Pratyush Tiwary (P Tiwary)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 53

Top Topics

Molecular Dynamics

Top Venues

Journal of chemical theory and computation

The journal of physical chemistry. B

Journal of chemical information and modeling

The Journal of chemical physics

This page only lists publications with an associated author ORCID identifier.

Publications

Ruiyu Wang, Shams Mehdi, Ziyue Zou, Pratyush Tiwary
Is the Local Ion Density Sufficient to Drive NaCl Nucleation from the Melt and Aqueous Solution? The journal of physical chemistry. B 128 (4) (2024)
Vanessa J Meraz, Ziyue Zou, Pratyush Tiwary
Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck Based Enhanced Sampling. The journal of physical chemistry. B (2024)
Eric R Beyerle, Pratyush Tiwary
Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation. The journal of physical chemistry. B 128 (3) (2024)
Zachary Smith, Michael Strobel, Bodhi P Vani, Pratyush Tiwary
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention. Journal of chemical information and modeling 64 (7) (2024)
Zachary Smith, Michael Strobel, Bodhi P Vani, Pratyush Tiwary
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention. Journal of chemical information and modeling 64 (7) (2024)
Ruiyu Wang, Shams Mehdi, Ziyue Zou, Pratyush Tiwary
Is the Local Ion Density Sufficient to Drive NaCl Nucleation from the Melt and Aqueous Solution? The journal of physical chemistry. B (2024)
Vanessa J Meraz, Ziyue Zou, Pratyush Tiwary
Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck Based Enhanced Sampling. The journal of physical chemistry. B 128 (34) (2024)
Shams Mehdi, Pratyush Tiwary
Thermodynamics-inspired explanations of artificial intelligence. Nature communications 15 (1) (2024)
Vanessa J Meraz, Ziyue Zou, Pratyush Tiwary
Simulating Crystallization in a Colloidal System Using State Predictive Information Bottleneck Based Enhanced Sampling. The journal of physical chemistry. B 128 (34) (2024)
Ruiyu Wang, Pratyush Tiwary
Atomic scale insights into NaCl nucleation in nanoconfined environments. Chemical science (2024)
Ziyue Zou, Pratyush Tiwary
Enhanced Sampling of Crystal Nucleation with Graph Representation Learnt Variables. The journal of physical chemistry. B (2024)
Suemin Lee, Dedi Wang, Markus A Seeliger, Pratyush Tiwary
Calculating Protein-Ligand Residence Times through State Predictive Information Bottleneck Based Enhanced Sampling. Journal of chemical theory and computation (2024)
Ziyue Zou, Pratyush Tiwary
Enhanced Sampling of Crystal Nucleation with Graph Representation Learnt Variables. The journal of physical chemistry. B 128 (12) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation 20 (12) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation 20 (12) (2024)
Suemin Lee, Dedi Wang, Markus A Seeliger, Pratyush Tiwary
Calculating Protein-Ligand Residence Times through State Predictive Information Bottleneck Based Enhanced Sampling. Journal of chemical theory and computation (2024)
Zachary Smith, Michael Strobel, Bodhi P Vani, Pratyush Tiwary
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention. Journal of chemical information and modeling 64 (7) (2024)
Eric R Beyerle, Pratyush Tiwary
Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation. The journal of physical chemistry. B (2024)
Xinyu Gu, Akashnathan Aranganathan, Pratyush Tiwary
Empowering AlphaFold2 for protein conformation selective drug discovery with AlphaFold2-RAVE. eLife 13 (2024)
Zachary Smith, Michael Strobel, Bodhi P Vani, Pratyush Tiwary
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention. Journal of chemical information and modeling 64 (7) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation 20 (12) (2024)
Dedi Wang, Yihang Wang, Luke Evans, Pratyush Tiwary
From Latent Dynamics to Meaningful Representations. Journal of chemical theory and computation 20 (9) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation 20 (12) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation 20 (12) (2024)
Dedi Wang, Yunrui Qiu, Eric R Beyerle, Xuhui Huang, Pratyush Tiwary
Information Bottleneck Approach for Markov Model Construction. Journal of chemical theory and computation (2024)
Zachary Smith, Michael Strobel, Bodhi P Vani, Pratyush Tiwary
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention. Journal of chemical information and modeling (2024)
Zachary Smith, Michael Strobel, Bodhi P Vani, Pratyush Tiwary
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention. Journal of chemical information and modeling 64 (7) (2024)
Dedi Wang, Yihang Wang, Luke Evans, Pratyush Tiwary
From Latent Dynamics to Meaningful Representations. Journal of chemical theory and computation (2024)
Zachary Smith, Michael Strobel, Bodhi P Vani, Pratyush Tiwary
Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention. Journal of chemical information and modeling (2024)
