation before lunch.  Proceedings\nof the International Conference for High Performance Computing, Networking,\nStorage and Analysis, 2021, pp 1\u201311.","DOI":"10.1145\/3458817.3487397"},{"key":"2026090808095876900_cit7","doi-asserted-by":"publisher","first-page":"1885","DOI":"10.1038\/s41467-023-36956-5","article-title":"Structural mechanism\nof a drug-binding process involving\na large conformational change of the protein target","volume":"14","author":"Ayaz","year":"2023","journal-title":"Nat. Commun."},{"key":"2026090808095876900_cit8","doi-asserted-by":"publisher","first-page":"2644","DOI":"10.1021\/acs.jcim.3c00236","article-title":"Discovery and Validation of the Binding Poses of Allosteric\nFragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics\nSimulations to X-ray Crystallography","volume":"63","author":"Greisman","year":"2023","journal-title":"J. Chem.\nInf. and Model"},{"key":"2026090808095876900_cit9","doi-asserted-by":"publisher","DOI":"10.1126\/science.adv9817","article-title":"Scalable emulation of protein equilibrium ensembles\nwith generative deep learning","volume":"389","author":"Lewis","year":"2025","journal-title":"Science"},{"key":"2026090808095876900_cit10","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1016\/j.bbagen.2014.10.019","article-title":"Enhanced sampling techniques\nin molecular\ndynamics simulations of biological systems","volume":"1850","author":"Bernardi","year":"2015","journal-title":"Biochim. Biophys. Acta Gen. Subj."},{"key":"2026090808095876900_cit11","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1002\/1097-0282(2001)60:2&lt;96::AID-BIP1007&gt;3.0.CO;2-F","article-title":"Generalized-ensemble\nalgorithms for\nmolecular simulations of biopolymers","volume":"60","author":"Mitsutake","year":"2001","journal-title":"Biomolecules"},{"key":"2026090808095876900_cit12","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1016\/0021-9991(77)90121-8","article-title":"Nonphysical sampling\ndistributions in Monte Carlo free-energy\nestimation: Umbrella sampling","volume":"23","author":"Torrie","year":"1977","journal-title":"J. Comput. Phys."},{"key":"2026090808095876900_cit13","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1016\/S1093-3263(00)00133-9","article-title":"Steered molecular\ndynamics investigations of protein function","volume":"19","author":"Isralewitz","year":"2001","journal-title":"J. Mol. Graph. Model."},{"key":"2026090808095876900_cit14","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/0263-7855(94)80072-3","article-title":"Targeted molecular\ndynamics: a new\napproach for searching pathways of conformational transitions","volume":"12","author":"Schlitter","year":"1994","journal-title":"J. Mol. Graph."},{"key":"2026090808095876900_cit15","doi-asserted-by":"publisher","first-page":"2904","DOI":"10.1063\/1.1773132","article-title":"Overcoming free energy\nbarriers using unconstrained\nmolecular dynamics simulations","volume":"121","author":"He\u0301nin","year":"2004","journal-title":"J. Chem. Phys."},{"key":"2026090808095876900_cit16","doi-asserted-by":"publisher","first-page":"12562","DOI":"10.1073\/pnas.202427399","article-title":"Escaping free-energy minima","volume":"99","author":"Laio","year":"2002","journal-title":"Proc. Natl. Acad. Sci. 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Chem."},{"key":"2026090808095876900_cit20","doi-asserted-by":"publisher","first-page":"3696","DOI":"10.1073\/pnas.80.12.3696","article-title":"Dynamics of\na small globular protein\nin terms of low-frequency vibrational modes","volume":"80","author":"Go","year":"1983","journal-title":"Proc. Natl. Acad. Sci. U.S.A"},{"key":"2026090808095876900_cit21","doi-asserted-by":"publisher","first-page":"1129","DOI":"10.1093\/protein\/8.11.1129","article-title":"Essential\ndynamics of the cellular retinol-binding protein evidence for ligand-induced\nconformational changes","volume":"8","author":"Aalten","year":"1995","journal-title":"Protein Eng."