{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T22:17:21Z","timestamp":1775254641950,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2021,5,8]],"date-time":"2021-05-08T00:00:00Z","timestamp":1620432000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM123055"],"award-info":[{"award-number":["R01GM123055"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM133840"],"award-info":[{"award-number":["R01GM133840"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS1614777"],"award-info":[{"award-number":["DMS1614777"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CMMI1825941"],"award-info":[{"award-number":["CMMI1825941"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB1925643"],"award-info":[{"award-number":["MCB1925643"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016599","name":"Purdue Institute of Drug Discovery","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016599","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"NIGMS","doi-asserted-by":"publisher","award":["T32 GM132024"],"award-info":[{"award-number":["T32 GM132024"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Protein complexes are involved in many important processes in living cells. To understand the mechanisms of these processes, it is necessary to solve the 3D structures of the protein complexes. When protein complex structures have not yet been determined by experiment, protein-protein docking tools can be used to computationally model the structures of these complexes. Here, we present a webserver which provides access to LZerD and Multi-LZerD protein docking tools. The protocol provided by the server have performed consistently among the top in the CAPRI blind evaluation. LZerD docks pairs of structures, while Multi-LZerD can dock three or more structures simultaneously. LZerD uses a soft protein surface representation with 3D Zernike descriptors and explores the binding pose space using geometric hashing. Multi-LZerD performs multi-chain docking by combining pairwise solutions by LZerD. Both methods output full-atom docked models of the input proteins. Users can also input distance constraints between interacting or non-interacting residues as well as residues that locate at the interface or far from the interface. The webserver is equipped with a user-friendly panel that visualizes the distribution and structures of binding poses of top scoring models. The LZerD webserver is available at https:\/\/lzerd.kiharalab.org.<\/jats:p>","DOI":"10.1093\/nar\/gkab336","type":"journal-article","created":{"date-parts":[[2021,4,19]],"date-time":"2021-04-19T22:31:51Z","timestamp":1618871511000},"page":"W359-W365","source":"Crossref","is-referenced-by-count":95,"title":["LZerD webserver for pairwise and multiple protein\u2013protein docking"],"prefix":"10.1093","volume":"49","author":[{"given":"Charles","family":"Christoffer","sequence":"first","affiliation":[{"name":"Department of Computer Science, Purdue University, West Lafayette, IN\u00a047907, USA"}]},{"given":"Siyang","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Purdue University, West Lafayette, IN\u00a047907, USA"}]},{"given":"Vijay","family":"Bharadwaj","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Purdue University, West Lafayette, IN\u00a047907, USA"}]},{"given":"Tunde","family":"Aderinwale","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Purdue University, West Lafayette, IN\u00a047907, USA"}]},{"given":"Vidhur","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Purdue University, West Lafayette, IN\u00a047907, USA"}]},{"given":"Matin","family":"Hormati","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Purdue University, West Lafayette, IN\u00a047907, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4091-6614","authenticated-orcid":false,"given":"Daisuke","family":"Kihara","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Purdue University, West Lafayette, IN\u00a047907, USA"},{"name":"Department of Biological Sciences, Purdue University, West Lafayette IN, 47907, USA"},{"name":"Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN\u00a047907, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,5,8]]},"reference":[{"key":"2021070812053563700_B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.sbi.2020.05.017","article-title":"Computational structure modeling for diverse categories of macromolecular interactions","volume":"64","author":"Aderinwale","year":"2020","journal-title":"Curr. Opin. Struct. 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