Senior Scientist: Cheminformatics & Computational Chemistry
Resume:
Vinaya Kumar Golla, Ph.D.
Computational Chemistry, Molecular Biology, and Biochemistry expert
# ***********@*****.*** 860-***-**** Charlottesville, Virginia, USA
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§ GitHub English, Hindi, Telugu, German (A2)
Summary
• Strong expertise, including over 12 years of experience in molecular modeling methods such as molecular dynamics simulations, free energy calculations, force field development and validation, quantum chemical calculations, homology modeling, molecular docking, drug design, quantitative structure-activity relationship (QSAR) modeling, pharmacophore modeling, ADMET (absorption, distribution, metabolism, excretion, and toxicity), and virtual screening approaches
• Experience in applying AI and ML methods to protein and peptide structure prediction and activity analysis
• Dedicated biochemist with extensive experience in protein biochemistry and structural biology. Proficient in recombinant protein expression, purification, and analytical characterization. Skilled in cell culture work, chromatography techniques, and cryo-em methods
• Development of Chemoinformatics and Bioinformatics tools
• Excellent in science communication and technical writing skills
• Ability to achieve research targets by managing multiple projects simultaneously
• Proven ability to work in multidisciplinary and collaborative environments
• Extensive experience in supervising, mentoring, and training lab personnel Skills
Molecular Dynamics Molecular Docking Free Energy Calculations/FEP Homology Modeling AlphaFold/Rosetta Virtual Screening QSAR LBDD, SBDD Quantum calculations ADMET analysis Schrödinger Maestro Accelrys Discovery Studio PyMOL, VMD Machine learning Chemo and Bioinformatic tools QM/MM Protein expression Protein purification Gene editing/cloning Protein mutations AKTA/FPLC Cryo-EM/Negative staining DLS IXE/HIC/SEC/AC SDS-PAGE Immunoblotting Nanodiscs Native-PAGE
Scientific Writing C, C++, Python, R Bash, awk, and PHP Windows, Linux Education
Apr 2016 – Dec 2020 Jacobs University Bremen, Bremen, Germany PhD in Biochemical Engineering
Aug 2011 – July
2013
National Institute of Pharmaceutical Education and Research, Mohali, India M.S. (Pharm.) in Pharmacoinformatics - 8.44 CGPA
Sep 2007 – May
2011
GIET School of Pharmacy, Rajahmundry, India
Bachelors in Pharmacy - 8.56 CGPA
Work Experience
Jun 2023 - Ongoing Research Associate
University of Virginia, Charlottesville, Virginia, USA
• Modeled novel antimicrobial peptides and screened a library of 2 million compounds
• Integrated AI, ML, and in-silico screening approaches to identify peptide activity and ability to cross the Blood Brain Barrier selectively
• Applied structural biology methods such as cryo-electron microscopy (cryoEM) and compu- tational modeling (AlphaFold/Rosetta) to determine the protein structures
• Implementing the AI and ML methods to predict the structure and functions for the hypothetical proteins obtained using unbiased screening
• Applied protein biochemistry and structural biology techniques with a focus on recombinant protein expression and purification
• Utilized FPLC systems (AKTA) for protein purification, employing techniques such as affinity chromatography, ion exchange chromatography, hydrophobic interaction chromatography, and size exclusion chromatography
• Performed analytical characterization of proteins using SDS-PAGE, western blotting, an- alytical SEC (size exclusion chromatography), and Dynamic Light Scattering methods
(DLS)
• Produced and characterized membrane proteins, including E. coli inner and outer membrane proteins, transporters, and receptors
• Employed nanodiscs for the stabilization and structural study of membrane proteins Dec 2020 - June 2023 Postdoctoral Research Associate University of Connecticut, Storrs, Connecticut, USA
