{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T18:38:46Z","timestamp":1725993526426},"reference-count":107,"publisher":"Elsevier","isbn-type":[{"type":"print","value":"9780128114322"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1016\/b978-0-12-809633-8.20186-6","type":"book-chapter","created":{"date-parts":[[2018,3,15]],"date-time":"2018-03-15T22:45:15Z","timestamp":1521153915000},"page":"1142-1150","source":"Crossref","is-referenced-by-count":0,"title":["Dedicated Bioinformatics Analysis Hardware"],"prefix":"10.1016","author":[{"given":"Bertil","family":"Schmidt","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andreas","family":"Hildebrandt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20186-6_bib94","doi-asserted-by":"crossref","first-page":"5342","DOI":"10.1016\/j.jcp.2008.01.047","article-title":"General purpose molecular dynamics simulations fully implemented on graphics processing units","volume":"227","author":"Anderson","year":"2008","journal-title":"Journal of Computational Physics"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20186-6_bib1","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1109\/TCBB.2016.2535385","article-title":"Leveraging FPGAs for accelerating short read alignment","volume":"14","author":"Arram","year":"2017","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20186-6_bib2","first-page":"241","article-title":"Polarizable force fields for molecular dynamics simulations of biomolecules","volume":"5","author":"Baker","year":"2015","journal-title":"Wiley Interdisciplinary Reviews: Computational Molecular Science"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib3","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1007\/978-1-4939-1465-4_7","article-title":"Coarse-grained force fields for molecular simulations","volume":"1215","author":"Barnoud","year":"2015","journal-title":"Methods in Molecular Biology"},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20186-6_bib4","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1109\/TVLSI.2008.2005314","article-title":"A highly parameterized and efficient FPGA-based skeleton for pairwise biological sequence alignment","volume":"17","author":"Benkrid","year":"2009","journal-title":"IEEE Transactions on VLSI"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20186-6_bib5","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.jpdc.2012.04.004","article-title":"G-MSA \u2013 A GPU-based, fast and accurate algorithm for multiple sequence alignment","volume":"73","author":"Blazewicz","year":"2013","journal-title":"Journal of Parallel and Distributed Computing"},{"issue":"16","key":"10.1016\/B978-0-12-809633-8.20186-6_bib6","doi-asserted-by":"crossref","first-page":"7762","DOI":"10.1093\/nar\/gkv784","article-title":"High speed BLASTN: An accelerated MegaBLAST search tool","volume":"43","author":"Chen","year":"2015","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20186-6_bib7","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/1471-2105-14-67","article-title":"A hybrid short read mapping accelerator","volume":"14","author":"Chen","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib8","first-page":"142760","article-title":"Opportunities and obstacles for deep learning in biology and medicine","author":"Ching","year":"2017","journal-title":"bioRxiv"},{"issue":"6255","key":"10.1016\/B978-0-12-809633-8.20186-6_bib9","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1126\/science.aab1369","article-title":"Structural origin of slow diffusion in protein folding","volume":"349","author":"Chung","year":"2015","journal-title":"Science"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20186-6_bib10","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.1016\/j.cpc.2011.01.009","article-title":"Highly accelerated simulations of glassy dynamics using GPUs: Caveats on limited floating-point precision","volume":"182","author":"Colberg","year":"2011","journal-title":"Computer Physics Communications"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20186-6_bib91","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1145\/508352.508353","article-title":"Reconfigurable computing: A survey of systems and software","volume":"34","author":"Compton","year":"2002","journal-title":"ACM Computing Surveys"},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20186-6_bib11","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle mesh Ewald: An N log( N ) method for Ewald sums in large systems","volume":"98","author":"Darden","year":"1993","journal-title":"The Journal of Chemical Physics"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib12","unstructured":"DePristo, M., Poplin, R., 2017. DeepVariant: Highly accurate genomes with deep neural networks. Available at: