{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:44:25Z","timestamp":1753875865438,"version":"3.41.2"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2024,11,5]],"date-time":"2024-11-05T00:00:00Z","timestamp":1730764800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The advent of AlphaFold and other protein Artificial Intelligence (AI) models has transformed protein design, necessitating efficient handling of large-scale data and complex workflows. Using existing programming packages that predate recent AI advancements often leads to inefficiencies in human coding and slow code execution. To address this gap, we developed the Afpdb package.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Afpdb, built on AlphaFold\u2019s NumPy architecture, offers a high-performance core. It uses RFDiffusion's contig syntax to streamline residue and atom selection, making coding simpler and more readable. Integrating PyMOL\u2019s visualization capabilities, Afpdb allows automatic visual quality control. With over 180 methods commonly used in protein AI design, which are otherwise hard to find, Afpdb enhances productivity in structural biology by supporting the development of concise, high-performance code.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Code and documentation are available on GitHub (https:\/\/github.com\/data2code\/afpdb) and PyPI (https:\/\/pypi.org\/project\/afpdb). An interactive tutorial is accessible through Google Colab.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae654","type":"journal-article","created":{"date-parts":[[2024,11,5]],"date-time":"2024-11-05T14:41:02Z","timestamp":1730817662000},"source":"Crossref","is-referenced-by-count":0,"title":["Afpdb: an efficient structure manipulation package for AI protein design"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-7496-152X","authenticated-orcid":false,"given":"Yingyao","family":"Zhou","sequence":"first","affiliation":[{"name":"Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","place":["United States"]}]},{"given":"Jiayi","family":"Cox","sequence":"additional","affiliation":[{"name":"Biologics Research Center, Novartis Biomedical Research , San Diego, CA 92121,","place":["United States"]}]},{"given":"Bin","family":"Zhou","sequence":"additional","affiliation":[{"name":"Biologics Research 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