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Ada Sedova
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Supercomputer-based ensemble docking drug discovery pipeline with application to COVID-19
A Acharya, R Agarwal, MB Baker, J Baudry, D Bhowmik, S Boehm, ...
Journal of chemical information and modeling 60 (12), 5832-5852, 2020
1562020
GPU-accelerated drug discovery with docking on the Summit supercomputer: porting, optimization, and application to COVID-19 research
S LeGrand, A Scheinberg, AF Tillack, M Thavappiragasam, JV Vermaas, ...
Proceedings of the 11th ACM international conference on bioinformatics …, 2020
722020
High-throughput virtual laboratory for drug discovery using massive datasets
J Glaser, JV Vermaas, DM Rogers, J Larkin, S LeGrand, S Boehm, ...
The International Journal of High Performance Computing Applications 35 (5 …, 2021
412021
High-Performance Molecular Dynamics Simulation for Biological and Materials Sciences: Challenges of Performance Portability
A Sedova, JD Eblen, R Budiardja, A Tharrington, JC Smith
2018 IEEE/ACM International Workshop on Performance, Portability and …, 2018
332018
Supercomputing pipelines search for therapeutics against COVID-19
JV Vermaas, A Sedova, MB Baker, S Boehm, DM Rogers, J Larkin, ...
Computing in Science & Engineering 23 (1), 7-16, 2020
262020
Hit expansion of a noncovalent SARS-CoV-2 main protease inhibitor
J Glaser, A Sedova, S Galanie, DW Kneller, RB Davidson, E Maradzike, ...
ACS Pharmacology & Translational Science 5 (4), 255-265, 2022
222022
Sequence and Temperature Influence on Kinetics of DNA Strand Displacement at Gold Electrode Surfaces
K Biala, A Sedova, GU Flechsig
ACS Applied Materials & Interfaces 7 (36), 19948-19959, 2015
202015
Porting Adaptive Ensemble Molecular Dynamics Workflows to the Summit Supercomputer
J Ossyra, A Sedova, A Tharrington, F Noé, C Clementi, JC Smith
High Performance Computing. ISC High Performance 2019. Lecture Notes in …, 2019
152019
Dips-plus: The enhanced database of interacting protein structures for interface prediction
A Morehead, C Chen, A Sedova, J Cheng
Scientific Data 10 (1), 509, 2023
142023
RNA approaches the B‐form in stacked single strand dinucleotide contexts
A Sedova, NK Banavali
Biopolymers 105 (2), 65-82, 2016
112016
High-performance deep learning toolbox for genome-scale prediction of protein structure and function
M Gao, P Lund-Andersen, A Morehead, S Mahmud, C Chen, X Chen, ...
2021 IEEE/ACM Workshop on Machine Learning in High Performance Computing …, 2021
102021
SARS-CoV2 billion-compound docking
DM Rogers, R Agarwal, JV Vermaas, MD Smith, RT Rajeshwar, C Cooper, ...
Scientific Data 10 (1), 173, 2023
82023
Proteome-scale Deployment of Protein Structure Prediction Workflows on the Summit Supercomputer
M Gao, M Coletti, RB Davidson, R Prout, S Abraham, B Hernandez, ...
2022 IEEE International Parallel and Distributed Processing Symposium …, 2022
82022
Geometric patterns for neighboring bases near the stacked state in nucleic acid strands
A Sedova, NK Banavali
Biochemistry 56 (10), 1426-1443, 2017
82017
Addressing load imbalance in bioinformatics and biomedical applications: Efficient scheduling across multiple GPUs
M Thavappiragasam, V Kale, O Hernandez, A Sedova
2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM …, 2021
72021
Amplified detection of single base mismatches with the competing-strand assay reveals complex kinetic and thermodynamic behavior of strand displacement at the electrode surface
K Biała, A Sedova, M Mix, K Bär, P Orsag, M Fojta, GU Flechsig
Electrochimica Acta 285, 272-283, 2018
72018
tinyIFD: A High-Throughput Binding Pose Refinement Workflow Through Induced-Fit Ligand Docking
DJ Hsu, RB Davidson, A Sedova, J Glaser
Journal of Chemical Information and Modeling, 2023
62023
Performance portability of molecular docking miniapp on leadership computing platforms
M Thavappiragasam, A Scheinberg, W Elwasif, O Hernandez, A Sedova
2020 IEEE/ACM International Workshop on Performance, Portability and …, 2020
62020
Highly Interactive, Steered Scientific Workflows on HPC Systems: Optimizing Design Solutions.
JR Ossyra, A Sedova, MB Baker, JC Smith
High Performance Computing. ISC High Performance 2019. Lecture Notes in …, 2019
62019
Exposing Key Vibrational Contributions to Properties of Organic Molecular Solids with High Signal, Low Frequency Neutron Spectroscopy and Ab Initio Simulations
A Pandey, A Sedova, LL Daemen, Y Cheng, AJ Ramirez-Cuesta
Crystal Growth & Design 18 (9), 4815-4821, 2018
62018
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