https:\/\/research.googleblog.com\/2017\/12\/deepvariant-highly-accurate-genomes.html"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20186-6_bib13","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1002\/cphc.201100681","article-title":"Classical reactive molecular dynamics implementations: State of the art","volume":"13","author":"Farah","year":"2012","journal-title":"ChemPhysChem"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20186-6_bib14","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1109\/TCBB.2015.2405333","article-title":"FHAST: Fpga-based acceleration of Bowtie in hardware","volume":"12","author":"Fernandez","year":"2015","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20186-6_bib15","doi-asserted-by":"crossref","first-page":"2985","DOI":"10.1002\/cber.18940270364","article-title":"Einfluss der Konfiguration auf die Wirkung der Enzyme","volume":"27","author":"Fischer","year":"1894","journal-title":"Berichte Der Deutschen Chemischen Gesellschaft"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib16","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.cpc.2015.02.028","article-title":"Strong scaling of general-purpose molecular dynamics simulations on GPUs","volume":"192","author":"Glaser","year":"2015","journal-title":"Computer Physics Communications"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20186-6_bib17","doi-asserted-by":"crossref","first-page":"1542","DOI":"10.1021\/ct200909j","article-title":"Routine microsecond molecular dynamics simulations with AMBER on GPUs","volume":"8","author":"G\u00f6tz","year":"2012","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20186-6_bib18","doi-asserted-by":"crossref","first-page":"e88901","DOI":"10.1371\/journal.pone.0088901","article-title":"QuickProbs \u2013 A fast multiple sequence alignment algorithm designed for graphics processors","volume":"9","author":"Gudy","year":"2014","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib19","doi-asserted-by":"crossref","first-page":"2371","DOI":"10.1021\/ct900275y","article-title":"An implementation of the smooth particle-mesh Ewald (PME) method on GPU hardware","volume":"5","author":"Harvey","year":"2009","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20186-6_bib20","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1021\/ct9000685","article-title":"ACEMD: Accelerating biomolecular dynamics in the microsecond time scale","volume":"5","author":"Harvey","year":"2009","journal-title":"Journal of Chemical Theory and Computation"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib21","first-page":"183","article-title":"FPGA implementation of systolic sequence alignment","author":"Hoang","year":"1992","journal-title":"International Workshop on Field Programmable Logic and Applications"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib22","doi-asserted-by":"crossref","unstructured":"Houtgast, E.J., et al., 2017. An efficient GPU-accelerated implementation of genomic short read mapping with BWA-MEM. ACM SIGARCH Computer Architecture News 44 (4), 38\u201343.","DOI":"10.1145\/3039902.3039910"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib23","doi-asserted-by":"crossref","unstructured":"Houtgast, E.J., et al., 2015. An FPGA-based systolic array to accelerate the BWA-MEM genomic mapping algorithm. In: 2015 International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation (SAMOS), IEEE.","DOI":"10.1109\/SAMOS.2015.7363679"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib24","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.compbiolchem.2015.05.004","article-title":"CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs","volume":"58","author":"Hung","year":"2015","journal-title":"Computational Biology and Chemistry"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20186-6_bib25","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nphys3553","article-title":"The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time","volume":"12","author":"Hu","year":"2015","journal-title":"Nature Physics"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20186-6_bib26","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1145\/1371579.1371581","article-title":"Mercury BLASTP: Accelerating protein sequence alignment","volume":"1","author":"Jacob","year":"2008","journal-title":"ACM Transactions on Reconfigurable Technology and Systems"},{"issue":"9","key":"10.1016\/B978-0-12-809633-8.20186-6_bib27","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1038\/nsb0902-646","article-title":"Molecular dynamics simulations of biomolecules","volume":"9","author":"Karplus","year":"2002","journal-title":"Nature Structural Biology"},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20186-6_bib28","doi-asserted-by":"crossref","first-page":"2195","DOI":"10.1073\/pnas.89.6.2195","article-title":"Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques","volume":"89","author":"Katchalski-Katzir","year":"1992","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib29","series-title":"High-Performance