Location: Bengaluru, Karnataka, India

Company: Quantumzyme

About Quantumzyme

Quantumzyme is a leading biocatalysis company leveraging advanced computational chemistry, AI, and

enzyme engineering to deliver sustainable and effective solutions for chemical and pharmaceutical

manufacturing. Our mission is to revolutionize chemical production through greener, cost-effective,

and precision-driven enzyme design.

Position Overview

We are seeking a highly motivated Scientist (Computational Chemistry / Computational Biology /

Bioinformatics) with 0.6 to 4 years of post-PhD experience to join our Bengaluru team.

This role requires a strong hands-on computational researcher who can independently execute

projects while mentoring junior team members. The candidate will be responsible for on-time project

delivery, working on industrial and academic collaborations, with a strong emphasis on MD

simulations for enzyme engineering and catalytic mechanism.

Key Responsibilities

- Perform hands-on computational research in molecular simulations and enzyme modelling.

- Lead specific project modules while mentoring junior researchers.

- Ensure timely completion and delivery of project milestones.

- Perform Molecular Dynamics (MD) simulations of biological macromolecular systems

(proteins, enzymes, protein–ligand complexes).

- Design and execute QM/MM simulations to:

o Study enzyme catalytic mechanisms

o Model reaction pathways

o Perform transition state and electronic structure calculations

o Evaluate reaction energetics and free energy profiles

- Apply enhanced sampling techniques such as:

o Umbrella Sampling

o Meta dynamics

o FEP

1

o MMPBSA / MMGBSA

- Automate simulation setup, workflow pipelines, and post-MD analysis using scripting.

- Work efficiently in Linux-based HPC environments.





- Contribute to reports, technical documentation, and publications.

- Analyse reaction mechanisms and interpret computational results to guide experimental

design.

- Collaborate with interdisciplinary teams and communicate scientific insights effectively.

Qualifications

- PhD in Computational Chemistry / Computational Biology / Bioinformatics or related field

- 0.6 – 4 years of post-PhD hands-on research experience

- Strong background in enzyme systems and biomolecular simulations

Mandatory Skills

Core Computational Biology/Chemistry

- GROMACS (Minimum 3 years hands-on experience)

- CP2K

- Molecular Dynamics (MD) simulations

- QM/MM simulations

- Reaction mechanism analysis

- Umbrella Sampling, Metadynamics, Free Energy methods

- Protein–ligand and enzyme system modelling

- Experience working with biological macromolecules (proteins, enzymes, AI-assisted

workflows)

Visualization & Analysis

- VMD

- PyMOL

- Chimera

- Discovery Studio

- ChemDraw / Biovia Draw

QM/MM & Electronic Structure Tools

Experience with one or more of:

2

- CP2K

- Gaussian

- ORCA

- ChemShell

- Turbomole

Programming & Automation:

- Python

- BASH

- Shell scripting for automation

- C / C++

- Workflow automation for MD simulations

- Post-processing and trajectory analysis scripting

- Experience working in Linux / HPC clusters

Additional Skills (Preferred)

Enzyme Engineering & Bioinformatics

- Enzyme structure–function analysis

- Active-site modelling

- Mutational scanning and hotspot prediction

- Sequence alignment & homology modelling (BLAST, Clustal Omega, MEGA)

- Understanding of enzyme kinetics and catalytic selectivity

Advanced Sampling & AI

- Replica MD, aMD, REMD

- TI, LIE, MMPBSA

- Exposure to AI/ML tools (scikit-learn, PyTorch, TensorFlow)

- RF Diffusion

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📌 Job Description - Scientist - Insilico (Bengaluru)
🏢 Quantumzyme
📍 Bengaluru