Omar N A Demerdash
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Explore the profile of Omar N A Demerdash including associated specialties, affiliations and a list of published articles.
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11
Citations
234
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Recent Articles
1.
TCR-H: explainable machine learning prediction of T-cell receptor epitope binding on unseen datasets
Rajeshwar T R, Demerdash O, Smith J
Front Immunol
. 2024 Sep;
15:1426173.
PMID: 39221256
Artificial-intelligence and machine-learning (AI/ML) approaches to predicting T-cell receptor (TCR)-epitope specificity achieve high performance metrics on test datasets which include sequences that are also part of the training set but...
2.
Cope K, Prates E, Miller J, Demerdash O, Shah M, Kainer D, et al.
Comput Struct Biotechnol J
. 2023 Feb;
21:1122-1139.
PMID: 36789259
For plants, distinguishing between mutualistic and pathogenic microbes is a matter of survival. All microbes contain microbe-associated molecular patterns (MAMPs) that are perceived by plant pattern recognition receptors (PRRs). Lysin...
3.
Demerdash O
J Comput Aided Mol Des
. 2021 Oct;
35(11):1095-1123.
PMID: 34708263
The advent of computational drug discovery holds the promise of significantly reducing the effort of experimentalists, along with monetary cost. More generally, predicting the binding of small organic molecules to...
4.
Zhu X, Ericksen S, Demerdash O, Mitchell J
Proteins
. 2013 Sep;
81(12):2221-8.
PMID: 24038640
We describe methods and results for four new types of challenge in the Critical Assessment of PRedicted Interactions (CAPRI). Two new challenges asked predictors to create models related to protein...
5.
Moretti R, Fleishman S, Agius R, Torchala M, Bates P, Kastritis P, et al.
Proteins
. 2013 Jul;
81(11):1980-7.
PMID: 23843247
Community-wide blind prediction experiments such as CAPRI and CASP provide an objective measure of the current state of predictive methodology. Here we describe a community-wide assessment of methods to predict...
6.
Demerdash O, Mitchell J
Proteins
. 2013 Jun;
81(11):1919-30.
PMID: 23760773
Protein-protein interactions are a fundamental aspect of many biological processes. The advent of recombinant protein and computational techniques has allowed for the rational design of proteins with novel binding capabilities....
7.
Demerdash O, Mitchell J
Proteins
. 2012 Mar;
80(7):1766-79.
PMID: 22434479
Normal mode analysis has emerged as a useful technique for investigating protein motions on long time scales. This is largely due to the advent of coarse-graining techniques, particularly Hooke's Law-based...
8.
Fleishman S, Whitehead T, Strauch E, Corn J, Qin S, Zhou H, et al.
J Mol Biol
. 2011 Oct;
414(2):289-302.
PMID: 22001016
The CAPRI (Critical Assessment of Predicted Interactions) and CASP (Critical Assessment of protein Structure Prediction) experiments have demonstrated the power of community-wide tests of methodology in assessing the current state...
9.
Hendrickson M, Rao A, Demerdash O, Kalil R
PLoS One
. 2011 Apr;
6(4):e18535.
PMID: 21490921
Neurons and glial cells in the developing brain arise from neural progenitor cells (NPCs). Nestin, an intermediate filament protein, is thought to be expressed exclusively by NPCs in the normal...
10.
Demerdash O, Buyan A, Mitchell J
Proteins
. 2010 Aug;
78(15):3156-65.
PMID: 20715288
We present a computationally efficient method for flexible refinement of docking predictions that reflects observed motions within a protein's structural class. Using structural homologs, we derive deformation models that capture...