Publications by authors named "Sameer Varma"

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Phosphates and Phosphorylated Amino Acids for the AMOEBA-HFC Polarizable Force Field.
Julian M Delgado, Giorgio Schillaci, Sameer Varma

J Chem Theory Comput· November 2025

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ATP-Ion Complexation and Lithium's Bioactive Form in Cellular Solutions.
Julian M Delgado, Peter S Klein, Sameer Varma

J Am Chem Soc· June 2025

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A semi-automated workflow for DIA-based global discovery to pathway-driven PRM analysis.
Jennifer Guergues, Jessica Wohlfahrt, John M Koomen, Jonathan R Krieger, Sameer Varma

Proteomics· February 2025

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Structural Adaptation of Secondary p53 Binding Sites on MDM2 and MDMX.
Pirada Serena Higbee, Guy W Dayhoff, Asokan Anbanandam, Sameer Varma, Gary Daughdrill

J Mol Biol· July 2024

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Polarizable AMOEBA Model for Simulating Mg·Protein·Nucleotide Complexes.
Julian M Delgado, Péter R Nagy, Sameer Varma

J Chem Inf Model· January 2024

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Biochemical properties of naturally occurring human bloom helicase variants.
Rachel R Cueny, Sameer Varma, Kristina H Schmidt, James L Keck

PLoS One· June 2023

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Biochemical Properties of Naturally Occurring Human Bloom Helicase Variants.
Rachel R Cueny, Sameer Varma, Kristina H Schmidt, James L Keck

bioRxiv· January 2023

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Inclusion of High-Field Target Data in AMOEBA's Calibration Improves Predictions of Protein-Ion Interactions.
Julián A Delgado, Vered Wineman-Fisher, Sagar Pandit, Sameer Varma

J Chem Inf Model· October 2022

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High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular Simulations.
Matthew Saunders, Vered Wineman-Fisher, Eric Jakobsson, Sameer Varma, Sagar A Pandit

Langmuir· March 2022

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Cellular Uptake Pathways of Nanoparticles: Process of Endocytosis and Factors Affecting their Fate.
Sameer Varma, Smita Dey, Dhanabal Palanisamy

Curr Pharm Biotechnol· February 2022

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Molecular basis for higher affinity of SARS-CoV-2 spike RBD for human ACE2 receptor.
Julián M Delgado, Nalvi Duro, David M Rogers, Alexandre Tkatchenko, Sagar A Pandit, Sameer Varma

Proteins· September 2021

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Contrasting Local and Macroscopic Effects of Collagen Hydroxylation.
Sameer Varma, Joseph P R O Orgel, Jay D Schieber

Int J Mol Sci· August 2021

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Methyl-Induced Polarization Destabilizes the Noncovalent Interactions of N-Methylated Lysines.
Sanim Rahman, Vered Wineman-Fisher, Péter R Nagy, Yasmine Al-Hamdani, Alexandre Tkatchenko, Sameer Varma

Chemistry· July 2021

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Site-specific identification and validation of hepatic histone nitration in vivo: Implications for alcohol-induced liver injury.
Crystina L Kriss, Nalvi Duro, Owen W Nadeau, Jennifer Guergues, Omar Chavez-Chiang, Sameer Varma

J Mass Spectrom· June 2021

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Predictive QM/MM Modeling of Modulations in Protein-Protein Binding by Lysine Methylation.
Sanim Rahman, Vered Wineman-Fisher, Yasmine Al-Hamdani, Alexandre Tkatchenko, Sameer Varma

J Mol Biol· February 2021

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Improved description of ligand polarization enhances transferability of ion-ligand interactions.
Vered Wineman-Fisher, Yasmine Al-Hamdani, Péter R Nagy, Alexandre Tkatchenko, Sameer Varma

J Chem Phys· September 2020

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Transferable interactions of Li and Mg ions in polarizable models.
Vered Wineman-Fisher, Julián Meléndez Delgado, Péter R Nagy, Eric Jakobsson, Sagar A Pandit, Sameer Varma

J Chem Phys· September 2020

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Role of Structural Fluctuations in Allosteric Stimulation of Paramyxovirus Hemagglutinin-Neuraminidase.
Nalvi Duro, Sameer Varma

Structure· October 2019

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Interactions of Monovalent and Divalent Cations at Palmitoyl-Oleoyl-Phosphatidylcholine Interface.
James Kruczek, See-Wing Chiu, Sameer Varma, Eric Jakobsson, Sagar A Pandit

Langmuir· August 2019

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Interaction of salt with ether- and ester-linked phospholipid bilayers.
Matthew Saunders, Mark Steele, Wyatt Lavigne, Sameer Varma, Sagar A Pandit

Biochim Biophys Acta Biomembr· May 2019

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Ion-Hydroxyl Interactions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields.
Vered Wineman-Fisher, Yasmine Al-Hamdani, Iqbal Addou, Alexandre Tkatchenko, Sameer Varma

J Chem Theory Comput· April 2019

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An effective treatment approach of DPP-IV inhibitor encapsulated polymeric nanoparticles conjugated with anti-CD-4 mAb for type 1 diabetes.
Mahesh Thondawada, Ashish Devidas Wadhwani, Dhanabal S Palanisamy, Hanumant Singh Rathore, Ramesh C Gupta, Sameer Varma

Drug Dev Ind Pharm· July 2018

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Machine learning approaches to evaluate correlation patterns in allosteric signaling: A case study of the PDZ2 domain.
Mohsen Botlani, Ahnaf Siddiqui, Sameer Varma

J Chem Phys· June 2018

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Stimulation of Nipah Fusion: Small Intradomain Changes Trigger Extensive Interdomain Rearrangements.
Priyanka Dutta, Ahnaf Siddiqui, Mohsen Botlani, Sameer Varma

Biophys J· October 2016

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Nanomechanics of Type I Collagen.
Sameer Varma, Joseph P R O Orgel, Jay D Schieber

Biophys J· July 2016

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