Author details

Full Name

Omar Demerdash

Affiliation

ORCID

Career Start Year

2009

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37260016	Predictive understanding of the surface tension and velocity of sound in ionic liquids using machine learning.		2023
36789259	Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop <i>Populus</i>.	Comput Struct Biotechnol J	2022
36075915	Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.	Nature Communications	2022
34816264	Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.		2021
33636998	From Intermolecular Interaction Energies and Observable Shifts to Component Contributions and Back Again: A Tale of Variational Energy Decomposition Analysis.	Annual Review of Physical Chemistry	2021
32941612	Potential Pathogenicity Determinants Identified from Structural Proteomics of SARS-CoV and SARS-CoV-2.	Mol Biol Evol	2021
34708263	Using diverse potentials and scoring functions for the development of improved machine-learned models for protein-ligand affinity and docking pose prediction.	Journal of Computer-Aided Molecular Design	2021
33200117	Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.	ChemRxiv	2020
31954798	Prediction of peptide binding to MHC using machine learning with sequence and structure-based feature sets.	Biochimica et Biophysica Acta - General Subjects	2020
31819058	Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum.	Nat Commun	2019
30428257	Improvements to the AMOEBA Force Field by Introducing Anisotropic Atomic Polarizability of the Water Molecule.	Journal of Chemical Theory and Computation	2018
29096520	Assessing many-body contributions to intermolecular interactions of the AMOEBA force field using energy decomposition analysis of electronic structure calculations.	Journal of Chemical Physics	2017
27709939	Assessing Ion-Water Interactions in the AMOEBA Force Field Using Energy Decomposition Analysis of Electronic Structure Calculations.	Journal of Chemical Theory and Computation	2016
27405002	Convergence of the Many-Body Expansion for Energy and Forces for Classical Polarizable Models in the Condensed Phase.	Journal of Chemical Theory and Computation	2016
26854760	CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.	J Mol Biol	2016
27513316	Advanced Potential Energy Surfaces for Molecular Simulation.	J Phys Chem B	2016
26547155	An efficient and stable hybrid extended Lagrangian/self-consistent field scheme for solving classical mutual induction.	Journal of Chemical Physics	2015
24328448	Advanced potential energy surfaces for condensed phase simulation.	Annual Review of Physical Chemistry	2014
23843247	Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.	Proteins	2013
24038640	Data-driven models for protein interaction and design.	Proteins: Structure, Function and Bioinformatics	2013
23760773	Using physical potentials and learned models to distinguish native binding interfaces from de novo designed interfaces that do not bind.	Proteins: Structure, Function and Bioinformatics	2013
22434479	Density-cluster NMA: A new protein decomposition technique for coarse-grained normal mode analysis.	Proteins: Structure, Function and Bioinformatics	2012
22001016	Community-wide assessment of protein-interface modeling suggests improvements to design methodology.	J Mol Biol	2011
21490921	Expression of nestin by neural cells in the adult rat and human brain.	PLoS ONE	2011
20715288	ReplicOpter: a replicate optimizer for flexible docking.	Proteins: Structure, Function and Bioinformatics	2010
19816556	Structure-based predictive models for allosteric hot spots.	PLoS Computational Biology	2009