Explanipedia

MLMD: Machine Learning Velocities to Propagate Molecular Dynamics Simulations Open

Guy W. Dayhoff, Sameer Varma · 2025

Temporal evolution in molecular dynamics (MD) simulations requires updates on particle velocities. These updates are obtained from forces that are computed traditionally from physics-based Hamiltonians, and more recently from machine-learn…

A semi-automated workflow for DIA-based global discovery to pathway-driven PRM analysis Open

Jennifer Guergues, Jessica Wohlfahrt, John M. Koomen, Jonathan R. Krieger, Sameer Varma , et al. · 2024

Targeted proteomics, which includes parallel reaction monitoring (PRM), is typically utilized for more precise detection and quantitation of key proteins and/or pathways derived from complex discovery proteomics datasets. Initial discovery…

Structural Adaptation of Secondary P53 Binding Sites on Mdm2 and Mdmx Open

Pirada S. Higbee, Guy W. Dayhoff, Asokan Anbanandam, Sameer Varma, Gary W. Daughdrill · 2024

Polarizable AMOEBA Model for Simulating Mg 2+ ·Protein·Nucleotide Complexes Open

Julián M. Delgado, Péter R. Nagy, Sameer Varma · 2023

Molecular mechanics (MM) simulations have the potential to provide detailed insights into the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities of these enzymes also require the binding of divalent …

Polarizable AMOEBA Model for Simulating Mg2+·Protein·Nucleotide Complexes Open

Julián M. Delgado, Peter R. Nagy, Sameer Varma · 2023

Molecular mechanics (MM) simulations have the potential to provide detailed insights into the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities of these enzymes also require the binding of divalent …

Biochemical properties of naturally occurring human bloom helicase variants Open

Rachel R. Cueny, Sameer Varma, Kristina Schmidt, James L. Keck · 2023

Bloom syndrome helicase (BLM) is a RecQ-family helicase implicated in a variety of cellular processes, including DNA replication, DNA repair, and telomere maintenance. Mutations in human BLM cause Bloom syndrome (BS), an autosomal recessiv…

Characterizing and Mapping Volcanic Flow Deposits on Mount St. Helens via Dual-Band SAR Imagery Open

Nikola Rogic, Sylvain Charbonnier, Franco Garin, Guy W. Dayhoff, Eric Gagliano , et al. · 2023

Mapping volcanic flow deposits can be achieved by considering backscattering characteristics as a metric of surface roughness. In this study, we developed an approach to extract a measure of surface roughness from dual-band airborne Synthe…

Biochemical Properties of Naturally Occurring Human Bloom Helicase Variants Open

Rachel R. Cueny, Sameer Varma, Kristina Schmidt, James L. Keck · 2023

Bloom syndrome helicase (BLM) is a RecQ-family helicase implicated in a variety of cellular processes, including DNA replication, DNA repair, and telomere maintenance. Mutations in human BLM cause Bloom syndrome (BS), an autosomal recessiv…

Inclusion of High-Field Target Data in AMOEBA’s Calibration Improves Predictions of Protein–Ion Interactions Open

Julián A. Delgado, Vered Wineman‐Fisher, Sagar A. Pandit, Sameer Varma · 2022

The reliability of molecular mechanics simulations to predict effects of ion binding to proteins depends on their ability to simultaneously describe ion-protein, ion-water, and protein-water interactions. Force fields (FFs) to describe pro…

High-Dimensional Parameter Search Method to Determine Force Field Mixing Terms in Molecular Simulations Open

Matthew Saunders, Vered Wineman‐Fisher, Eric Jakobsson, Sameer Varma, Sagar Pandit · 2022

Molecular dynamics (MD) force fields for lipids and ions are typically developed independently of one another. In simulations consisting of both lipids and ions, lipid-ion interaction energies are estimated using a predefined set of mixing…

Contrasting Local and Macroscopic Effects of Collagen Hydroxylation Open

Sameer Varma, Joseph Orgel, Jay D. Schieber · 2021

Collagen is heavily hydroxylated. Experiments show that proline hydroxylation is important to triple helix (monomer) stability, fibril assembly, and interaction of fibrils with other molecules. Nevertheless, experiments also show that even…

Methyl‐Induced Polarization Destabilizes the Noncovalent Interactions of N‐Methylated Lysines Open

Sanim Rahman, Vered Wineman‐Fisher, Péter R. Nagy, Yasmine S. Al-Hamdani, Alexandre Tkatchenko , et al. · 2021

Lysine methylation can modify noncovalent interactions by altering lysine's hydrophobicity as well as its electronic structure. Although the ramifications of the former are documented, the effects of the latter remain largely unknown. Unde…

Molecular basis for higher affinity of SARS‐CoV‐2 spike RBD for human ACE2 receptor Open

Julián M. Delgado, Nalvi Duro, David Rogers, Alexandre Tkatchenko, Sagar A. Pandit , et al. · 2021

Severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) has caused substantially more infections, deaths, and economic disruptions than the 2002‐2003 SARS‐CoV. The key to understanding SARS‐CoV‐2's higher infectivity lies partly in it…

Molecular basis for higher affinity of SARS-CoV-2 spike RBD for human ACE2 receptor Open

Julián M. Delgado, Nalvi Duro, David Rogers, Alexandre Tkatchenko, Sagar Pandit , et al. · 2021

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused substantially more infections, deaths, and economic disruptions than the 2002-2003 SARS-CoV. The key to understanding SARS-CoV-2’s higher infectivity lies partly in it…

Predictive QM/MM Modeling of Modulations in Protein–Protein Binding by Lysine Methylation Open

Sanim Rahman, Vered Wineman‐Fisher, Yasmine S. Al-Hamdani, Alexandre Tkatchenko, Sameer Varma · 2020

Transferable interactions of Li+ and Mg2+ ions in polarizable models Open

Vered Wineman‐Fisher, Julián M. Delgado, Péter R. Nagy, Eric Jakobsson, Sagar A. Pandit , et al. · 2020

Therapeutic implications of Li+, in many cases, stem from its ability to inhibit certain Mg2+-dependent enzymes, where it interacts with or substitutes for Mg2+. The underlying details of its action are, however, unknown. Molecular simulat…

Molecular basis for SARS-CoV-2 spike affinity for human ACE2 receptor Open

Julián M. Delgado, Nalvi Duro, David Rogers, Alexandre Tkatchenko, Sagar Pandit , et al. · 2020

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused substantially more infections, deaths, and economic disruptions than the 2002-2003 SARS-CoV. The key to understanding SARS-CoV-2’s higher infectivity may lie in its ho…

Improved description of ligand polarization enhances transferability of ion–ligand interactions Open

Vered Wineman‐Fisher, Yasmine S. Al-Hamdani, Péter R. Nagy, Alexandre Tkatchenko, Sameer Varma · 2020

The reliability of molecular mechanics (MM) simulations in describing biomolecular ion-driven processes depends on their ability to accurately model interactions of ions simultaneously with water and other biochemical groups. In these mode…

Identifying Time-Resolved Allosteric Signaling Pathways in Proteins using Supervised Machine Learning Open

Nalvi Duro, Sameer Varma · 2020

Improved Description of Ligand Polarization Enhances Transferability of Ionic Interactions Open

Vered Wineman‐Fisher, Yasmine S. Al-Hamdani, Alexandre Tkatchenko, Sameer Varma · 2020

Role of Structural Fluctuations in Allosteric Stimulation of Paramyxovirus Hemagglutinin-Neuraminidase Open

Nalvi Duro, Sameer Varma · 2019

Ion-Hydroxyl Interactions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields Open

Vered Wineman‐Fisher, Yasmine S. Al-Hamdani, Iqbal Addou, Alexandre Tkatchenko, Sameer Varma · 2019

Ion descriptors in molecular mechanics models are calibrated against reference data on ion-water interactions. It is then typically assumed that these descriptors will also satisfactorily describe interactions of ions with other functional…

Interaction of salt with ether- and ester-linked phospholipid bilayers Open

Matthew Saunders, Mark Steele, Wyatt Lavigne, Sameer Varma, Sagar Pandit · 2019

Effects of Monovalent Salt on Ether-Linked Phospholipid Bilayers Open

Matthew Saunders, Mark Steele, Wyatt Lavigne, Sameer Varma, Sagar Pandit · 2019

Ion-Hydroxyl Interactions: From High-Level Quantum Benchmarks to Transferable Polarizable Force Fields Open

Vered Wineman‐Fisher, Yasmine S. Al-Hamdani, Iqbal Adduo, Alexandre Tkatchenko, Sameer Varma · 2019

Hydroxylation of Type I Collagen: Effects on Fibrillar Structure and Mechanics Open

Alekhya A. Kandoor, Michele Kirchner, Vered Wineman‐Fisher, Yujia Xu, Sameer Varma · 2019

Structural Fluctuations are Key to Allosteric Stimulation of NDV Hemagglutinin-Neuraminidase Open

Nalvi Duro, Sameer Varma · 2019

Molecular Basis for the Hierarchical Dependency of Collagen Mechanics Open

Sameer Varma, Joseph Orgel, Jay D. Schieber · 2018

Dynamic Allostery in Regulated Entry of Newcastle Disease Virus into Host Cells Open

Nalvi Duro, Sameer Varma · 2017

Incorporation of Multi-State Information Improves Molecular Modelling of Dynamic Allostery: A Case Study of PDZ Domains Computational Quantitative Characterization of Entropic Signaling Pathways in Proteins: A Case Study on Human PDZ2 Domain of PTP1E Open

Mohsen Botlani, Sameer Varma · 2017

Sameer Varma YOU? Author Swipe