{"id":7808,"date":"2012-06-26T23:51:31","date_gmt":"2012-06-26T20:51:31","guid":{"rendered":"http:\/\/hgpu.org\/?p=7808"},"modified":"2012-06-26T23:51:31","modified_gmt":"2012-06-26T20:51:31","slug":"gpu-based-cloud-computing-for-comparing-the-structure-of-protein-binding-sites","status":"publish","type":"post","link":"https:\/\/hgpu.org\/?p=7808","title":{"rendered":"GPU-based Cloud Computing for Comparing the Structure of Protein Binding Sites"},"content":{"rendered":"<p>In this paper, we present a novel approach for using a GPU-based Cloud computing infrastructure to efficiently perform a structural comparison of protein binding sites. The original CPU-based Java version of a recent graph-based algorithm called SEGA has been rewritten in OpenCL to run on NVIDIA GPUs in parallel on a set of Amazon EC2 Cluster GPU Instances. This new implementation of SEGA has been tested on a subset of protein structure data contained in the CavBase, providing a structural comparison of protein binding sites on a much larger scale than in previous research efforts reported in the literature.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>In this paper, we present a novel approach for using a GPU-based Cloud computing infrastructure to efficiently perform a structural comparison of protein binding sites. The original CPU-based Java version of a recent graph-based algorithm called SEGA has been rewritten in OpenCL to run on NVIDIA GPUs in parallel on a set of Amazon EC2 [&hellip;]<\/p>\n","protected":false},"author":351,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_memberships_contains_paid_content":false,"footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[10,90,3],"tags":[1781,946,387,20,974,1793,931],"class_list":["post-7808","post","type-post","status-publish","format-standard","hentry","category-biology","category-opencl","category-paper","tag-biology","tag-java","tag-macromolecule","tag-nvidia","tag-nvidia-geforce-gtx-580","tag-opencl","tag-tesla-m2050"],"views":2752,"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/7808","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/users\/351"}],"replies":[{"embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=7808"}],"version-history":[{"count":0,"href":"https:\/\/hgpu.org\/index.php?rest_route=\/wp\/v2\/posts\/7808\/revisions"}],"wp:attachment":[{"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=7808"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=7808"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/hgpu.org\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=7808"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}