},{"key":"2026090808095876900_cit22","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1002\/prot.340230207","article-title":"Harmonicity\nand anharmonicity in\nprotein dynamics: a normal mode analysis and principal component analysis","volume":"23","author":"Hayward","year":"1995","journal-title":"Proteins. Struct. Funct. Bioinf."},{"key":"2026090808095876900_cit23","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1016\/j.str.2005.02.002","article-title":"Usefulness\nand limitations of normal mode analysis in modeling dynamics of biomolecular\ncomplexes","volume":"13","author":"Ma","year":"2005","journal-title":"Structure"},{"key":"2026090808095876900_cit24","doi-asserted-by":"publisher","first-page":"5481","DOI":"10.1021\/acs.jctc.2c01309","article-title":"Frequency-Selective Anharmonic Mode\nAnalysis of Thermally\nExcited Vibrations in Proteins","volume":"19","author":"Sauer","year":"2023","journal-title":"J. Chem. Theory\nComput."},{"key":"2026090808095876900_cit25","doi-asserted-by":"publisher","first-page":"2696","DOI":"10.1103\/PhysRevLett.68.2696","article-title":"Large-amplitude\nnonlinear motions in proteins","volume":"68","author":"Garci\u0301a","year":"1992","journal-title":"Phys. Rev. Lett."},{"key":"2026090808095876900_cit26","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1002\/prot.340170408","article-title":"Essential\ndynamics of proteins","volume":"17","author":"Amadei","year":"1993","journal-title":"Proteins Struct. Funct.\nBioinf."},{"key":"2026090808095876900_cit27","doi-asserted-by":"publisher","first-page":"215102","DOI":"10.1063\/1.4834695","article-title":"Slow dynamics\nof a protein backbone in molecular dynamics\nsimulation revealed by time-structure based independent component\nanalysis","volume":"139","author":"Naritomi","year":"2013","journal-title":"J. Chem. Phys."},{"key":"2026090808095876900_cit28","doi-asserted-by":"publisher","first-page":"5002","DOI":"10.1021\/acs.jctc.5b00553","article-title":"Kinetic distance\nand kinetic maps from molecular dynamics\nsimulation","volume":"11","author":"Noe\u0301","year":"2015","journal-title":"J. Chem. Theory Comput."},{"key":"2026090808095876900_cit29","doi-asserted-by":"publisher","DOI":"10.1080\/00268976.2020.1737742","article-title":"Machine Learning\nfor Collective Variable\nDiscovery and Enhanced Sampling in Biomolecular Simulation","volume":"118","author":"Sidky","year":"2020","journal-title":"Mol. Phys."},{"key":"2026090808095876900_cit30","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.sbi.2019.12.016","article-title":"Machine learning approaches for analyzing\nand enhancing molecular dynamics simulations","volume":"61","author":"Wang","year":"2020","journal-title":"Curr. Opin. Struct. Biol."},{"key":"2026090808095876900_cit31","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1146\/annurev-physchem-042018-052331","article-title":"Machine Learning for\nMolecular Simulation","volume":"71","author":"Noe\u0301","year":"2020","journal-title":"Annu. Rev. Phys. Chem."},{"key":"2026090808095876900_cit32","doi-asserted-by":"publisher","first-page":"164101","DOI":"10.1063\/5.0258483","article-title":"Data efficient learning\nof molecular slow modes from nonequilibrium\nmetadynamics","volume":"162","author":"Hanni","year":"2025","journal-title":"J. Chem. Phys."},{"key":"2026090808095876900_cit33","doi-asserted-by":"publisher","first-page":"1774","DOI":"10.1021\/acs.jpclett.3c03542","article-title":"Collective Variable-based\nEnhanced Sampling: From Human Learning to Machine Learning","volume":"15","author":"Fu","year":"2024","journal-title":"J. Phys. Chem. Lett."},{"key":"2026090808095876900_cit34","doi-asserted-by":"publisher","first-page":"174109","DOI":"10.1063\/5.0202156","article-title":"Deep Learning Path-like\nCollective Variable for Enhanced sampling molecular dynamics","volume":"160","author":"Fro\u0308hlking","year":"2024","journal-title":"J. Chem. Phys."