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However, docking methods often perform poorly for metalloproteins due to additional complexity from the three-way interactions among amino-acid residues, metal ions and ligands. This is a significant problem because zinc proteins alone comprise about 10% of all available protein structures in the protein databank. Here, we developed GM-DockZn that is dedicated for ligand docking to zinc proteins. Unlike the existing docking methods developed specifically for zinc proteins, GM-DockZn samples ligand conformations directly using a geometric grid around the ideal zinc-coordination positions of seven discovered coordination motifs, which were found from the survey of known zinc proteins complexed with a single ligand.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>GM-DockZn has the best performance in sampling near-native poses with correct coordination atoms and numbers within the top 50 and top 10 predictions when compared to several state-of-the-art techniques. This is true not only for a non-redundant dataset of zinc proteins but also for a homolog set of different ligand and zinc-coordination systems for the same zinc proteins. Similar superior performance of GM-DockZn for near-native-pose sampling was also observed for docking to apo-structures and cross-docking between different ligand complex structures of the same protein. The highest success rate for sampling nearest near-native poses within top 5 and top 1 was achieved by combining GM-DockZn for conformational sampling with GOLD for ranking. The proposed geometry-based sampling technique will be useful for ligand docking to other metalloproteins.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>GM-DockZn is freely available at www.qmclab.com\/ for academic users.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa292","type":"journal-article","created":{"date-parts":[[2020,4,27]],"date-time":"2020-04-27T11:09:23Z","timestamp":1587985763000},"page":"4004-4011","source":"Crossref","is-referenced-by-count":11,"title":["GM-DockZn: a geometry matching-based docking algorithm for zinc proteins"],"prefix":"10.1093","volume":"36","author":[{"given":"Kai","family":"Wang","sequence":"first","affiliation":[{"name":"Guangdong Provincial Key Laboratory of New Drug Design and Evaluation , School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006"},{"name":"School of Agriculture and Biology , Zhongkai University of Agriculture and Engineering, Guangzhou 510000"}]},{"given":"Nan","family":"Lyu","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Key Laboratory of New Drug Design and Evaluation , School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006"}]},{"given":"Hongjuan","family":"Diao","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Key Laboratory of New Drug Design and Evaluation , School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006"}]},{"given":"Shujuan","family":"Jin","sequence":"additional","affiliation":[{"name":"Peking University Shenzhen Graduate School , Shenzhen 518055"},{"name":"Shenzhen Bay Laboratory , Shenzhen 518055, China"}]},{"given":"Tao","family":"Zeng","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Key Laboratory of New Drug Design and Evaluation , School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9958-5699","authenticated-orcid":false,"given":"Yaoqi","family":"Zhou","sequence":"additional","affiliation":[{"name":"Peking University Shenzhen Graduate School , Shenzhen 518055"},{"name":"Shenzhen Bay Laboratory , Shenzhen 518055, China"},{"name":"Institute for Glycomics and School of Information and Communication Technology , Griffith University, Southport, QLD 4222, Australia"}]},{"given":"Ruibo","family":"Wu","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Key Laboratory of New Drug Design and Evaluation , School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006"},{"name":"Institute for Glycomics and School of Information and Communication Technology , Griffith University, Southport, QLD 4222, Australia"}]}],"member":"286","published-online":{"date-parts":[[2020,5,5]]},"reference":[{"key":"2023062312040069000_btaa292-B1","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.jinorgbio.2011.11.020","article-title":"A bioinformatics view of zinc enzymes","volume":"111","author":"Andreini","year":"2012","journal-title":"J. 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