Computing Using FPGAs","first-page":"105135","article-title":"FPGA-accelerated molecular dynamics","author":"Khan","year":"2013"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20186-6_bib30","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s12859-016-1434-6","article-title":"Accelerating metagenomic read classification on CUDA-enabled GPUs","volume":"18","author":"Kobus","year":"2017","journal-title":"BMC Bioinformatics"},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20186-6_bib31","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1021\/ci100459b","article-title":"Accelerating molecular docking calculations using graphics processing units","volume":"51","author":"Korb","year":"2011","journal-title":"Journal of Chemical Information and Modeling"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20186-6_bib32","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1073\/pnas.44.2.98","article-title":"Application of a theory of enzyme specificity to protein synthesis","volume":"44","author":"Koshland","year":"1958","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib33","doi-asserted-by":"crossref","first-page":"e606","DOI":"10.7717\/peerj.606","article-title":"Massively parallel read mapping on GPUs with the q-group index and PEANUT","volume":"2","author":"Koster","year":"2014","journal-title":"PeerJ"},{"issue":"13","key":"10.1016\/B978-0-12-809633-8.20186-6_bib34","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1002\/jcc.23899","article-title":"New ways to boost molecular dynamics simulations","volume":"36","author":"Krieger","year":"2015","journal-title":"Journal of Computational Chemistry"},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20186-6_bib35","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.micpro.2009.02.007","article-title":"Acceleration of ungapped extension in Mercury BLAST","volume":"33","author":"Lancaster","year":"2009","journal-title":"Microprocessors and Microsystems"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib36","first-page":"42","article-title":"SWhybrid: A hybrid-parallel framework for large-scale protein sequence database search","volume":"2017","author":"Lan","year":"2017","journal-title":"IEEE IPDPS"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib37","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.ymeth.2016.02.020","article-title":"MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices","volume":"102","author":"Li","year":"2016","journal-title":"Methods"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20186-6_bib95","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.cpc.2012.09.022","article-title":"SPFP: Speed without compromise \u2013 A mixed precision model for GPU accelerated molecular dynamics simulations","volume":"184","author":"Le Grand","year":"2013","journal-title":"Computer Physics Communications"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib38","unstructured":"Lipton, R.J., Lopresti, D., 1985. A systolic array for rapid string comparison. In: Proceedings of the Chapel Hill Conference on VLSI. 363\u2013376."},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20186-6_bib39","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1186\/1756-0500-3-93","article-title":"CUDASW++2.0: Enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions","volume":"3","author":"Liu","year":"2010","journal-title":"BMC Research Notes"},{"issue":"9","key":"10.1016\/B978-0-12-809633-8.20186-6_bib40","doi-asserted-by":"crossref","first-page":"634","DOI":"10.1016\/j.cpc.2008.05.008","article-title":"Accelerating molecular dynamics simulations using Graphics Processing Units with CUDA","volume":"179","author":"Liu","year":"2008","journal-title":"Computer Physics Communications"},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20186-6_bib41","doi-asserted-by":"crossref","first-page":"1678","DOI":"10.1109\/TCBB.2011.33","article-title":"CUDA-BLASTP: Accelerating BLASTP on CUDA-enabled graphics hardware","volume":"8","author":"Liu","year":"2011","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20186-6_bib42","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1186\/1756-0500-2-73","article-title":"CUDASW++: Optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units","volume":"2","author":"Liu","year":"2009","journal-title":"BMC Research Notes"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib43","unstructured":"Liu, Y., Schmidt, B., Maskell, D., 2009b. MSA-CUDA: Multiple sequence alignment on graphics processing units with CUDA. In: Proceedings of the 20th IEEE International Conference Application-specific Systems, Architectures and Processors."