},{"key":"2026090808095876900_cit35","doi-asserted-by":"publisher","first-page":"7112","DOI":"10.1021\/acs.jpcb.4c02743","article-title":"Exploring\nConformational Landscapes\nAlong Anharmonic Low-Frequency Vibrations","volume":"128","author":"Mondal","year":"2024","journal-title":"J.\nPhys. Chem. B"},{"key":"2026090808095876900_cit36","doi-asserted-by":"publisher","first-page":"10739","DOI":"10.1021\/acs.jpcb.5c04622","article-title":"High-Throughput Computation\nof Anharmonic Low-Frequency Protein Vibrations","volume":"129","author":"Sauer","year":"2025","journal-title":"J. Phys. Chem. B"},{"key":"2026090808095876900_cit37","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.aea4617","article-title":"Fast sampling\nof protein conformational dynamics","volume":"12","author":"Sauer","year":"2026","journal-title":"Sci. Adv."},{"key":"2026090808095876900_cit38","doi-asserted-by":"publisher","first-page":"arXiv:2601.02699","DOI":"10.48550\/arXiv.2601.02699","article-title":"Protein-Water Energy Transfer via\nAnharmonic Low-Frequency\nVibrations","author":"Neff","year":"2026","journal-title":"arXiv"},{"key":"2026090808095876900_cit39","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1088\/0034-4885\/47\/1\/001","article-title":"Protein dynamics","volume":"47","author":"McCammon","year":"1984","journal-title":"Rep. Prog. Phys."},{"key":"2026090808095876900_cit40","doi-asserted-by":"publisher","first-page":"736","DOI":"10.1021\/jp504920s","article-title":"A time-independent\nfree energy estimator for metadynamics","volume":"119","author":"Tiwary","year":"2015","journal-title":"J. Phys.\nChem. B"},{"key":"2026090808095876900_cit41","doi-asserted-by":"publisher","first-page":"915","DOI":"10.1073\/pnas.0508452103","article-title":"HIV-1 protease\nflaps spontaneously open and reclose in molecular dynamics simulations","volume":"103","author":"Hornak","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U.S.A"},{"key":"2026090808095876900_cit42","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1016\/j.csbj.2019.12.004","article-title":"The current\nunderstanding of KRAS protein structure and dynamics","volume":"18","author":"Pantsar","year":"2020","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"2026090808095876900_cit43","doi-asserted-by":"publisher","first-page":"5599","DOI":"10.3390\/cancers13225599","article-title":"Oncogenic\nKRAS:\nsignaling and drug resistance","volume":"13","author":"Kim","year":"2021","journal-title":"Cancers"},{"key":"2026090808095876900_cit44","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1021\/acs.jctc.2c00599","article-title":"MDexciteR: Enhanced\nSampling Molecular Dynamics by Excited Normal Modes or Principal Components\nObtained from Experiments","volume":"19","author":"Costa","year":"2023","journal-title":"J. Chem. Theory Comput."},{"key":"2026090808095876900_cit45","doi-asserted-by":"publisher","first-page":"1853","DOI":"10.1021\/acs.jctc.7b01226","article-title":"Replica exchange Gaussian\naccelerated\nmolecular dynamics: Improved enhanced sampling and free energy calculation","volume":"14","author":"Huang","year":"2018","journal-title":"J. Chem. Theory Comput."},{"key":"2026090808095876900_cit46","doi-asserted-by":"publisher","first-page":"2898","DOI":"10.1021\/acs.jpcb.0c11600","article-title":"Unraveling\nthe coupling between conformational changes and ligand binding in\nribose binding protein using multiscale molecular dynamics and free-energy\ncalculations","volume":"125","author":"Ren","year":"2021","journal-title":"J. Phys. Chem. B"},{"key":"2026090808095876900_cit47","doi-asserted-by":"publisher","first-page":"3172","DOI":"10.1021\/acs.jcim.0c00315","article-title":"Insights into\nMcl-1 conformational states and allosteric inhibition mechanism from\nmolecular dynamics simulations, enhanced sampling, and pocket crosstalk\nanalysis","volume":"60","author":"Benabderrahmane","year":"2020","journal-title":"J. Chem. Inf. Model."