{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:22Z","timestamp":1772138062954,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,2,23]],"date-time":"2024-02-23T00:00:00Z","timestamp":1708646400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001502","name":"Department of Atomic Energy","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001502","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100021014","name":"Department of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100021014","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Science Engineering and Research Board","award":["SPG\/2020\/000475"],"award-info":[{"award-number":["SPG\/2020\/000475"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Integrative structural modeling combines data from experiments, physical principles, statistics of previous structures, and prior models to obtain structures of macromolecular assemblies that are challenging to characterize experimentally. The choice of model representation is a key decision in integrative modeling, as it dictates the accuracy of scoring, efficiency of sampling, and resolution of analysis. But currently, the choice is usually made ad hoc, manually.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we report NestOR (Nested Sampling for Optimizing Representation), a fully automated, statistically rigorous method based on Bayesian model selection to identify the optimal coarse-grained representation for a given integrative modeling setup. Given an integrative modeling setup, it determines the optimal representations from given candidate representations based on their model evidence and sampling efficiency. The performance of NestOR was evaluated on a benchmark of four macromolecular assemblies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>NestOR is implemented in the Integrative Modeling Platform (https:\/\/integrativemodeling.org) and is available at https:\/\/github.com\/isblab\/nestor. Data for the benchmark is at https:\/\/www.doi.org\/10.5281\/zenodo.10360718.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae106","type":"journal-article","created":{"date-parts":[[2024,2,21]],"date-time":"2024-02-21T00:41:06Z","timestamp":1708476066000},"source":"Crossref","is-referenced-by-count":8,"title":["Optimizing representations for integrative structural modeling using Bayesian model selection"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9945-8534","authenticated-orcid":false,"given":"Shreyas","family":"Arvindekar","sequence":"first","affiliation":[{"name":"National Center for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-2821-7243","authenticated-orcid":false,"given":"Aditi S","family":"Pathak","sequence":"additional","affiliation":[{"name":"National Center for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-3190-7977","authenticated-orcid":false,"given":"Kartik","family":"Majila","sequence":"additional","affiliation":[{"name":"National Center for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9061-8407","authenticated-orcid":false,"given":"Shruthi","family":"Viswanath","sequence":"additional","affiliation":[{"name":"National Center for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India"}]}],"member":"286","published-online":{"date-parts":[[2024,2,23]]},"reference":[{"key":"2024030911145259600_btae106-B1","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1038\/nature06404","article-title":"Determining the architectures of macromolecular assemblies","volume":"450","author":"Alber","year":"2007","journal-title":"Nature"},{"key":"2024030911145259600_btae106-B2","doi-asserted-by":"crossref","first-page":"7131","DOI":"10.1074\/jbc.M413038200","article-title":"Structures of complete RNA polymerase II and its subcomplex, Rpb4\/7","volume":"280","author":"Armache","year":"2005","journal-title":"J Biol Chem"},{"key":"2024030911145259600_btae106-B3","doi-asserted-by":"crossref","first-page":"e4387","DOI":"10.1002\/pro.4387","article-title":"Molecular architecture of nucleosome remodeling and deacetylase Sub-complexes by integrative structure determination","volume":"31","author":"Arvindekar","year":"2022","journal-title":"Protein Sci"},{"key":"2024030911145259600_btae106-B4","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1038\/s43586-022-00121-x","article-title":"Nested sampling for physical scientists","volume":"2","author":"Ashton","year":"2022","journal-title":"Nat Rev Methods Primers"},{"key":"2024030911145259600_btae106-B5","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.str.2018.09.011","article-title":"Bayesian weighing of electron cryo-microscopy data for integrative structural