Omar N. A. Demerdash

发表

Expression of Nestin by Neural Cells in the Adult Rat and Human Brain

Abigail J. Rao, R. Kalil, Michael L. Hendrickson, 2011, PloS one.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

John A. Gunnels, Julie C. Mitchell, Matthew B. Baker, 2020, Journal of chemical information and modeling.

From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis.

Daniel S. Levine, Paul R. Horn, M. Head‐Gordon, 2021, Annual review of physical chemistry.

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

Duncan Poole, John A. Gunnels, Arvind Ramanathan, 2020, J. Chem. Inf. Model..

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.

Julie C. Mitchell, Andrej Sali, Dina Schneidman-Duhovny, 2016, Journal of molecular biology.

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

Julie C. Mitchell, S. Irle, I. Mathews, 2022, Nature Communications.

Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus

Daniel A. Jacobson, T. Tschaplinski, D. Jacobson, 2022, Computational and structural biotechnology journal.

Convergence of the Many-Body Expansion for Energy and Forces for Classical Polarizable Models in the Condensed Phase.

Teresa Head-Gordon, Omar Demerdash, Omar N. A. Demerdash, 2016, Journal of chemical theory and computation.

Advanced potential energy surfaces for condensed phase simulation.

Teresa Head-Gordon, Omar Demerdash, Eng-Hui Yap, 2014, Annual review of physical chemistry.

Advanced models for water simulations

Lee‐Ping Wang, T. Head-Gordon, O. Demerdash, 2018 .

Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins

Julie C. Mitchell, Jeremy C. Smith, Utsab R. Shrestha, 2019, Front. Mol. Biosci..

Functional Immune Deficiency Syndrome via Intestinal Infection in COVID-19

Daniel A. Jacobson, Eric E. Bardes, B. Aronow, 2020, bioRxiv.

Confronting the COVID-19 Pandemic with Systems Biology

Daniel A. Jacobson, Eric E. Bardes, B. Aronow, 2020 .

Potential Pathogenicity Determinants Identified from Structural Proteomics of SARS-CoV and SARS-CoV-2

Daniel A. Jacobson, D. Jacobson, O. Demerdash, 2020, Molecular biology and evolution.

Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions

Julie C. Mitchell, Jeffrey J. Gray, Z. Weng, 2013, Proteins.

Community-wide assessment of protein-interface modeling suggests improvements to design methodology.

Kengo Kinoshita, Haruki Nakamura, Genki Terashi, 2011, Journal of molecular biology.

Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum

Julie C. Mitchell, A. Bateman, J. Markley, 2019, Nature Communications.

Density‐cluster NMA: A new protein decomposition technique for coarse‐grained normal mode analysis

Julie C. Mitchell, Julie C Mitchell, Omar N A Demerdash, 2012, Proteins.

Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations.

M. Head‐Gordon, T. Head-Gordon, O. Demerdash, 2016, Journal of chemical theory and computation.

Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule.

Omar N. A. Demerdash, A. Das, T. Head‐Gordon, 2018, Journal of chemical theory and computation.

Structure-Based Predictive Models for Allosteric Hot Spots

Julie C. Mitchell, Michael D. Daily, Omar N. A. Demerdash, 2009, PLoS Comput. Biol..

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, 2021, Journal of Computer-Aided Molecular Design.

Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets.

Julie C. Mitchell, Julie C Mitchell, Bogdan Czejdo, 2020, Biochimica et biophysica acta. General subjects.

Data‐driven models for protein interaction and design

Julie C. Mitchell, Julie C Mitchell, Spencer S Ericksen, 2013, Proteins.

Using physical potentials and learned models to distinguish native binding interfaces from de novo designed interfaces that do not bind

Julie C. Mitchell, Julie C Mitchell, Omar N A Demerdash, 2013, Proteins.

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

Julie C. Mitchell, Daniel A. Jacobson, D. Jacobson, 2021, bioRxiv.

Advanced Potential Energy Surfaces for Molecular Simulation.

Jonathan W Essex, Qiao Zeng, Jay W Ponder, 2016, The journal of physical chemistry. B.

An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction.

Teresa Head-Gordon, Omar Demerdash, Alex Albaugh, 2015, The Journal of chemical physics.

Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations.

M. Head‐Gordon, T. Head-Gordon, O. Demerdash, 2017, The Journal of chemical physics.

Quantum Chemistry-Driven Machine Learning Approach for the Prediction of the Surface Tension and Speed of Sound in Ionic Liquids

Jeremy C. Smith, B. Simmons, Seema Singh, 2023, ACS Sustainable Chemistry & Engineering.

Predictive understanding of the surface tension and velocity of sound in ionic liquids using machine learning.

Jeremy C. Smith, M. Kidder, MicholasDean Smith, 2023, The Journal of chemical physics.

ReplicOpter: A replicate optimizer for flexible docking

Julie C. Mitchell, O. Demerdash, Amanda Buyan, 2010, Proteins.

Normal Mode Analysis of Macromolecules: From Enzyme Active Sites to Molecular Machines

Guohui Li, Q. Cui, O. Demerdash, 2005 .

Accurate Prediction of Carbon Dioxide Capture by Deep Eutectic Solvents using Quantum Chemistry and a Neural Network

B. Simmons, Seema Singh, M. Kidder, 2023, Green Chemistry.