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Protein Folding Neural Networks Are Not Robust


Sep 19, 2021
Sumit Kumar Jha , Arvind Ramanathan , Rickard Ewetz , Alvaro Velasquez , Susmit Jha

* 8 pages, 5 figures 

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CrossedWires: A Dataset of Syntactically Equivalent but Semantically Disparate Deep Learning Models


Aug 29, 2021
Max Zvyagin , Thomas Brettin , Arvind Ramanathan , Sumit Kumar Jha

* 13 pages 

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Protein-Ligand Docking Surrogate Models: A SARS-CoV-2 Benchmark for Deep Learning Accelerated Virtual Screening


Jun 30, 2021
Austin Clyde , Thomas Brettin , Alexander Partin , Hyunseung Yoo , Yadu Babuji , Ben Blaiszik , Andre Merzky , Matteo Turilli , Shantenu Jha , Arvind Ramanathan , Rick Stevens


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Achieving 100X faster simulations of complex biological phenomena by coupling ML to HPC ensembles


Apr 26, 2021
Alexander Brace , Hyungro Lee , Heng Ma , Anda Trifan , Matteo Turilli , Igor Yakushin , Todd Munson , Ian Foster , Shantenu Jha , Arvind Ramanathan


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Scaffold Embeddings: Learning the Structure Spanned by Chemical Fragments, Scaffolds and Compounds


Mar 11, 2021
Austin Clyde , Arvind Ramanathan , Rick Stevens


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Pandemic Drugs at Pandemic Speed: Accelerating COVID-19 Drug Discovery with Hybrid Machine Learning- and Physics-based Simulations on High Performance Computers


Mar 04, 2021
Agastya P. Bhati , Shunzhou Wan , Dario Alfè , Austin R. Clyde , Mathis Bode , Li Tan , Mikhail Titov , Andre Merzky , Matteo Turilli , Shantenu Jha , Roger R. Highfield , Walter Rocchia , Nicola Scafuri , Sauro Succi , Dieter Kranzlmüller , Gerald Mathias , David Wifling , Yann Donon , Alberto Di Meglio , Sofia Vallecorsa , Heng Ma , Anda Trifan , Arvind Ramanathan , Tom Brettin , Alexander Partin , Fangfang Xia , Xiaotan Duan , Rick Stevens , Peter V. Coveney


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Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins


Dec 01, 2020
Arvind Ramanathan , Heng Ma , Akash Parvatikar , Chakra S. Chennubhotla

* 9 pages, 2 figures 

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