},{"key":"2026090808095876900_cit48","doi-asserted-by":"publisher","first-page":"6571","DOI":"10.1073\/pnas.80.21.6571","article-title":"Harmonic dynamics of proteins: normal\nmodes and fluctuations\nin bovine pancreatic trypsin inhibitor","volume":"80","author":"Brooks","year":"1983","journal-title":"Proc.\nNatl. Acad. Sci. U.S.A"},{"key":"2026090808095876900_cit49","doi-asserted-by":"publisher","first-page":"072301","DOI":"10.1063\/1.5025487","article-title":"Reweighted autoencoded\nvariational Bayes for enhanced sampling (RAVE)","volume":"149","author":"Ribeiro","year":"2018","journal-title":"J. Chem. Phys."},{"key":"2026090808095876900_cit50","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1038\/s41467-019-11405-4","article-title":"Past\u2013future\ninformation bottleneck\nfor sampling molecular reaction coordinate simultaneously with thermodynamics\nand kinetics","volume":"10","author":"Wang","year":"2019","journal-title":"Nat. Commun."},{"key":"2026090808095876900_cit51","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1021\/acs.jcim.4c01022","article-title":"FESTA: A Polygon-Based Approach for Extracting Relevant\nStructures from Free Energy Surfaces Obtained in Molecular Simulations","volume":"65","author":"Istomin","year":"2025","journal-title":"J. Chem. Inf. Model."},{"key":"2026090808095876900_cit52","doi-asserted-by":"publisher","first-page":"1561","DOI":"10.1021\/acs.jctc.4c01603","article-title":"Acceleration with interpretability:\nA surrogate model-based collective\nvariable for enhanced sampling","volume":"21","author":"Chatterjee","year":"2025","journal-title":"J. Chem. Theory\nComput."},{"key":"2026090808095876900_cit53","doi-asserted-by":"publisher","first-page":"6480","DOI":"10.1021\/bi4007513","article-title":"Characterization\nof the interdomain motions in hen lysozyme using residual dipolar\ncouplings as replica-averaged structural restraints in molecular dynamics\nsimulations","volume":"52","author":"De Simone","year":"2013","journal-title":"Biochemistry"},{"key":"2026090808095876900_cit54","doi-asserted-by":"publisher","first-page":"1954","DOI":"10.1021\/acs.jcim.0c01470","article-title":"Mutation-induced impacts on the switch transformations of the GDP-and\nGTP-bound K-ras: insights from multiple replica Gaussian accelerated\nmolecular dynamics and free energy analysis","volume":"61","author":"Chen","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"2026090808095876900_cit55","doi-asserted-by":"publisher","first-page":"020603","DOI":"10.1103\/PhysRevLett.100.020603","article-title":"Well-tempered metadynamics: a smoothly\nconverging and tunable free-energy method","volume":"100","author":"Barducci","year":"2008","journal-title":"Phys.\nRev. Lett."},{"key":"2026090808095876900_cit56","unstructured":"Sauer, M. A.; Mondal, S.; Heyden, M.\n          FRESEAN Metadynamics\nwith Weighted DCCM Analysis, 2026."}],"container-title":["Journal of Chemical Theory\nand Computation"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jctc.6c00914","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jctcce\/article-pdf\/22\/17\/9145\/67425556\/acs.jctc.6c00914.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jctcce\/article-pdf\/22\/17\/9145\/67425556\/acs.jctc.6c00914.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T12:30:53Z","timestamp":1788870653000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jctcce\/article\/22\/17\/9145\/5330338\/From-Enhanced-Sampling-to-Human-Readable"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,26]]},"references-count":56,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,8,26]]},"published-print":{"date-parts":[[2026,9,8]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jctc.6c00914","relation":{},"ISSN":["1549-9618","1549-9626"],"issn-type":[{"value":"1549-9618","type":"print"},{"value":"1549-9626","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,26]]}}}