Pratyush Tiwary

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 23 papers. Top paper: “Interrogating RNA-small molecule interactions with structure probing and AI augmented-molecular simulations”.

Interrogating RNA-small molecule interactions with structure probing and AI augmented-molecular simulations

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.28.462207

N/A

0DataRank · unranked

1 citations

Shaifaly Parmar, John S. Schneekloth, Pratyush Tiwary, Yihang Wang

Protein Flexibility and Dissociation Pathway Differentiation Can Explain Onset of Resistance Mutations in Kinases**

Angewandte Chemie International Edition(2022)10.1002/anie.202200983

N/A

0DataRank · unranked

51 citations

Zachary Smith, Markus A. Seeliger, Pratyush Tiwary, Mrinal Shekhar

Path sampling of recurrent neural networks by incorporating known physics

Nature Communications(2022)10.1038/s41467-022-34780-x

N/A

0DataRank · unranked

34 citations

Eric Fields, Yijia Xu, En-Jui Kuo, Pratyush Tiwary, Sun-Ting Tsai

AlphaFold2-RAVE: From sequence to Boltzmann ensemble

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.25.493365

N/A

0DataRank · unranked

11 citations

Akashnathan Aranganathan, Dedi Wang, Pratyush Tiwary, Bodhi P. Vani

AlphaFold2-RAVE: From Sequence to Boltzmann Ranking

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00290

N/A

0DataRank · unranked

121 citations

Akashnathan Aranganathan, Dedi Wang, Pratyush Tiwary, Bodhi P. Vani

Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c01436

N/A

0DataRank · unranked

54 citations

Akashnathan Aranganathan, Pratyush Tiwary, Bodhi P. Vani

Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.25.550565

N/A

0DataRank · unranked

13 citations

Michael Strobel, Bodhi P. Vani, Pratyush Tiwary, Zachary Smith

Inferring phase transitions and critical exponents from limited observations with Thermodynamic Maps

arXiv (Cornell University)(2023)10.48550/arxiv.2308.14885

N/A

0DataRank · unranked

9 citations

Kinjal Mondal, John S. Schneekloth, Pratyush Tiwary, Lukas Herron

Good Things Take Time: Tiwary–Seeliger Collaboration for Predictive Pharmacodynamics

Angewandte Chemie International Edition(2023)10.1002/anie.202303339

N/A

0DataRank · unranked

0 citations

Pratyush Tiwary, Markus A. Seeliger

Enhanced Sampling with Machine Learning

Annual Review of Physical Chemistry(2024)10.1146/annurev-physchem-083122-125941

N/A

0DataRank · unranked

124 citations

Zachary A. Smith, Lukas Herron, Ziyue Zou, Pratyush Tiwary, Shams Mehdi

Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.3c01698

N/A

0DataRank · unranked

35 citations

Michael Strobel, Bodhi P. Vani, Pratyush Tiwary, Zachary Smith

Thermodynamics-inspired explanations of artificial intelligence

Nature Communications(2024)10.1038/s41467-024-51970-x

N/A

0DataRank · unranked

34 citations

Pratyush Tiwary, Shams Mehdi

Empowering AlphaFold2 for protein conformation selective drug discovery with AlphaFold2-RAVE

eLife(2024)10.7554/elife.99702

N/A

0DataRank · unranked

23 citations

Akashnathan Aranganathan, Pratyush Tiwary, Xinyu Gu

Calculating Protein–Ligand Residence Times through State Predictive Information Bottleneck Based Enhanced Sampling

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00503

N/A

0DataRank · unranked

23 citations

Dedi Wang, Markus A. Seeliger, Pratyush Tiwary, Suemin Lee

Information Bottleneck Approach for Markov Model Construction

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00449

N/A

0DataRank · unranked

21 citations

Yunrui Qiu, Eric R. Beyerle, Xuhui Huang, Pratyush Tiwary, Dedi Wang

Augmenting Human Expertise in Weighted Ensemble Simulations through Deep Learning-Based Information Bottleneck

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00919

N/A

0DataRank · unranked

8 citations

Pratyush Tiwary, Dedi Wang

Generative artificial intelligence for computational chemistry: a roadmap to predicting emergent phenomena

arXiv (Cornell University)(2024)10.48550/arxiv.2409.03118

N/A

0DataRank · unranked

5 citations

Lukas Herron, Richard S. John, Suemin Lee, Disha Sanwal, Ruiyu Wang +1 more

Calculating Protein-Ligand Residence Times Through State Predictive Information Bottleneck based Enhanced Sampling

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.04.16.589710

N/A

0DataRank · unranked

1 citations

Dedi Wang, Markus A. Seeliger, Pratyush Tiwary, Suemin Lee

Unveiling the intricate role of S100A1 in regulating RyR1 activity: A commentary on “Structural insights into the regulation of RyR1 by S100A1”

Cell Calcium(2024)10.1016/j.ceca.2024.102947

N/A

0DataRank · unranked

0 citations

Kristen M. Varney, Pratyush Tiwary, David J. Weber, Erick O. Hernández‐Ochoa, Megan L. Perry

Modeling Boltzmann-weighted structural ensembles of proteins using artificial intelligence–based methods

Current Opinion in Structural Biology(2025)10.1016/j.sbi.2025.103000

N/A

0DataRank · unranked

30 citations

Xinyu Gu, Dedi Wang, Bodhi P. Vani, Pratyush Tiwary, Akashnathan Aranganathan

Generative AI for computational chemistry: A roadmap to predicting emergent phenomena

Proceedings of the National Academy of Sciences(2025)10.1073/pnas.2415655121

N/A

0DataRank · unranked

16 citations

Lukas Herron, Richard John, Suemin Lee, Disha Sanwal, Ruiyu Wang +1 more

af2rave: protein ensemble generation with physics-based sampling

Digital Discovery(2025)10.1039/d5dd00201j

N/A

0DataRank · unranked

7 citations

Vanessa J. Meraz, Akashnathan Aranganathan, Xinyu Gu, Pratyush Tiwary, Da Teng

Using Time Dependent Rate Analysis to Evaluate the Quality of Machine Learned Reaction Coordinates for Biasing and Computing Kinetics

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.03.662600

N/A

0DataRank · unranked

0 citations

Suemin Lee, Pilar Cossio, Pratyush Tiwary, Glen M. Hocky, Nicodemo Mazzaferro