},{"issue":"16","key":"10.1016\/B978-0-12-809633-8.20186-6_bib44","doi-asserted-by":"crossref","first-page":"1958","DOI":"10.1093\/bioinformatics\/btq338","article-title":"MSAProbs: Multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities","volume":"26","author":"Liu","year":"2010","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20186-6_bib45","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1186\/1471-2105-12-85","article-title":"DecGPU: Distributed error correction on massively parallel graphics processing units using CUDA and MPI","volume":"12","author":"Liu","year":"2011","journal-title":"BMC Bioinformatics"},{"issue":"14","key":"10.1016\/B978-0-12-809633-8.20186-6_bib46","doi-asserted-by":"crossref","first-page":"1830","DOI":"10.1093\/bioinformatics\/bts276","article-title":"CUSHAW: A CUDA compatible short read aligner to large genomes based on the BurrowsWheeler transform","volume":"28","author":"Liu","year":"2012","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20186-6_bib47","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1186\/1471-2105-12-466","article-title":"Accelerated large-scale multiple sequence alignment","volume":"12","author":"Lloyd","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib48","doi-asserted-by":"crossref","unstructured":"Lu, M., et al., 2011. GSNP: A DNA single-nucleotide polymorphism detection system with GPU acceleration. In: 2011 International Conference on Parallel Processing (ICPP), IEEE.","DOI":"10.1109\/ICPP.2011.51"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20186-6_bib49","doi-asserted-by":"crossref","first-page":"e65632","DOI":"10.1371\/journal.pone.0065632","article-title":"SOAP3-dp: Fast, accurate and sensitive GPU-based short read aligner","volume":"8","author":"Luo","year":"2013","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib50","doi-asserted-by":"crossref","first-page":"e421","DOI":"10.7717\/peerj.421","article-title":"BALSA: Integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU","volume":"2","author":"Luo","year":"2014","journal-title":"PeerJ"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib51","doi-asserted-by":"crossref","unstructured":"Mahram, A., Herbordt, M.C., 2012. FMSA: FPGA-accelerated ClustalW-based multiple sequence alignment through pipelined prefiltering. In: Proceedings of the 20th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM), IEEE.","DOI":"10.1109\/FCCM.2012.38"},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20186-6_bib52","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1145\/2629691","article-title":"NCBI BLASTP on high-performance reconfigurable computing systems","volume":"7","author":"Mahram","year":"2015","journal-title":"ACM Transactions on Reconfigurable Technology and Systems"},{"issue":"S2","key":"10.1016\/B978-0-12-809633-8.20186-6_bib53","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-9-S2-S10","article-title":"CUDA compatible GPU cards as efficient hardware accelerators for Smith Waterman sequence alignment","volume":"9","author":"Manavski","year":"2008","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20186-6_bib92","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1186\/s13073-015-0221-8","article-title":"A 26-h system of highly sensitive whole genome sequencing for emergency management of genetic diseases","volume":"7","author":"Miller","year":"2015","journal-title":"Genome Medicine"},{"issue":"16","key":"10.1016\/B978-0-12-809633-8.20186-6_bib54","doi-asserted-by":"crossref","first-page":"2785","DOI":"10.1002\/jcc.21256","article-title":"AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility","volume":"30","author":"Morris","year":"2009","journal-title":"Journal of Computational Chemistry"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20186-6_bib55","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1109\/TCBB.2015.2495149","article-title":"BowMapCL: Burrows-wheeler mapping on multiple heterogeneous accelerators","volume":"13","author":"Nogueira","year":"2016","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"issue":"2012","key":"10.1016\/B978-0-12-809633-8.20186-6_bib56","article-title":"MDGRAPE-4: A special-purpose computer system for molecular dynamics simulations","volume":"372","author":"Ohmura","year":"2014","journal-title":"Philosophical Transactions Series A, Mathematical, Physical, and Engineering Sciences"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20186-6_bib90","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1109\/JPROC.2008.917757","article-title":"GPU computing","volume":"96","author":"Owens","year":"2008","journal-title":"Proceedings of the IEEE"},{"issue":"22","key":"10.1016\/B978-0-12-809633-8.20186-6_bib57","doi-asserted-by":"crossref","first-page":"3281","DOI":"10.1093\/bioinformatics\/btu532","article-title":"MEGADOCK 4.0: An ultra-high-performance protein-protein docking software for heterogeneous