A fast local embedded boundary method suitable for high power electromagnetic sources
Thavappiragasam, Mathialakan, Christlieb, Andrew, Luginsland, John, Guthrey, Pierson
Published in AIP advances (01.11.2020)
Published in AIP advances (01.11.2020)
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Journal Article
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Acharya, A, Agarwal, R, Baker, M. B, Baudry, J, Bhowmik, D, Boehm, S, Byler, K. G, Chen, S. Y, Coates, L, Cooper, C. J, Demerdash, O, Daidone, I, Eblen, J. D, Ellingson, S, Forli, S, Glaser, J, Gumbart, J. C, Gunnels, J, Hernandez, O, Irle, S, Kneller, D. W, Kovalevsky, A, Larkin, J, Lawrence, T. J, LeGrand, S, Liu, S.-H, Mitchell, J.C, Park, G, Parks, J.M, Pavlova, A, Petridis, L, Poole, D, Pouchard, L, Ramanathan, A, Rogers, D. M, Santos-Martins, D, Scheinberg, A, Sedova, A, Shen, Y, Smith, J. C, Smith, M. D, Soto, C, Tsaris, A, Thavappiragasam, M, Tillack, A. F, Vermaas, J. V, Vuong, V. Q, Yin, J, Yoo, S, Zahran, M, Zanetti-Polzi, L
Published in Journal of chemical information and modeling (28.12.2020)
Published in Journal of chemical information and modeling (28.12.2020)
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Journal Article
OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances
Davidson, Russell B, Woods, Jess, Effler, T Chad, Thavappiragasam, Mathialakan, Mitchell, Julie C, Parks, Jerry M, Sedova, Ada
Published in Bioinformatics (13.06.2022)
Published in Bioinformatics (13.06.2022)
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Journal Article
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Acharya, Atanu, Agarwal, Rupesh, Baker, M. B., Baudry, Jerome Y., Bhowmik, Debsindhu, Boehm, Swen, Byler, Kendall G., Chen, S. Y., Coates, Leighton, Cooper, Connor J., Demerdash, Omar, Daidone, Isabella, Eblen, John D., Ellingson, Sally R., Forli, Stefano, Glaser, Jens, Gumbart, James C., Gunnels, John, Hernandez, Oscar, Irle, Stephan, Kneller, Daniel W., Kovalevsky, Andrii Y., Larkin, Jeffrey, Lawrence, Travis J., LeGrand, Scott, Liu, S.-H. Kevin, Mitchell, Julie C., Park, Gilchan, Parks, Jerry M., Pavlova, Anna, Petridis, Loukas, Poole, Duncan, Pouchard, Line, Ramanathan, Arvind, Rogers, David M., Santos-Martins, Diogo, Scheinberg, Aaron, Sedova, Ada, Shen, Yue, Smith, Jeremy C., Smith, Micholas D., Soto, Carlos, Tsaris, Aristeidis, Thavappiragasam, Mathialakan, Tillack, Andreas F., Vermaas, Josh V., Vuong, Van Quan, Yin, Junqi, Yoo, Shinjae, Zahran, Mai, Zanetti-Polzi, Laura
Published in Journal of chemical information and modeling (16.12.2020)
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Published in Journal of chemical information and modeling (16.12.2020)
Journal Article
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Acharya, Atanu, Agarwal, Rupesh, Baker, M. B., Baudry, Jerome Y., Bhowmik, Debsindhu, Boehm, Swen, Byler, Kendall G., Chen, S. Y., Coates, Leighton, Cooper, Connor J., Demerdash, Omar N., Daidone, Isabella, Eblen, John D., Ellingson, Sally R., Forli, Stefano, Glaser, Jens, Gumbart, James C., Gunnels, John, Hernandez, Oscar, Irle, Stephan, Kneller, Daniel W., Kovalevsky, Andrii Y., Larkin, Jeffrey, Lawrence, Travis J., LeGrand, Scott, Liu, S.-H. Kevin, Mitchell, Julie C., Park, Gilchan, Parks, Jerry M., Pavlova, Anna, Petridis, Loukas, Poole, Duncan, Pouchard, Line, Ramanathan, Arvind, Rogers, David M., Santos-Martins, Diogo, Scheinberg, Aaron, Sedova, Ada, Shen, Yue, Smith, Jeremy C., Smith, Micholas D., Soto, Carlos, Tsaris, Aristeidis, Thavappiragasam, Mathialakan, Tillack, Andreas F., Vermaas, Josh V., Vuong, Van Quan, Yin, Junqi, Yoo, Shinjae, Zahran, Mai, Zanetti-Polzi, Laura
Published in Journal of chemical information and modeling (16.12.2020)
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Published in Journal of chemical information and modeling (16.12.2020)
Journal Article
Portability for GPU-accelerated molecular docking applications for cloud and HPC: can portable compiler directives provide performance across all platforms?
Thavappiragasam, Mathialakan, Elwasif, Wael, Sedova, Ada
Published in 2022 22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid) (01.05.2022)
Published in 2022 22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid) (01.05.2022)
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Conference Proceeding
Addressing Load Imbalance in Bioinformatics and Biomedical Applications: Efficient Scheduling across Multiple GPUs
Thavappiragasam, Mathialakan, Kale, Vivek, Hernandez, Oscar, Sedova, Ada
Published in 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (09.12.2021)
Published in 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (09.12.2021)
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Conference Proceeding
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research
LeGrand, Scott, Scheinberg, Aaron, Tillack, Andreas F., Thavappiragasam, Mathialakan, Vermaas, Josh V., Agarwal, Rupesh, Larkin, Jeff, Poole, Duncan, Santos-Martins, Diogo, Solis-Vasquez, Leonardo, Koch, Andreas, Forli, Stefano, Hernandez, Oscar, Smith, Jeremy C., Sedova, Ada
Published in ArXiv.org (21.09.2020)
Published in ArXiv.org (21.09.2020)
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Journal Article
Performance Portability of Molecular Docking Miniapp On Leadership Computing Platforms
Thavappiragasam, Mathialakan, Scheinberg, Aaron, Elwasif, Wael, Hernandez, Oscar, Sedova, Ada
Published in 2020 IEEE/ACM International Workshop on Performance, Portability and Productivity in HPC (P3HPC) (01.11.2020)
Published in 2020 IEEE/ACM International Workshop on Performance, Portability and Productivity in HPC (P3HPC) (01.11.2020)
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Conference Proceeding
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research
LeGrand, Scott, Scheinberg, Aaron, Tillack, Andreas F, Thavappiragasam, Mathialakan, Vermaas, Josh V, Agarwal, Rupesh, Larkin, Jeff, Poole, Duncan, Santos-Martins, Diogo, Solis-Vasquez, Leonardo, Koch, Andreas, li, Stefano, Hernandez, Oscar, Smith, Jeremy C, Sedova, Ada
Published in arXiv.org (06.07.2020)
Published in arXiv.org (06.07.2020)
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Paper
Journal Article
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research
LeGrand, Scott, Scheinberg, Aaron, Tillack, Andreas F, Thavappiragasam, Mathialakan, Vermaas, Josh V, Agarwal, Rupesh, Larkin, Jeff, Poole, Duncan, Santos-Martins, Diogo, Solis-Vasquez, Leonardo, Koch, Andreas, li, Stefano, Hernandez, Oscar, Smith, Jeremy C, Sedova, Ada
Published in ArXiv (06.07.2020)
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Published in ArXiv (06.07.2020)
Paper