Suemin Lee, Dedi Wang, Markus A Seeliger, Pratyush Tiwary
Calculating Protein-Ligand Residence Times through State Predictive Information Bottleneck Based Enhanced Sampling. Journal of chemical theory and computation 20 (14) (2024)
Bodhi P Vani, Akashnathan Aranganathan, Dedi Wang, Pratyush Tiwary
AlphaFold2-RAVE: From Sequence to Boltzmann Ranking. Journal of chemical theory and computation (2023)
Bodhi P Vani, Akashnathan Aranganathan, Pratyush Tiwary
Exploring Kinase Asp-Phe-Gly (DFG) Loop Conformational Stability with AlphaFold2-RAVE. Journal of chemical information and modeling (2023)
Renjie Zhao, Ziyue Zou, John D Weeks, Pratyush Tiwary
Quantifying the Relevance of Long-Range Forces for Crystal Nucleation in Water. Journal of chemical theory and computation (2023)
Bodhi P Vani, Akashnathan Aranganathan, Dedi Wang, Pratyush Tiwary
AlphaFold2-RAVE: From Sequence to Boltzmann Ranking. Journal of chemical theory and computation (2023)
Dedi Wang, Renjie Zhao, John D Weeks, Pratyush Tiwary
Influence of Long-Range Forces on the Transition States and Dynamics of NaCl Ion-Pair Dissociation in Water. The journal of physical chemistry. B 126 (2) (2022)
L Evans, Maria Cameron, Pratyush Tiwary
Computing committors via Mahalanobis diffusion maps with enhanced sampling data. The Journal of chemical physics 157 (21) (2022)
Eric R Beyerle, Shams Mehdi, Pratyush Tiwary
Quantifying Energetic and Entropic Pathways in Molecular Systems. The journal of physical chemistry. B 126 (21) (2022)
Sun-Ting Tsai, Eric Fields, Yijia Xu, En-Jui Kuo, Pratyush Tiwary
Path sampling of recurrent neural networks by incorporating known physics. Nature communications 13 (1) (2022)
Shams Mehdi, Dedi Wang, Shashank Pant, Pratyush Tiwary
Accelerating All-Atom Simulations and Gaining Mechanistic Understanding of Biophysical Systems through State Predictive Information Bottleneck. Journal of chemical theory and computation 18 (5) (2022)
Mrinal Shekhar, Zachary Smith, Markus A Seeliger, Pratyush Tiwary
Protein Flexibility and Dissociation Pathway Differentiation Can Explain Onset of Resistance Mutations in Kinases. Angewandte Chemie (International ed. in English) 61 (28) (2022)
Yihang Wang, Shaifaly Parmar, John S Schneekloth, Pratyush Tiwary
Interrogating RNA-Small Molecule Interactions with Structure Probing and Artificial Intelligence-Augmented Molecular Simulations. ACS central science 8 (6) (2022)
Zachary Smith, Pratyush Tiwary
Making High-Dimensional Molecular Distribution Functions Tractable through Belief Propagation on Factor Graphs. The journal of physical chemistry. B 125 (40) (2021)
Shashank Pant, Zachary Smith, Yihang Wang, Emad Tajkhorshid, Pratyush Tiwary
Confronting pitfalls of AI-augmented molecular dynamics using statistical physics. The Journal of chemical physics 153 (23) (2021)
Sun-Ting Tsai, Zachary Smith, Pratyush Tiwary
SGOOP-d: Estimating Kinetic Distances and Reaction Coordinate Dimensionality for Rare Event Systems from Biased/Unbiased Simulations. Journal of chemical theory and computation 17 (11) (2021)
Ziyue Zou, Sun-Ting Tsai, Pratyush Tiwary
Toward Automated Sampling of Polymorph Nucleation and Free Energies with the SGOOP and Metadynamics. The journal of physical chemistry. B 125 (47) (2021)
Dedi Wang, Pratyush Tiwary
State predictive information bottleneck. The Journal of chemical physics 154 (13) (2021)
Zachary Smith, Pavan Ravindra, Yihang Wang, Rory Cooley, Pratyush Tiwary
Discovering Protein Conformational Flexibility through Artificial-Intelligence-Aided Molecular Dynamics. The journal of physical chemistry. B 124 (38) (2020)
Yihang Wang, Pratyush Tiwary
Understanding the role of predictive time delay and biased propagator in RAVE. The Journal of chemical physics 152 (14) (2020)
Debabrata Pramanik, Zachary Smith, Adam Kells, Pratyush Tiwary
Can One Trust Kinetic and Thermodynamic Observables from Biased Metadynamics Simulations?: Detailed Quantitative Benchmarks on Millimolar Drug Fragment Dissociation. The journal of physical chemistry. B 123 (17) (2019)
Sun-Ting Tsai, Zachary Smith, Pratyush Tiwary
Reaction coordinates and rate constants for liquid droplet nucleation: Quantifying the interplay between driving force and memory. The Journal of chemical physics 151 (15) (2019)
João Marcelo Lamim Ribeiro, Pratyush Tiwary
Toward Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE. Journal of chemical theory and computation 15 (1) (2018)
João Marcelo Lamim Ribeiro, Sun-Ting Tsai, Debabrata Pramanik, Yihang Wang, Pratyush Tiwary
Kinetics of Ligand-Protein Dissociation from All-Atom Simulations: Are We There Yet? Biochemistry 58 (3) (2018)
Pratyush Tiwary
Molecular Determinants and Bottlenecks in the Dissociation Dynamics of Biotin-Streptavidin. The journal of physical chemistry. B 121 (48) (2017)