• Applied molecular modeling methods and free energy calculations to probe the dynamics of viral and membrane lipid systems
• Developed software tools for setting up and analyzing molecular dynamics simulations using Python, and incorporated advanced simulation techniques into research workflows
• Displayed a leadership role within the research group, providing guidance and mentorship to graduate and undergraduate students
• Supported the design and development of new projects, including assisting in the preparation and submission of research project proposals for grants and resources Apr 2016 - Dec 2020 Ph.D. Research Associate
Jacobs University Bremen, Bremen, Germany
• Worked on my Ph.D. thesis project entitled “Translocation of Phosphonic Acid Antibiotics Through Bacterial Membrane Channels”
• Performed applied field molecular dynamics (MD) simulations and free energy calculations on various bacterial membrane channels to understand the physiological aspects of antibiotic translocation mechanisms at the atomistic level
• Generated diffusion models to study the permeation of small molecules
• Collaborated closely with the experimental team to characterize bacterial membrane proteins, contributing to experimental design, data analysis, and interpretation July 2014 - Mar 2016 Associate Scientist: Computational Chemist Akamara Therapeutics, Delhi, India
• Worked on the design and development of Antibody Drug Conjugates (ADC) for cancer treatment
• Conducted In silico screening of designed molecules by using molecular modeling techniques such as docking, molecular dynamics simulations, binding free energy calculations, ADMET, and virtual screening methods
• Performed protein-ligand binding affinity calculations to support experimental affinity studies and participated in isothermal titration calorimetry (ITC) experiments
• Reviewed and analyzed scientific data, presenting findings in scientific reviews and general meetings
• Collaborated effectively with the team to enhance and implement project plans, as well as to design new projects
Oct 2013 - July2014 Junior Research Associate
GVK Biosciences Pvt. Ltd., Hyderabad, India
• Played a role in the generation of the Clinical Trial Outcome Database (CTOD) for various indications
• Experience in clinical trial practices, procedures, and methodologies
• Work experience on different clinical trial designs, including blinded, parallel, controlled, randomized, and multicenter for various indications
• Maintained quality control on the database according to required guidelines
• Provided efficient support to the team and evaluated all data collection activities Software tools developed
• Developed in-silico pipeline to screen lacritin N-104 contrivologs
• Build unique membranes in the Python (BUMPy) tool optimization
• Tested the performance of the “BRODEA” tool (Brownian dynamics including explicit atoms).
• Generated diffusion models to study antibiotic/small molecule permeation through protein transporters
• C++ program to calculate the Kappa Shaped descriptor index for a given chemical compound
• CPMD IFGen web application to semi-automate the input file preparation for CPMD (Car-Parrinello Molecular Dynamics)
Workshops/Conferences/Posters/Talks
• Research computing workshop - UVA, April 2025
• Talk on Cryo-EM of a small, monomeric membrane protein at UVA Molecular Electron Microscopy symposium, January 2025
• Invited Talk on Molecular Modeling Applications in Drug Discovery at MIT-WPU, India, September 2024
• 66th Annual Biophysical Society meeting – San Francisco, February 2022
• Alchemical Free Energy Workshop, Göttingen, May 2019
• Workshop on Computer Simulation and Theory of Macromolecules - Hünfeld, February 2019 (Talk)
• Biennial Meeting of the German Biophysical Society- Düsseldorf, September 2018
