Pratyush Tiwary
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Explore the profile of Pratyush Tiwary including associated specialties, affiliations and a list of published articles.
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79
Citations
1481
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Recent Articles
1.
Tribello G, Bonomi M, Bussi G, Camilloni C, Armstrong B, Arsiccio A, et al.
J Chem Phys
. 2025 Mar;
162(9).
PMID: 40035582
In computational physics, chemistry, and biology, the implementation of new techniques in shared and open-source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software...
2.
Aranganathan A, Gu X, Wang D, Vani B, Tiwary P
Curr Opin Struct Biol
. 2025 Feb;
91:103000.
PMID: 39923288
This review highlights recent advances in AI-driven methods for generating Boltzmann-weighted structural ensembles, which are crucial for understanding biomolecular dynamics and drug discovery. With the rise of deep learning models...
3.
Alkhalaf L, Arrowsmith C, Balskus E, Bergamini G, Bhandari R, Chang C, et al.
Nat Chem Biol
. 2024 Dec;
21(1):6-15.
PMID: 39719500
No abstract available.
4.
Inferring phase transitions and critical exponents from limited observations with thermodynamic maps
Herron L, Mondal K, Schneekloth Jr J, Tiwary P
Proc Natl Acad Sci U S A
. 2024 Dec;
121(52):e2321971121.
PMID: 39680772
Phase transitions are ubiquitous across life, yet hard to quantify and describe accurately. In this work, we develop an approach for characterizing generic attributes of phase transitions from very limited...
5.
Wang D, Tiwary P
J Chem Theory Comput
. 2024 Nov;
20(23):10371-10383.
PMID: 39589127
The weighted ensemble (WE) method stands out as a widely used segment-based sampling technique renowned for its rigorous treatment of kinetics. The WE framework typically involves initially mapping the configuration...
6.
Fullenkamp C, Mehdi S, Jones C, Tenney L, Pichling P, Prestwood P, et al.
bioRxiv
. 2024 Sep;
PMID: 39314358
The challenge of targeting RNA with small molecules necessitates a better understanding of RNA-ligand interaction mechanisms. However, the dynamic nature of nucleic acids, their ligand-induced stabilization, and how conformational changes...
7.
Mehdi S, Tiwary P
Nat Commun
. 2024 Sep;
15(1):7859.
PMID: 39251574
In recent years, predictive machine learning models have gained prominence across various scientific domains. However, their black-box nature necessitates establishing trust in them before accepting their predictions as accurate. One...
8.
Gu X, Aranganathan A, Tiwary P
Elife
. 2024 Sep;
13.
PMID: 39240197
Small-molecule drug design hinges on obtaining co-crystallized ligand-protein structures. Despite AlphaFold2's strides in protein native structure prediction, its focus on apo structures overlooks ligands and associated holo structures. Moreover, designing...
9.
Wang R, Tiwary P
Chem Sci
. 2024 Sep;
PMID: 39234215
In this work we examine the nucleation from NaCl aqueous solutions within nano-confined environments, employing enhanced sampling molecular dynamics simulations integrated with machine learning-derived reaction coordinates. Through our simulations, we...
10.
Perry M, Varney K, Tiwary P, Weber D, Hernandez-Ochoa E
Cell Calcium
. 2024 Sep;
123():102947.
PMID: 39226841
S100A1, a calcium-binding protein, plays a crucial role in regulating Ca signaling pathways in skeletal and cardiac myocytes via interactions with the ryanodine receptor (RyR) to affect Ca release and...