{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T22:01:11Z","timestamp":1773439271102,"version":"3.50.1"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2016,11,7]],"date-time":"2016-11-07T00:00:00Z","timestamp":1478476800000},"content-version":"vor","delay-in-days":824,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The application of protein\u2013protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of &amp;gt;97% strong scaling.<\/jats:p>\n               <jats:p>Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http:\/\/www.bi.cs.titech.ac.jp\/megadock .<\/jats:p>\n               <jats:p>Contact: \u00a0akiyama@cs.titech.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu532","type":"journal-article","created":{"date-parts":[[2014,8,7]],"date-time":"2014-08-07T03:03:22Z","timestamp":1407380602000},"page":"3281-3283","source":"Crossref","is-referenced-by-count":93,"title":["MEGADOCK 4.0: an ultra\u2013high-performance protein\u2013protein docking software for heterogeneous supercomputers"],"prefix":"10.1093","volume":"30","author":[{"given":"Masahito","family":"Ohue","sequence":"first","affiliation":[{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan"},{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan"}]},{"given":"Takehiro","family":"Shimoda","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan"},{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan"}]},{"given":"Shuji","family":"Suzuki","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan"},{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan"},{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan"}]},{"given":"Yuri","family":"Matsuzaki","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan"}]},{"given":"Takashi","family":"Ishida","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan"}]},{"given":"Yutaka","family":"Akiyama","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, Japan"},{"name":"1 Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 W8-76, Ookayama, Meguro-ku, Tokyo 152-8550, Japan, 2 Japan Society for the Promotion of Science (JSPS) and 3 Education Academy of Computational Life Sciences (ACLS), Tokyo Institute of Technology, 2-12-1 W8-93, Ookayama, Meguro-ku, Tokyo 152-8550, 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