supercomputers","volume":"30","author":"Ohue","year":"2014","journal-title":"Bioinformatics"},{"issue":"16","key":"10.1016\/B978-0-12-809633-8.20186-6_bib58","doi-asserted-by":"crossref","first-page":"3431","DOI":"10.1093\/bioinformatics\/bti508","article-title":"Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW","volume":"21","author":"Oliver","year":"2005","journal-title":"Bioinformatics"},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20186-6_bib96","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1109\/TCSII.2005.853340","article-title":"Reconfigurable architectures for bio-sequence database scanning on FPGAs","volume":"52","author":"Oliver","year":"2005","journal-title":"IEEE Transactions on Circuits and Systems II"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib59","series-title":"Tackling Exascale Software Challenges in Molecular Dynamics Simulations With GROMACS","first-page":"3","author":"Pall","year":"2015"},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20186-6_bib60","doi-asserted-by":"crossref","first-page":"2641","DOI":"10.1016\/j.cpc.2013.06.003","article-title":"A flexible algorithm for calculating pair interactions on SIMD architectures","volume":"184","author":"Pall","year":"2013","journal-title":"Computer Physics Communications"},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20186-6_bib61","doi-asserted-by":"crossref","first-page":"3372","DOI":"10.1021\/acs.jctc.7b00172","article-title":"Quantitative characterization of the binding and unbinding of millimolar drug fragments with molecular dynamics simulations","volume":"13","author":"Pan","year":"2017","journal-title":"Journal of Chemical Theory and Computation"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib62","doi-asserted-by":"crossref","unstructured":"Pechan, I., Feher, B., 2011. Molecular docking on FPGA and GPU platforms. In: 2011 Proceedings of the 21st International Conference on Field Programmable Logic and Applications, pp. 474\u2013477. IEEE.","DOI":"10.1109\/FPL.2011.93"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib63","doi-asserted-by":"crossref","unstructured":"Ramachandran, A., et al., 2015. FPGA accelerated DNA error correction. In: Design, Automation & Test in Europe Conference & Exhibition (DATE), IEEE.","DOI":"10.7873\/DATE.2015.0983"},{"year":"2004","series-title":"The Art of Molecular Dynamics Simulation","author":"Rapaport","key":"10.1016\/B978-0-12-809633-8.20186-6_bib64"},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20186-6_bib65","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1006\/jmbi.1996.0477","article-title":"A fast flexible docking method using an incremental construction algorithm","volume":"261","author":"Rarey","year":"1996","journal-title":"Journal of Molecular Biology"},{"issue":"19","key":"10.1016\/B978-0-12-809633-8.20186-6_bib66","doi-asserted-by":"crossref","first-page":"2398","DOI":"10.1093\/bioinformatics\/btq444","article-title":"Ultra-fast FFT protein docking on graphics processors","volume":"26","author":"Ritchie","year":"2010","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20186-6_bib67","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/jcc.23763","article-title":"A comparison between parallelization approaches in molecular dynamics simulations on GPUs","volume":"36","author":"Rovigatti","year":"2015","journal-title":"Journal of Computational Chemistry"},{"issue":"9","key":"10.1016\/B978-0-12-809633-8.20186-6_bib68","doi-asserted-by":"crossref","first-page":"3878","DOI":"10.1021\/ct400314y","article-title":"Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. explicit solvent particle mesh ewald","volume":"9","author":"Salomon-Ferrer","year":"2013","journal-title":"Journal of Chemical Theory and Computation"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20186-6_bib69","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1145\/1837853.1693473","article-title":"CUDAlign: Using GPU to accelerate the comparison of megabase genomic sequences","volume":"45","author":"Sandes","year":"2010","journal-title":"ACM SIGPLAN Notices"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20186-6_bib70","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1109\/TPDS.2012.194","article-title":"Retrieving Smith-Waterman alignments with optimizations for megabase biological sequences using GPU","volume":"24","author":"Sandes","year":"2013","journal-title":"IEEE Transactions on Parallel and Distributed Systems"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20186-6_bib71","doi-asserted-by":"crossref","first-page":"2838","DOI":"10.1109\/TPDS.2016.2515597","article-title":"CUDAlign 4.0: Incremental speculative traceback for exact chromosome-wide alignment in GPU clusters","volume":"27","author":"Sandes","year":"2016","journal-title":"IEEE Transactions on Parallel and Distributed