modeling","volume":"27","author":"Bonomi","year":"2019","journal-title":"Structure"},{"key":"2024030911145259600_btae106-B6","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1016\/j.sbi.2016.12.004","article-title":"Principles of protein structural ensemble determination","volume":"42","author":"Bonomi","year":"2017","journal-title":"Curr Opin Struct Biol"},{"key":"2024030911145259600_btae106-B7","doi-asserted-by":"crossref","first-page":"e65168","DOI":"10.7554\/eLife.65168","article-title":"CM1-driven assembly and activation of yeast \u03b3-tubulin small complex underlies microtubule nucleation","volume":"10","author":"Brilot","year":"2021","journal-title":"Elife"},{"key":"2024030911145259600_btae106-B8","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1214\/23-SS144","article-title":"Nested sampling methods","volume":"17","author":"Buchner","year":"2023","journal-title":"Stat Surv"},{"key":"2024030911145259600_btae106-B9","doi-asserted-by":"crossref","first-page":"7824","DOI":"10.1073\/pnas.1910364117","article-title":"Bayesian inference of chromatin structure ensembles from population-averaged contact data","volume":"117","author":"Carstens","year":"2020","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024030911145259600_btae106-B10","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1111\/j.1365-2966.2007.12353.x","article-title":"Multimodal nested sampling: an efficient and robust alternative to Markov Chain Monte Carlo methods for astronomical data analyses","volume":"384","author":"Feroz","year":"2008","journal-title":"Monthly Notices R Astronomical Soc"},{"key":"2024030911145259600_btae106-B11","doi-asserted-by":"crossref","first-page":"5610","DOI":"10.1021\/acs.jpcb.7b11871","article-title":"Model selection using BICePs: a bayesian approach for force field validation and parameterization","volume":"122","author":"Ge","year":"2018","journal-title":"J Phys Chem B"},{"key":"2024030911145259600_btae106-B12","first-page":"486","author":"Habeck","year":"2012"},{"key":"2024030911145259600_btae106-B13","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1515\/hsz-2023-0145","article-title":"Bayesian methods in integrative structure modeling","volume":"404","author":"Habeck","year":"2023","journal-title":"Biol Chem"},{"key":"2024030911145259600_btae106-B14","doi-asserted-by":"crossref","first-page":"891","DOI":"10.1007\/s11222-018-9844-0","article-title":"Dynamic nested sampling: an improved algorithm for parameter estimation and evidence calculation","volume":"29","author":"Higson","year":"2019","journal-title":"Stat Comput"},{"key":"2024030911145259600_btae106-B15","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1017\/S030500410001330X","article-title":"Some tests of significance, treated by the theory of probability","volume":"31","author":"Jeffreys","year":"1935","journal-title":"Math Proc Camb Phil Soc"},{"key":"2024030911145259600_btae106-B16","doi-asserted-by":"crossref","first-page":"L51","DOI":"10.1086\/501068","article-title":"A nested sampling algorithm for cosmological model selection","volume":"638","author":"Mukherjee","year":"2006","journal-title":"ApJ"},{"key":"2024030911145259600_btae106-B17","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1093\/sysbio\/syz003","article-title":"Marginal likelihoods in phylogenetics: a review of methods and applications","volume":"68","author":"Oaks","year":"2019","journal-title":"Syst Biol"},{"key":"2024030911145259600_btae106-B18","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.3390\/life11111183","article-title":"A framework for stochastic optimization of parameters for integrative modeling of macromolecular assemblies","volume":"11","author":"Pasani","year":"2021","journal-title":"Life"},{"key":"2024030911145259600_btae106-B19","doi-asserted-by":"crossref","first-page":"e1006641","DOI":"10.1371\/journal.pcbi.1006641","article-title":"Bayesian inference of protein conformational ensembles from limited structural data","volume":"14","author":"Potrzebowski","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2024030911145259600_btae106-B20","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1016\/j.cell.2019.05.016","article-title":"Principles for integrative structural biology studies","volume":"177","author":"Rout","year":"2019","journal-title":"Cell"},{"key":"2024030911145259600_btae106-B21","doi-asserted-by":"crossref","first-page":"e1001244","DOI":"10.1371\/journal.pbio.1001244","article-title":"Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies","volume":"10","author":"Russel","year":"2012","journal-title":"PLoS Biol"},{"key":"2024030911145259600_btae106-B22","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1093\/sysbio\/syy050","article-title":"Model selection and parameter inference in phylogenetics