Naeyma Islam

I develop and use theoretical and computational techniques to characterize and study bio-molecular systems to aid computer-aided drug design with a focus on docking-based and pharmacophore-based virtual screening, homology modeling of proteins, hit identification and hit to lead and multi-parameter optimization. Experience with statistical mechanics, conventional and enhanced-sampling molecular dynamics (MD) simulations, constant pH simulation, coarse-grained simulation, and quantum mechanical (QM) calculations. Skilled in free energy calculations specially using the free energy perturbation (FEP) method to study receptor-ligand binding and the importance of water to binding. Strong background in python and machine learning. Enjoy interacting with scientists from different disciplines and the challenges of designing models to complement experimental needs. Able to work in high-stress situations and can handle multiple projects at the same time. A highly motivated researcher who is keen to pick up new skills rapidly. Hardworking Postdoctoral Research Fellow with demonstrated record of research success in. Self-directed and motivated professional with highly-ethical, meticulous and thorough approach.

• Machine Learning, Stanford University, USA, LINK
• Computer-Aided Drug Design, Schrodinger, USA, LINK
• Drug Discovery, The University of California San Diego, USA, LINK

• First Prize in Chemistry department poster competition, University of New Orleans, LINK
• Best mentor for mentoring high school students in the Summer Research Program, Advanced Materials Research Institute (AMRI), University of New Orleans

• Coarse grained models for constant pH simulations of carboxylic acids, Naeyma Islam; Sharma, Arjun; Gyawali, Gaurav; Kumar, Revati; Rick, Steven, J. Chem. Theory Comput., 2019, 15, 8
• Water hydrogen degrees of freedom and the hydrophobic effect, Naeyma Islam, Mahalia Flint and Steven Rick, J. Chem. Phys, 2019, 150, 1
• Molecular dynamics simulations of the flexibility and inhibition of SARS-CoV-2 NSP 13 helicase, Raubenolt, Bryan; Islam, Naeyma; Summa, Christoper & Rick, Steven, Journal of Molecular Graphics and Modelling, 2022, 112, 108122
• The Small Molecule Antagonist KCI807 Disrupts Association of the Amino-terminal Domain of the Androgen Receptor with ELK1 by Modulating the Adjacent DNA Binding Domain, Soave, Claire; Ducker, Charles ;Islam, Naeyma; Kim, Seongho; Yurgelevic, Sally; Nicely, Nathan; Pardy, Luke; et al., Molecular Pharmacology April 2023, 103 (4) 211-220; DOI: https://doi.org/10.1124/molpharm.122.000589
• Statistical Mechanics Metrics in Pairing and Parsing In Silico and Phenotypic Data of a Novel Genetic NFκB1 (c. T638A) Variant, Eman N Chaudhri, Jessica M Abbott, Naeyma N Islam, Caleb A Weber, Mathew A Coban, Ahmet Bilgili, Jacqueline D Squire, Sarah Mantia, Klaas J Wierenga, Thomas R Caulfield., Genes 2023, 14(10), 1855; https://doi.org/10.3390/genes14101855
• Structure of Boranes Based on the Topology of Molecular Electron Density, Naeyma Islam, Diss. Middle Tennessee State University, 2016

• Dr. Thomas Caulfield, Associate Professor, Neuroscience Department, Mayo Clinic, Jacksonvile, FL, caulfield.thomas@mayo.edu
• Dr. Steven W. Rick, Professor, Chemistry Departmenrt, University of New Orleans, srick@uno.edu
• Dr. Guido Scarabelli, Senior Scientist II, Application Science, Schrödinger Inc., guido.scarabelli@schrodinger.com
• Dr. Weilie Zhou, Professor, Chemistry Departmenrt, University of New Orleans, wzhou@uno.edu