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Hire Dr. Sruthi M.

United States

USD 100 /hr

Ph.D. Computational Chemist | MD, QM/MM, FEP, Docking, RDKit | 8+ Years in Drug Discovery & Simulation

Profile Summary

I am a Ph.D.-trained computational chemist with over 8 years of experience in academic and industry settings, specializing in molecular dynamics (MD), free energy calculations (FEP, MM/PBSA), QM/MM methods, and cheminformatics. My work bridges physics-based modeling and drug discovery, with demonstrated success in automating and scaling scientific workflows for ligand binding prediction, binding site analysis, and compound prioritization. 🔬 Core Expertise: Molecular Dynamics (GROMACS, AMBER, NAMD) Free Energy Calculations (QM/MM FEP, ABF, MMPBSA, SEEKR2) Docking & Binding Site Analysis (AutoDock Vina, RDKit, PyMOL, Chimera) Cheminformatics (RDKit, molecular fingerprinting, ligand conformers) Workflow Automation (Python, Bash, HPC/Cloud deployment on AWS, Google Cloud, Azure) 🧪 Key Experience Highlights: Quantum Simulation Technologies (QSimulate) As a Computational Chemist at a fast-growing quantum chemistry startup, I developed and automated QM/MM FEP protocols using AMBER/GENESIS, built conformer pipelines using RDKit, and helped design scalable workflows for evaluating small molecules in early-stage drug discovery. Postdoctoral Research At University of Pennsylvania and University of Delaware, I investigated the mechanism of anesthetics and antiretrovirals, applying MD and FEP to study ligand-receptor interactions, conformational changes, and validate binding affinities in collaboration with experimentalists. Ph.D. Research (Rutgers University) My doctoral work focused on ligand-gated ion channels (GABA(A), VDAC, GLIC/ELIC), using adaptive biasing force (ABF) and alchemical methods to explore mutation effects, lipid interactions, and drug modulation. 🛠️ Technical Skills: Programming: Python, Bash, C/C++, Java, TCL, R, MATLAB Libraries & Tools: RDKit, NumPy, Scikit-learn, TensorFlow (ML Foundations) Software: GROMACS, AMBER, AutoDock, GENESIS, PyMOL, Chimera, CHARMM-GUI, NWChem Cloud & HPC: AWS, Google Cloud, Azure, Linux, SLURM Scientific Communication: Multiple first-author publications, conference talks, and collaborative research with academic labs in the U.S., Canada, France, and Switzerland.

Subject Matter Expertise

• ★ Molecular Modeling
• ★ Molecular Docking
• ★ Computational Chemistry
• ☆ Computational Biology
• ☆ Neuroscience
• ☆ Computational Neuroscience
• ☆ Biophysics
• ☆ Data Analysis
• ☆ Computer Simulation/Computational Modeling
• ☆ Data Visualization
• ☆ Python

Services

• Research
• Consulting

Research Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Work Experience

Computational Chemist

Qsimulate

March 2020 - September 2023

Postdoctoral Researcher

University of the Sciences in Philadelphia

July 2019 - March 2020

Postdoctoral Researcher

University of Delaware

September 2018 - June 2019

Education

Graduate Assistant (Computational And Integrative Biology)

Rutgers University

September 2012 - May 2018

Certifications

• Complete A.I and Machine learning , Data Science Bootcamp

  udemy

  https://www.udemy.com/certificate/UC-7468dcf0-d5a8-4d0e-864b-36b68fa27adf/

  January 2025 - Present

Publications

JOURNAL ARTICLE

Wang, Yuhang, Murlidaran, Sruthi, Pearlman, David A(2021). Quantum simulations of SARS-CoV-2 main protease Mpro enable high-quality scoring of diverse ligands. Journal of Computer-Aided Molecular Design. 35. (9). p. 963--971. Springer International Publishing Cham

Murlidaran, Sruthi, Bu, Weiming, Eckenhoff, Roderic G, Brannigan, Grace H, Joseph, Thomas T(2020). Relative Affinities of General Anesthetics for Experimentally Identified Binding Sites in Ryanodine Receptors (RyR1). Biophysical Journal. 118. (3). p. 115a. Elsevier

Böhm, Raphael, Amodeo, Giuseppe Federico, Murlidaran, Sruthi, Chavali, Shashank, Wagner, Gerhard, Winterhalter, Mathias, Brannigan, Grace, Hiller, Sebastian(2020). The structural basis for low conductance in the membrane protein VDAC upon $β$-NADH binding and voltage gating. Structure. 28. (2). p. 206--214. Elsevier

Murlidaran, Sruthi, Hénin, Jér̂ome, Brannigan, Grace(2019). Competitive dewetting underlies site-specific binding of general anesthetics to GABA (A) receptors. bioRxiv. p. 694612. Cold Spring Harbor Laboratory

