{"doi":"10.1016/j.csbj.2024.09.025","title":"Multiscale molecular modeling of chromatin with MultiMM: From nucleosomes to the whole genome","abstract":"<h2>Abstract</h2> <b>Motivation:</b> We present a user-friendly 3D chromatin simulation model for the human genome based on OpenMM, addressing the challenges posed by existing models with use-specific implementations. Our approach employs a multi-scale energy minimization strategy, capturing chromatin's hierarchical structure. Initiating with a Hilbert curve-based structure, users can input files specifying nucleosome positioning, loops, compartments, or subcompartments. <b>Results:</b> The model utilizes an energy minimization approach with a large choice of numerical integrators, providing the entire genome's structure within minutes. Output files include the generated structures for each chromosome, offering a versatile and accessible tool for chromatin simulation in bioinformatics studies. Furthermore, MultiMM is capable of producing nucleosome-resolution structures by making simplistic geometric assumptions about the structure and the density of nucleosomes on the DNA. <b>Code availability:</b> Open-source software and the manual are freely available on https://github.com/SFGLab/MultiMM or via pip https://pypi.org/project/MultiMM/.","journal":"Computational and Structural Biotechnology Journal","year":2024,"id":466477,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9102,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":910253,"name":"Krzysztof Banecki","orcid":"0000-0001-9573-0804","position":1,"is_corresponding":false},{"id":62171,"name":"Dariusz Plewczyński","orcid":"0000-0002-3840-7610","position":2,"is_corresponding":false},{"id":963307,"name":"Sevastianos Korsak","orcid":"0000-0002-7357-3315","position":0,"is_corresponding":true}],"reference_count":77,"raw_metadata":null,"created_at":"2026-07-19T02:05:06.743102Z","pmid":"39435339","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}