{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T21:48:58Z","timestamp":1791841738106,"version":"4.3.4"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T00:00:00Z","timestamp":1791331200000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Materials and Process Simulation Center at Caltech"},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CBET-2311117"],"award-info":[{"award-number":["CBET-2311117"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>BioForge is the first macromolecular structure preparation library for Rust, complementing sequence-analysis libraries such as Rust-Bio with cleaning, geometry-based missing-atom repair, protonation, and solvation as a force-field-agnostic preprocessing stage. Across 22 structures (1439\u20133\u2009819\u2009839 atoms) on a single CPU core, BioForge scales linearly in wall time (fitted N0.89) versus super-linear N1.17 for PDBFixer and N1.25 for PDB2PQR, completing the 3.8M-atom 9MJN in 5.1\u2009s at 1.1 GB peak (PDBFixer: error, 273 GB); PDB2PQR is limited to fewer than 100\u2009000 atoms. BioForge also compiles to WebAssembly for browser deployment and supports direct embedding into simulation and parameterization pipelines via its application programming interface.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>An MIT-licensed Rust library crate (bio-forge) and a WebAssembly package (bio-forge-wasm) extend the Rust bioinformatics ecosystem with structure preparation, both published on https:\/\/crates.io and NPM respectively; the same WebAssembly binary powers a client-side web application at https:\/\/bio-forge.app that runs entirely in the browser without a server or data upload. Source code and precompiled command-line binaries are freely available at https:\/\/github.com\/TKanX\/bio-forge; an archival snapshot of the version used for all reported experiments is deposited at Zenodo (https:\/\/doi.org\/10.5281\/zenodo.21627953).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag616","type":"journal-article","created":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T11:55:22Z","timestamp":1791374122000},"source":"Crossref","is-referenced-by-count":0,"title":["BioForge: a fast and safe macromolecular structure preparation library in Rust"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-8671-1152","authenticated-orcid":false,"given":"Tony","family":"Kan","sequence":"first","affiliation":[{"name":"Materials and Process Simulation Center, Beckman Institute, California Institute of Technology , Pasadena, CA 91125,","place":["United 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California Institute of Technology , Pasadena, CA 91125,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-7392-1757","authenticated-orcid":false,"given":"Yixin C","family":"Xu","sequence":"additional","affiliation":[{"name":"Materials and Process Simulation Center, Beckman Institute, California Institute of Technology , Pasadena, CA 91125,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sejun","family":"Kim","sequence":"additional","affiliation":[{"name":"Materials and Process Simulation Center, Beckman Institute, California Institute of Technology , Pasadena, CA 91125,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0097-5716","authenticated-orcid":false,"suffix":"III","given":"William A","family":"Goddard","sequence":"additional","affiliation":[{"name":"Materials and Process Simulation Center, 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