Ara M. Abramyan Email & Phone Number

New York, New York, United States

San Diego, California, United States

• Offering feedback and suggestions to customers on how Schrödinger’s platform can facilitate their drug discovery endeavors, as a member of the Applications Science team
• Leading a project aimed at evaluating the incorporation of unnatural monomers into the ribosome using metadynamics simulations, in collaboration with the center for genetically encoded materials (C-GEM)
• Leading a project to validate Schrödinger’s free energy perturbation method (FEP+) for nucleic acid-small molecule systems, in collaboration with Schrödinger's Desmond team
• Leading two projects applying Schrödinger's IFD-MD and FEP+ to study ligands binding to the dopamine and serotonin neurotransmitter transporters
• Lead modeling services projects in collaboration with the Bill and Melinda Gates Foundation, to identify FEP-amenable targets as well as new hits for those targets
• Writing customized scripts for customers, to help Schrödinger's Python application team

San Diego, California

Baltimore, MD

• Elucidated molecular mechanisms of action of diverse classes of substrates and inhibitors binding to neurotransmitter transporters and receptors using a spectrum of computational chemistry methods (docking, extensive.
• Collaborated with cross-functional teams (chemists, pharmacologists, behavioral scientists) in multiple projects and led the molecular modeling aspect of discussions during project meetings
• Overall, contributions at NIDA resulted in 16 peer-reviewed journal articles, including 5 first-author publications

Philadelphia, PA

• Determined interaction binding modes of several sugar-foldamer recepor complexes.
• Identified mechanistic details of handedness induction by biasing groups on quinoline arylamide foldamers.
• Established structural and mechanistic details of water transport through foldamer channels.
• Overall, work at USciences resulted in 8 peer-reviewed articles, including 3 first-author publications.

Greater Philadelphia Area

• Determined the binding modes, conformational changes and binding/release mechanisms of foldamer capsule-ligand systems
• Identified structural pathways of folding-unfolding and handedness inversion of helical foldamers by NAMD metadynamics simulations
• Modified general AMBER force field (GAFF) torsional force field parameters to accurately describe aryl-amide foldamer conformations using quantum mechanics methods
• Determined the binding modes and structural deformations of foldamer-DNA complexes using the modified force field parameters
• Wrote codes in Python/Perl to calculate lipid order parameter, electron density, molecule cavity volume and other structural parameters; wrote R scripts for population network analysis

Summer 2014 - Organic Chemistry lab (~30 students) - CH203 Spring 2014 - Organic Chemistry recitations (~300 students/semester) - CH202Summer 2013 - Thermodynamics (senior chemistry undergraduate students) - GRE workshopFall 2012 - Thermodynamics (tutor) - CH321Summer 2012 - General Chemistry recitations (~40 students/semester) - CH102Fall 2011.

London, United Kingdom

• Identified flexible, potentially “druggable", regions in the Tripanosoma cruzi glutathione-dependant peroxidase I (TcGPXI) protein using molecular dynamics simulations based on the structure obtained from sequence.
• Generated cysteine to serine mutations in the TcGPXI by site-directed mutagenesis technique.

Moscow, Russian Federation

• Represented Xalatan and Xalacom drugs at hospitals in set areas
• Organized conferences and made presentations for doctors

Doctor Of Philosophy (Ph.D.), Biochemistry

Master'S Degree, Drug Discovery

Master'S Degree, Pharmacy