{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T06:27:44Z","timestamp":1758349664160,"version":"3.44.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,8,4]],"date-time":"2025-08-04T00:00:00Z","timestamp":1754265600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004901","name":"FAPEMIG","doi-asserted-by":"publisher","award":["11839"],"award-info":[{"award-number":["11839"]}],"id":[{"id":"10.13039\/501100004901","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Advances in the prediction of the 3D structures of most known proteins through machine learning have achieved unprecedented accuracies. However, although these computed models are remarkably good, they still challenge accuracy at the atomic level. The Occluded Surface (OS) algorithm is widely used for atomic packing analysis. But it lacks implementations in high-level languages.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce FIBOS, an R and Python package incorporating the OS methodology with enhancements. We show how FIBOS can be used to atomically compare experimental structures and AlphaFold predictions. Although the average packing was similar, AlphaFold models exhibited slightly greater variability, revealing a specific pattern of outliers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>FIBOS can be installed locally as a PyPi Python or CRAN R package, and it is also available at https:\/\/github.com\/insilico-unifei\/fibos-R and https:\/\/github.com\/insilico-unifei\/fibos-py.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf434","type":"journal-article","created":{"date-parts":[[2025,8,4]],"date-time":"2025-08-04T16:25:58Z","timestamp":1754324758000},"source":"Crossref","is-referenced-by-count":0,"title":["FIBOS: R and python packages for analyzing protein packing and structure"],"prefix":"10.1093","volume":"41","author":[{"given":"Herson H M","family":"Soares","sequence":"first","affiliation":[{"name":"Institute of Technological Sciences, Federal University of Itajub\u00e1 , Itabira, 35903-087,","place":["Brazil"]}]},{"given":"Jo\u00e3o P R","family":"Romanelli","sequence":"additional","affiliation":[{"name":"Institute of Applied and Pure Sciences, Federal University of Itajub\u00e1 , Itabira, 35903-087,","place":["Brazil"]}]},{"given":"Patrick J","family":"Fleming","sequence":"additional","affiliation":[{"name":"Thomas C. Jenkins Department of Biophysics, Johns Hopkins University , Baltimore, MD 21218,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6979-8469","authenticated-orcid":false,"given":"Carlos H","family":"da Silveira","sequence":"additional","affiliation":[{"name":"Institute of Technological Sciences, Federal University of Itajub\u00e1 , Itabira, 35903-087,","place":["Brazil"]}]}],"member":"286","published-online":{"date-parts":[[2025,8,4]]},"reference":[{"key":"2025091921100568500_btaf434-B1","doi-asserted-by":"crossref","first-page":"1662","DOI":"10.3390\/ph16121662","article-title":"Quality assessment of selected protein structures derived from homology modeling and AlphaFold","volume":"16","author":"Binbay","year":"2023","journal-title":"Pharmaceuticals"},{"key":"2025091921100568500_btaf434-B2","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1038\/d41586-022-03539-1","article-title":"Alphafold\u2019s new rival? META AI predicts shape of 600 million proteins","volume":"611","author":"Callaway","year":"2022","journal-title":"Nature"},{"key":"2025091921100568500_btaf434-B3","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1002\/prot.22187","article-title":"Protein cutoff scanning: a comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins","volume":"74","author":"da Silveira","year":"2009","journal-title":"Proteins"},{"volume-title":"The PyMOL Molecular Graphics System","year":"2015","author":"DeLano","key":"2025091921100568500_btaf434-B4"},{"key":"2025091921100568500_btaf434-B5","doi-asserted-by":"crossref","first-page":"39085","DOI":"10.1074\/jbc.M306214200","article-title":"The structural determination of an insect sterol carrier protein-2 with a ligand-bound C16 fatty acid at 1.35-\u00c5 resolution","volume":"278","author":"Dyer","year":"2003","journal-title":"J Biol Chem"},{"key":"2025091921100568500_btaf434-B6","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1006\/jmbi.2000.3750","article-title":"Protein packing: dependence on protein size, secondary structure and amino acid composition","volume":"299","author":"Fleming","year":"2000","journal-title":"J Mol Biol"},{"key":"2025091921100568500_btaf434-B7","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1080\/01621459.1974.10482962","article-title":"The influence curve and its role in robust estimation","volume":"69","author":"Hampel","year":"1974","journal-title":"J Am Stat Assoc"},{"key":"2025091921100568500_btaf434-B8","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1038\/s44320-024-00016-x","article-title":"Deep learning for protein structure prediction and design\u2014progress and applications","volume":"20","author":"J\u00e4nes","year":"2024","journal-title":"Mol Syst Biol"},{"key":"2025091921100568500_btaf434-B9","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1002\/jmr.300080603","article-title":"Occluded molecular surface: analysis of protein packing","volume":"8","author":"Pattabiraman","year":"1995","journal-title":"J Mol Recognit"},{"key":"2025091921100568500_btaf434-B11","doi-asserted-by":"publisher","first-page":"e1000188","DOI":"10.1371\/journal.pcbi.1000188","article-title":"Cavities and atomic packing in protein structures and interfaces","volume":"4","author":"Sonavane","year":"2008","journal-title":"PLoS Comput Biol"},{"first-page":"1","year":"1999","author":"Swinbank","key":"2025091921100568500_btaf434-B12"},{"key":"2025091921100568500_btaf434-B13","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf434\/63940409\/btaf434.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/9\/btaf434\/63940409\/btaf434.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/9\/btaf434\/63940409\/btaf434.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T01:10:14Z","timestamp":1758330614000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf434\/8221930"}},"subtitle":[],"editor":[{"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,8,4]]},"references-count":12,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2025,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf434","relation":{},"ISSN":["1367-4811"],"issn-type":[{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2025,9]]},"published":{"date-parts":[[2025,8,4]]},"article-number":"btaf434"}}