• 62nd Annual Biophysical Society meeting – San Francisco, February 2018
• IMI Translocation Meeting-2016 at Jacobs University, Bremen, July 2016
• 2nd UK-India MedChem Congress, Hyderabad, March 2013
• 3rd Indo-German conference on Modeling Chemical and Biological (Re) activity (MCBR3) at the National Institute of Pharmaceutical Education and Research (NIPER), Mohali, February 2013
• 62nd Indian Pharmaceutical Congress (IPC) at Manipal University, Manipal, December 2010 Distinctive Highlights/Extra Curricular
• Awarded the Project Management Foundation Certificate from the University of Virginia
• Professional Diploma in Drug Regulatory Affairs (PDDRA), from Satrishi Institute of Clinical Research (SICR), Noida, India, 2012
• Certified Base SAS 9.0 programmer
• Participated and volunteered in National Social Service (NSS) programs and camps
• Qualified ’A’ certificate in the National Cadet Corps (NCC) Accomplishments
• Serving as a Managing Editor for a journal focused on emerging investigators
• Reviewer for 20+ journals, providing critical feedback to improve research quality
• Pittsburgh Supercomputing Center (PSC) Anton 2 allocation award (2021)
• ‘Wow’ card from GVK Biosciences for quick learning and quality work, 2013
• Mandal first in the UTF (United Teachers Federation) talent test in SSC, 2004
• Gold medal with Pratibha award from Andhra Pradesh State Board of Secondary School Education in 2001, and received a scholarship from 2002 to 2004
• Mandal first in Srinivasa Ramanujan Math’s Talent Test, 2001 Publications
• V. K. Golla, R. Benz, U. Kleinekathöfer, and C. Pesille, "Glyphosate uptake pathway across the outer membrane of Pseudomonas aeruginosa", (Under review), 2026.
• P. Singh, V. K. Golla, N. Sharma, and N.Chaudhri,A comprehensive review on the advancement of supramolecular polymers and their pharmaceutical and biomedical applications, Coord. Chem. Rev. 548, 217223 (2025).
• N. Senoo, D.K. Chinthapalli, M.G. Baile, V. K. Golla, B. Saha, A.O. Oluwole, O.B. Ogunbona, J.A. Saba, T. Munteanu, Y. Valdez, K. Whited, M.S. Sheridan, D. Chorev, N.N. Alder, E.R. May, C.V. Robinson, S.M. Claypool, Functional diversity among cardiolipin binding sites on the mitochondrial ADP/ATP carrier, EMBO J. 43, 2979-3008 (2024).
• V. K. Golla, K. J. Boyd and E. R. May, Curvature-based lipid partitioning and localization in a mitochondrial inner membrane model, Nature Commun. Biol. 7, 29 (2024).
• C. Piselli, V. K. Golla, R. Benz and U. Kleinekathöfer, Importance of the Lysine Cluster in the Translocation of Anions through the Pyrophosphate Specific Channel OprO, Biochim. Biophy. Acta, Biomembr. 1865, 184086 (2023)
• P. Singh, J. Feng, V. K. Golla, A. Lotfi, D. Tyagi "Crosslinked and biofunctionalized γ-cyclodextrin metal-organic framework to enhance cellular binding efficiency", Mater. Chem. Phys. 126496 (2022)
• V. K. Golla, C. Pesile, R. Benz, and U. Kleinekathöfer, “Permeation of Fosfomycin through the Phosphate-Specific Channels OprP and OprO of Pseudomonas aeruginosa”, J. Phys. Chem. B. 126, 7, 1388–1403 (2022)
• V. K. Golla, J. D. Prajapati, and U. Kleinekathöfer, “Millisecond-long simulations for the transport of antibiotics”, J. Chem. Theory Comput. 17, 1, 549-559 (2021)
• V. K. Golla, J. D. Prajapati, M. Joshi and U. Kleinekathöfer, “Exploration of Free Energy Surfaces across a Membrane Channel Using Metadynamics and Umbrella Sampling", J. Chem. Theory Comput. 16, 4, 2751-2765 (2020)
• V. K. Golla, E. Sans-Serramitjana, K. R. Pothula, L. Benier, J. A. Bafna, M. Winterhalter and U. Kleinekathöfer,
“Fosfomycin Permeation through the Outer Membrane Porin OmpF", Biophys. J. 116, 258–269 (2019) Declaration
I hereby declare that the information furnished above is true to the best of my knowledge Date: April 6, 2026
Place: Charlottesville
G. Vinaya Kumar
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