using nested sampling","volume":"68","author":"Russel","year":"2019","journal-title":"Syst Biol"},{"key":"2024030911145259600_btae106-B23","doi-asserted-by":"crossref","first-page":"100743","DOI":"10.1016\/j.jbc.2021.100743","article-title":"From integrative structural biology to cell biology","volume":"296","author":"Sali","year":"2021","journal-title":"J Biol Chem"},{"key":"2024030911145259600_btae106-B24","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1002\/pro.3995","article-title":"Using integrative modeling platform to compute, validate, and archive a model of a protein complex structure","volume":"30","author":"Saltzberg","year":"2021","journal-title":"Protein Sci"},{"key":"2024030911145259600_btae106-B25","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.sbi.2014.08.001","article-title":"Uncertainty in integrative structural modeling","volume":"28","author":"Schneidman-Duhovny","year":"2014","journal-title":"Curr Opin Struct Biol"},{"key":"2024030911145259600_btae106-B26","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1111\/j.1365-2966.2007.11871.x","article-title":"Efficient bayesian inference for multimodal problems in cosmology","volume":"378","author":"Shaw","year":"2007","journal-title":"Monthly Notices R Astronomical Soc"},{"key":"2024030911145259600_btae106-B27","doi-asserted-by":"crossref","first-page":"2927","DOI":"10.1074\/mcp.M114.041673","article-title":"Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex","volume":"13","author":"Shi","year":"2014","journal-title":"Mol Cell Proteomics"},{"key":"2024030911145259600_btae106-B28","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1063\/1.1835238","article-title":"Nested sampling","volume":"735","author":"Skilling","year":"2004","journal-title":"AIP Conf Proc"},{"key":"2024030911145259600_btae106-B29","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1214\/06-BA127","article-title":"Nested sampling for general Bayesian computation","volume":"1","author":"Skilling","year":"2006","journal-title":"Bayesian Anal"},{"key":"2024030911145259600_btae106-B30","doi-asserted-by":"crossref","first-page":"3837","DOI":"10.1093\/bioinformatics\/btac400","article-title":"PrISM: precision for integrative structural models","volume":"38","author":"Ullanat","year":"2022","journal-title":"Bioinformatics"},{"key":"2024030911145259600_btae106-B31","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1016\/j.str.2018.03.011","article-title":"Development of a prototype system for archiving integrative\/hybrid structure models of biological macromolecules","volume":"26","author":"Vallat","year":"2018","journal-title":"Structure"},{"key":"2024030911145259600_btae106-B32","doi-asserted-by":"crossref","first-page":"2344","DOI":"10.1016\/j.bpj.2017.10.005","article-title":"Assessing exhaustiveness of stochastic sampling for integrative modeling of macromolecular structures","volume":"113","author":"Viswanath","year":"2017","journal-title":"Biophys J"},{"key":"2024030911145259600_btae106-B33","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1073\/pnas.1814649116","article-title":"Optimizing model representation for integrative structure determination of macromolecular assemblies","volume":"116","author":"Viswanath","year":"2019","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024030911145259600_btae106-B34","doi-asserted-by":"crossref","first-page":"661520","DOI":"10.3389\/fmolb.2021.661520","article-title":"Reconciling simulations and experiments with BICePs: a review","volume":"8","author":"Voelz","year":"2021","journal-title":"Front Mol Biosci"},{"key":"2024030911145259600_btae106-B35","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1093\/sysbio\/syq085","article-title":"Improving marginal likelihood estimation for Bayesian phylogenetic model selection","volume":"60","author":"Xie","year":"2011","journal-title":"Syst Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btae106\/56746263\/btae106.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/3\/btae106\/56912785\/btae106.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/40\/3\/btae106\/56912785\/btae106.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,9]],"date-time":"2024-03-09T06:15:35Z","timestamp":1709964935000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btae106\/7613065"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2024,2,23]]},"references-count":35,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,3,4]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btae106","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2023.12.12.571227","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,3,1]]},"published":{"date-parts":[[2024,2,23]]},"article-number":"btae106"}}