{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:27:08Z","timestamp":1763810828347,"version":"3.37.3"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T00:00:00Z","timestamp":1653436800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004515","name":"Universiti Kebangsaan Malaysia","doi-asserted-by":"publisher","award":["DIP-2019-016","FRGS\/1\/2020\/ICT01\/UKM\/02\/1"],"award-info":[{"award-number":["DIP-2019-016","FRGS\/1\/2020\/ICT01\/UKM\/02\/1"]}],"id":[{"id":"10.13039\/501100004515","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003093","name":"Ministry of Higher Education Malaysia","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100003093","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The GrAfSS (Graph theoretical Applications for Substructure Searching) webserver is a platform to search for three-dimensional substructures of: (i) amino acid side chains in protein structures; and (ii) base arrangements in RNA structures. The webserver interfaces the functions of five different graph theoretical algorithms \u2013 ASSAM, SPRITE, IMAAAGINE, NASSAM and COGNAC \u2013 into a single substructure searching suite. Users will be able to identify whether a three-dimensional (3D) arrangement of interest, such as a ligand binding site or 3D motif, observed in a protein or RNA structure can be found in other structures available in the Protein Data Bank (PDB). The webserver also allows users to determine whether a protein or RNA structure of interest contains substructural arrangements that are similar to known motifs or 3D arrangements. These capabilities allow for the functional annotation of new structures that were either experimentally determined or computationally generated (such as the coordinates generated by AlphaFold2) and can provide further insights into the diversity or conservation of functional mechanisms of structures in the PDB. The computed substructural superpositions are visualized using integrated NGL viewers. The GrAfSS server is available at http:\/\/mfrlab.org\/grafss\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac402","type":"journal-article","created":{"date-parts":[[2022,5,8]],"date-time":"2022-05-08T11:07:41Z","timestamp":1652008061000},"page":"W375-W383","source":"Crossref","is-referenced-by-count":10,"title":["GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA"],"prefix":"10.1093","volume":"50","author":[{"given":"Nur Syatila\u00a0Ab","family":"Ghani","sequence":"first","affiliation":[{"name":"Institute of Systems Biology, Universiti Kebangsaan Malaysia , 43600 UKM Bangi , Selangor , Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5956-2428","authenticated-orcid":false,"given":"Reeki","family":"Emrizal","sequence":"additional","affiliation":[{"name":"Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia , 43600 UKM Bangi , Selangor , Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabrina Mohamed","family":"Moffit","sequence":"additional","affiliation":[{"name":"Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia , 43600 UKM Bangi , Selangor , Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hazrina\u00a0Yusof","family":"Hamdani","sequence":"additional","affiliation":[{"name":"Advanced Medical and Dental Institute, Universiti Sains Malaysia , Bertam, Kepala Batas 13200 , Pulau Pinang , Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Effirul\u00a0Ikhwan","family":"Ramlan","sequence":"additional","affiliation":[{"name":"School of Medicine, University College Dublin, Belfield , Dublin 4 , Ireland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4275-4663","authenticated-orcid":false,"given":"Mohd","family":"Firdaus-Raih","sequence":"additional","affiliation":[{"name":"Institute of Systems Biology, Universiti Kebangsaan Malaysia , 43600 UKM Bangi , Selangor , Malaysia"},{"name":"Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia , 43600 UKM Bangi , Selangor , Malaysia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,25]]},"reference":[{"key":"2022070423582734000_B1","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1038\/newbio233223b0","article-title":"Crystallography: Protein data bank","volume":"233","author":"Nature New Biology","year":"1971","journal-title":"Nat. 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