Browsing by Author "Haddad, Yazan Abdulmajeed Eyadh"
Now showing items 1-4 of 4
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Homology modeling in the time of collective and artificial intelligence
(Elsevier Science BV, 2020)Homology modeling is a method for building protein 3D structures using protein primary sequence and utilizing prior knowledge gained from structural similarities with other proteins. The homology modeling process is done ... -
Peptide-Carbon Quantum Dots conjugate, Derived from Human Retinoic Acid Receptor Responder Protein 2, against Antibiotic-Resistant Gram Positive and Gram Negative Pathogenic Bacteria
(MDPI AG (Multidisciplinary Digital Publishing Institute-MDPI), 2020)Antibiotic-resistant bacterial infections have become global issues for public health, which increases the utter need to develop alternatives to antibiotics. Here, the HSER (Homo sapiens retinoic acid receptor) peptide was ... -
Rotamer Dynamics: Analysis of Rotamers in Molecular Dynamics Simulations of Proteins
(Biophysical Society, 2019)Given by χ torsional angles, rotamers describe the side-chain conformations of amino acid residues in a protein based on the rotational isomers (hence the word rotamer). Constructed rotamer libraries, based on either protein ... -
Solvent Accessibility Promotes Rotamer Errors during Protein Modeling with Major Side-Chain Prediction Programs
(American Chemical Society, 2023)Side-chain rotamer prediction is one of the most critical late stages in protein 3D structure building. Highly advanced and specialized algorithms (e.g., FASPR, RASP, SCWRL4, and SCWRL4v) optimize this process by use of ...