Systems"},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20186-6_bib88","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1016\/j.drudis.2017.01.014","article-title":"Next-generation seqeuncing: Big data meets high performance computing","volume":"22","author":"Schmidt","year":"2017","journal-title":"Drug Discovery Today"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20186-6_bib89","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1101\/gr.191684.115","article-title":"Biological data sciences in genome research","volume":"25","author":"Schatz","year":"2015","journal-title":"Genome Research"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib72","doi-asserted-by":"crossref","unstructured":"Shaw, D.E., et al., 2014. Anton 2: Raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer. In: SC14: International Conference for High Performance Computing, Networking, Storage and Analysis, pp. 41\u201353. IEEE.","DOI":"10.1109\/SC.2014.9"},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20186-6_bib73","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1089\/cmb.2009.0062","article-title":"A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware","volume":"17","author":"Shi","year":"2010","journal-title":"Journal of Computational Biology"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib87","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pbio.1002195","article-title":"Big Data: Astronomical or genomical?","volume":"13","author":"Stephens","year":"2015","journal-title":"PLOS Biology"},{"issue":"16","key":"10.1016\/B978-0-12-809633-8.20186-6_bib93","doi-asserted-by":"crossref","first-page":"2618","DOI":"10.1002\/jcc.20829","article-title":"Accelerating molecular modeling applications with graphics processors","volume":"28","author":"Stone","year":"2007","journal-title":"Journal of Computational Chemistry"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib75","doi-asserted-by":"crossref","unstructured":"Thall, A., 2006. Extended-precision floating-point numbers for GPU computation. ACM SIGGRAPH 2006 Research Posters, pp. 1\u201312.","DOI":"10.1145\/1179622.1179682"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib76","unstructured":"Vermij, E., 2011. Genetic sequence alignment on a supercomputing platform. MS Thesis, TU Delft, Netherlands."},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20186-6_bib77","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1093\/bioinformatics\/btq644","article-title":"GPU-BLAST: Using graphics processors to accelerate protein sequence alignment","volume":"27","author":"Vouzis","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib78","doi-asserted-by":"crossref","unstructured":"Waidyasooriya, H.M., Hariyama, M., Kasahara, K., 2016. Architecture of an FPGA accelerator for molecular dynamics simulation using OpenCL. In: 2016 IEEE\/ACIS Proceedings of the 15th International Conference on Computer and Information Science (ICIS), p. 15.","DOI":"10.1109\/ICIS.2016.7550743"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib79","first-page":"383","article-title":"The FPGA-based high-performance computer RIVY-ERA for applications in bioinformatics","author":"Wienbrandt","year":"2014","journal-title":"Conference on Computability in Europe"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib80","doi-asserted-by":"crossref","first-page":"e808","DOI":"10.7717\/peerj.808","article-title":"Arioc: High-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space","volume":"3","author":"Wilton","year":"2015","journal-title":"PeerJ"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib81","first-page":"1","article-title":"FPGASW: Accelerating large-scale Smith\u2013Waterman sequence alignment application with backtracking on FPGA linear systolic array","author":"Xia","year":"2017","journal-title":"Interdisciplinary Sciences: Computational Life Sciences"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib82","first-page":"293","article-title":"FPGA-accelerated molecular dynamics simulations: An overview","author":"Yang","year":"2007","journal-title":"Reconfigurable Computing: Architectures, Tools and Applications"},{"issue":"8","key":"10.1016\/B978-0-12-809633-8.20186-6_bib83","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1093\/bioinformatics\/btw769","article-title":"H-BLAST: A fast protein sequence alignment toolkit on heterogeneous computers with GPUs","volume":"33","author":"Ye","year":"2017","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib84","article-title":"cublastp: Fine-grained parallelization of protein sequence search on cpu+ gpu","author":"Zhang","year":"2015","journal-title":"IEEE\/ACM Transactions on Computational Biology and Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_bib85","doi-asserted-by":"crossref","unstructured":"Zhang, P., Tan, G., Gau, G.R., 2007. Implementation of the Smith-Waterman algorithm on a reconfigurable supercomputing platform. In: Proceedings of the 1st international workshop on high-performance reconfigurable computing technology and applications, pp. 39\u201348.","DOI":"10.1145\/1328554.1328565"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20186-6_bib86","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1093\/bioinformatics\/btu047","article-title":"G-BLASTN: Accelerating nucleotide alignment by graphics processors","volume":"30","author":"Zhao","year":"2014","journal-title":"Bioinformatics"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20186-6_fur1","doi-asserted-by":"crossref","first-page":"5342","DOI":"10.1016\/j.jcp.2008.01.047","article-title":"General purpose molecular dynamics simulations fully implemented on graphics processing units","volume":"227","author":"Anderson","year":"2008","journal-title":"Journal of Computational Physics"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20186-6_fur2","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1145\/508352.508353","article-title":"Reconfigurable computing: A survey of systems and software","volume":"34","author":"Compton","year":"2002","journal-title":"ACM Computing Surveys"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20186-6_fur3","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.cpc.2012.09.022","article-title":"SPFP: Speed without compromise \u2013 A mixed precision model for GPU accelerated molecular dynamics simulations","volume":"184","author":"Le Grand","year":"2013","journal-title":"Computer Physics Communications"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_fur4","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1186\/1471-2105-14-117","article-title":"CUDASW++3.0: Accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions","volume":"14","author":"Liu","year":"2013","journal-title":"BMC Bioinformatics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20186-6_fur5","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1186\/s13073-015-0221-8","article-title":"A 26-h system of highly sensitive whole genome sequencing for emergency management of genetic diseases","volume":"7","author":"Miller","year":"2015","journal-title":"Genome Medicine"},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20186-6_fur6","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1109\/TCSII.2005.853340","article-title":"Reconfigurable architectures for bio-sequence database scanning on FPGAs","volume":"52","author":"Oliver","year":"2005","journal-title":"IEEE Transactions on Circuits and Systems II"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20186-6_fur7","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1109\/JPROC.2008.917757","article-title":"GPU computing","volume":"96","author":"Owens","year":"2008","journal-title":"Proceedings of the IEEE"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20186-6_fur8","doi-asserted-by":"crossref","first-page":"1417","DOI":"10.1101\/gr.191684.115","article-title":"Biological data sciences in genome research","volume":"25","author":"Schatz","year":"2015","journal-title":"Genome Research"},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20186-6_fur9","doi-asserted-by":"crossref","first-page":"712","DOI":"10.1016\/j.drudis.2017.01.014","article-title":"Next-generation seqeuncing: Big data meets high performance computing","volume":"22","author":"Schmidt","year":"2017","journal-title":"Drug Discovery Today"},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20186-6_fur10","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1145\/1364782.1364802","article-title":"Anton, a special-purpose machine for molecular dynamics simulation","volume":"51","author":"Shaw","year":"2008","journal-title":"Communications of the ACM"},{"key":"10.1016\/B978-0-12-809633-8.20186-6_fur11","doi-asserted-by":"crossref","first-page":"e1002195","DOI":"10.1371\/journal.pbio.1002195","article-title":"Big Data: Astronomical or genomical?","volume":"13","author":"Stephens","year":"2015","journal-title":"PLOS Biology"},{"issue":"16","key":"10.1016\/B978-0-12-809633-8.20186-6_fur12","doi-asserted-by":"crossref","first-page":"2618","DOI":"10.1002\/jcc.20829","article-title":"Accelerating molecular modeling applications with graphics processors","volume":"28","author":"Stone","year":"2007","journal-title":"Journal of Computational Chemistry"}],"container-title":["Encyclopedia of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338201866?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338201866?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T16:52:51Z","timestamp":1693587171000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/B9780128096338201866"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9780128114322"],"references-count":107,"URL":"https:\/\/doi.org\/10.1016\/b978-0-12-809633-8.20186-6","relation":{},"subject":[],"published":{"date-parts":[[2019]]}}}