Murlidaran, Sruthi, Perilla, Juan R(2019). Molecular Mechanism of Potent Capsid-Targeting Antiretroviral Drugs. Biophysical Journal. 116. (3). p. 14a. Elsevier

Murlidaran, Sruthi, Brannigan, Grace(2018). Geny=-RTE In (e-(Ha (tr)-Ha (t)/RT)=-RTE In (e-(4-Ai+ 1) Hanw-lis/RT)∆ Genv=-RT. Chemical and Biochemical Approaches for the Study of Anesthetic Function, Part A. 602. p. 17. Academic Press

Murlidaran, Sruthi, Salari, Reza, Hénin, Jerome, Brannigan, Grace(2017). Relative Affinities of General Anesthetics for Pseudo-Symmetric Intersubunit Binding Sites of Heteromeric GABA (A) Receptors. Biophysical Journal. 112. (3). p. 555a. Elsevier

Woll, Kellie A, Murlidaran, Sruthi, Pinch, Benika J, Hénin, Jér̂ome, Wang, Xiaoshi, Salari, Reza, Covarrubias, Manuel, Dailey, William P, Brannigan, Grace, Garcia, Benjamin A, et al.(2016). A novel bifunctional alkylphenol anesthetic allows characterization of $γ$-aminobutyric acid, type A (GABAA), receptor subunit binding selectivity in synaptosomes. Journal of Biological Chemistry. 291. (39). p. 20473--20486. American Society for Biochemistry and Molecular Biology

Murlidaran, Sruthi, Salari, Reza, Hénin, Jér̂ome, Brannigan, Grace(2016). Relative Affinities of Positive and Negative Modulators of Heteromeric GABA (A) Receptors for Pseudo-Symmetric Intersubunit Binding Sites. Biophysical Journal. 110. (3). p. 454a. Elsevier

Carswell, Casey L, Hénault, Camille M, Murlidaran, Sruthi, Therien, JP Daniel, Juranka, Peter F, Surujballi, Julian A, Brannigan, Grace, Baenziger, John E(2015). Role of the fourth transmembrane $α$ helix in the allosteric modulation of pentameric ligand-gated ion channels. Structure. 23. (9). p. 1655--1664. Elsevier

Hénault, Camille M, Carswell, Casey L, Murlidaran, Sruthi, Therien, JP Daniel, Juranka, Peter F, Surujballi, Julian A, Brannigan, Grace, Baenziger, John E(2015). Role of the Transmembrane $α$-Helix M4 in the Potentiation of Pentameric Ligand-Gated Ion Channels. Biophysical Journal. 108. (2). p. 432a. Elsevier

Murlidaran, Sruthi, Salari, Reza, Brannigan, Grace(2015). Affinity Calculations for Lipophilic Modulators Binding to Isolated Sites on GABA (A) Receptors. Biophysical Journal. 108. (2). p. 19a. Elsevier

Salari, Reza, Murlidaran, Sruthi, Brannigan, Grace(2014). Pentameric ligand-gated ion channels: Insights from computation. Molecular simulation. 40. (10-11). p. 821--829. Taylor \& Francis

Murlidaran, Sruthi, Salari, Reza, Brannigan, Grace(2014). Effects of Disease-Associated Mutations on the Conformations of GABA (A) Receptors. Biophysical Journal. 106. (2). p. 550a. Elsevier

Hénin, Jér̂ome, Salari, Reza, Murlidaran, Sruthi, Brannigan, Grace(2014). A predicted binding site for cholesterol on the GABAA receptor. Biophysical journal. 106. (9). p. 1938--1949. Elsevier

Salari, R, Murlidaran, S, Brannigan, G, others(2014). A Predicted Binding Site for Cholesterol on the GABAA Receptor. BIOPHYSICAL JOURNAL. 106. (9). p. 1938--1949. Elsevier

Murlidaran, Sruthi, Hénin, Jér̂ome, Brannigan, Grace(2013). Competitive dewetting underlies subunit-specific binding of general anesthetics to GABA (A) receptors.

DISSERTATION THESIS

Murlidaran, Sruthi(2018). Mechanisms underlying effects of genetic variance and general anesthetics on pentameric ligand-gated ion channels.

BOOK CHAPTER

Murlidaran, Sruthi, Brannigan, Grace(2018). Physical Accuracy Leads to Biological Relevance: Best Practices For Simulating Ligand-Gated Ion Channels Interacting With General Anesthetics. Methods in enzymology. 602. p. 3--24. Academic Press

CONFERENCE PAPER

Woll, KA, Murlidaran, S, Henin, J, Brannigan, G, Eckenhoff, R(2016). SELECTIVE ALKYLPHENOL ANESTHETIC BINDING TO GABA A SUBUNITS IN NATIVE NEURONAL TISSUE. ANESTHESIA AND ANALGESIA. 122.