Publications by authors named "Omar Demerdash"

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Allosteric Prediction via Convolutional Neural Networks and Protein Structural and Dynamical Features.
T Rajitha Rajeshwar, John H Lagergren, Jeremy C Smith, Omar N A Demerdash

Biophys J· December 2025

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Divergent responses of branched and straight-chain lipid membranes to butanol stress revealed by molecular dynamics simulation.
Joshua O Aggrey, Micholas Dean Smith, Omar Demerdash, Robert F Standaert, Jeremy C Smith

Biophys J· October 2025

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Predicting receptor-ligand pairing preferences in plant-microbe interfaces via molecular dynamics and machine learning.
Erica T Prates, Omar Demerdash, Manesh Shah, Tomás A Rush, Udaya C Kalluri

Comput Struct Biotechnol J· June 2025

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TCR-H: explainable machine learning prediction of T-cell receptor epitope binding on unseen datasets.
Rajitha Rajeshwar T, Omar N A Demerdash, Jeremy C Smith

Front Immunol· September 2024

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Accurate Machine Learning for Predicting the Viscosities of Deep Eutectic Solvents.
Mood Mohan, Karuna Devi Jetti, Micholas Dean Smith, Omar N Demerdash, Michelle K Kidder

J Chem Theory Comput· May 2024

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Physics-Based Machine Learning Models Predict Carbon Dioxide Solubility in Chemically Reactive Deep Eutectic Solvents.
Mood Mohan, Omar N Demerdash, Blake A Simmons, Seema Singh, Michelle K Kidder

ACS Omega· April 2024

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Drugging the entire human proteome: Are we there yet?
Micholas Dean Smith, L Darryl Quarles, Omar Demerdash, Jeremy C Smith

Drug Discov Today· March 2024

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Predictive understanding of the surface tension and velocity of sound in ionic liquids using machine learning.
Mood Mohan, Micholas Dean Smith, Omar Demerdash, Michelle K Kidder, Jeremy C Smith

J Chem Phys· June 2023

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Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop .
Kevin R Cope, Erica T Prates, John I Miller, Omar N A Demerdash, Manesh Shah

Comput Struct Biotechnol J· December 2022

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Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.
Mikhail A Hameedi, Erica T Prates, Michael R Garvin, Irimpan I Mathews, B Kirtley Amos, Omar Demerdash

Nat Commun· September 2022

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Using diverse potentials and scoring functions for the development of improved machine-learned models for protein-ligand affinity and docking pose prediction.
Omar N A Demerdash

J Comput Aided Mol Des· November 2021

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Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.
Mikhail Ali Hameedi, Erica T Prates, Michael R Garvin, Irimpan Mathews, B Kirtley Amos, Omar Demerdash

bioRxiv· November 2021

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From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis.
Yuezhi Mao, Matthias Loipersberger, Paul R Horn, Akshaya Das, Omar Demerdash

Annu Rev Phys Chem· April 2021

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Potential Pathogenicity Determinants Identified from Structural Proteomics of SARS-CoV and SARS-CoV-2.
Erica T Prates, Michael R Garvin, Mirko Pavicic, Piet Jones, Manesh Shah, Omar Demerdash

Mol Biol Evol· January 2021

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Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets.
Michelle P Aranha, Catherine Spooner, Omar Demerdash, Bogdan Czejdo, Jeremy C Smith

Biochim Biophys Acta Gen Subj· April 2020

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Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum.
Valeriu Bortnov, Marco Tonelli, Woonghee Lee, Ziqing Lin, Douglas S Annis, Omar N Demerdash

Nat Commun· December 2019

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Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins.
Omar Demerdash, Utsab R Shrestha, Loukas Petridis, Jeremy C Smith, Julie C Mitchell

Front Mol Biosci· August 2019

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Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule.
Akshaya K Das, Omar N Demerdash, Teresa Head-Gordon

J Chem Theory Comput· December 2018

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Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations.
Omar Demerdash, Yuezhi Mao, Tianyi Liu, Martin Head-Gordon, Teresa Head-Gordon

J Chem Phys· October 2017

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Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations.
Yuezhi Mao, Omar Demerdash, Martin Head-Gordon, Teresa Head-Gordon

J Chem Theory Comput· November 2016

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Advanced Potential Energy Surfaces for Molecular Simulation.
Alex Albaugh, Henry A Boateng, Richard T Bradshaw, Omar N Demerdash, Jacek Dziedzic

J Phys Chem B· September 2016

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Convergence of the Many-Body Expansion for Energy and Forces for Classical Polarizable Models in the Condensed Phase.
Omar Demerdash, Teresa Head-Gordon

J Chem Theory Comput· August 2016

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CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.
Peter Cimermancic, Patrick Weinkam, T Justin Rettenmaier, Leon Bichmann, Daniel A Keedy, Omar N Demerdash

J Mol Biol· February 2016

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An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction.
Alex Albaugh, Omar Demerdash, Teresa Head-Gordon

J Chem Phys· November 2015

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Advanced potential energy surfaces for condensed phase simulation.
Omar Demerdash, Eng-Hui Yap, Teresa Head-Gordon

Annu Rev Phys Chem· April 2015

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