{"doi":"10.5281/zenodo.8388056","title":"Brownian dynamics simulations of biomolecular diffusional association processes","abstract":"Advanced Review: Brownian dynamics (BD) is a computational method to simulate molecular diffusion<br> processes. Although the BD method has been developed over several<br> decades and is well established, new methodological developments are improving<br> its accuracy, widening its scope, and increasing its application. In biological<br> applications, BD is used to investigate the diffusive behavior of molecules subject<br> to forces due to intermolecular interactions or interactions with material surfaces.<br> BD can be used to compute rate constants for diffusional association, generate<br> structures of encounter complexes for molecular binding partners, and<br> examine the transport properties of geometrically complex molecules. Often, a<br> series of simulations is performed, for example, for different protein mutants or<br> environmental conditions, so that the effects of the changes on diffusional properties<br> can be estimated. While biomolecules are commonly described at atomic<br> resolution and internal molecular motions are typically neglected, coarsegraining<br> and the treatment of conformational flexibility are increasingly<br> employed. Software packages for BD simulations of biomolecules are growing in<br> capabilities, with several new packages providing novel features that expand the<br> range of questions that can be addressed. These advances, when used in concert<br> with experiment or other simulation methods, such as molecular dynamics,<br> open new opportunities for application to biochemical and biological systems.<br> Here, we review some of the latest developments in the theory, methods, software,<br> and applications of BD simulations to study biomolecular diffusional association<br> processes and provide a perspective on their future use and application<br> to outstanding challenges in biology, bioengineering, and biomedicine.","journal":"Zenodo (CERN European Organization for Nuclear Research)","year":2022,"id":291756,"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":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9517,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":896244,"name":"Lane Votapka","orcid":"0000-0002-0865-5867","position":1,"is_corresponding":false},{"id":71085,"name":"Rommie E. Amaro","orcid":"0000-0002-9275-9553","position":2,"is_corresponding":false},{"id":819889,"name":"Rebecca C. Wade","orcid":"0000-0001-5951-8670","position":3,"is_corresponding":false},{"id":896243,"name":"Abraham Muñiz‐Chicharro","orcid":"0000-0002-2598-7687","position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T00:30:38.420009Z","pmid":null,"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":[]}