Research Advisor, Computational Chemistry

Xenon Seven

Computational chemist applying physics‑based modeling and cheminformatics in drug design for cardiometabolic diseases. Collaborating with teams to optimize chemically modified oligonucleotides in therapeutic portfolios.

Posted 6/29/2026full-timeRemote • 🇮🇳 IndiaMid-LevelSeniorWebsite

Tech Stack

Tools & technologies

CloudPythonRust

About the role

Key responsibilities & impact

Perform molecular dynamics simulations of chemically modified oligonucleotide duplexes and single‑stranded species to characterize the structural and thermodynamic consequences of sugar, backbone, and base modifications
Apply free energy methods (FEP, thermodynamic integration, MM/PBSA, MM/GBSA) to predict modification‑dependent binding affinities, duplex stability, and protein–oligonucleotide interactions
Develop and validate force field parameters for novel nucleotide analogs using quantum mechanical calculations, enabling rapid computational evaluation of new chemistries emerging from the medicinal chemistry team
Build and apply cheminformatics descriptors and QSAR/QSPR models adapted for chemically modified oligonucleotides, moving beyond sequence‑only representations to capture the full chemical diversity of the modification space
Collaborate with medicinal chemists and biologists to integrate computational predictions with experimental SAR data, contributing to the identification of optimal modification patterns for on‑target potency, selectivity, metabolic stability, and safety
Contribute to reusable computational workflows, data assets, and modeling platforms that support cross‑program learning and integration with the team’s unified machine learning models
Present findings to cross‑functional teams and contribute to scientific strategy discussions, publications, and patent applications

Requirements

What you’ll need

PhD in computational chemistry, physical chemistry, chemical physics, biophysics, or a closely related field
Demonstrated expertise in molecular dynamics simulation of nucleic acids or chemically modified biopolymers
Experience with free energy calculation methods applied to biomolecular systems
Proficiency in cheminformatics toolkits (RDKit, OpenEye, or equivalent) and/or commercial CADD platforms (Schrödinger, MOE)
Strong programming skills in Python, with experience in scientific computing libraries
Familiarity with machine learning and AI methods applied to molecular sciences, including experience with predictive modeling for molecular properties, chemical optimization, or structure–activity relationships
Excellent written and oral communication skills with ability to present complex computational results to diverse scientific audiences including medicinal chemists and biologists
Experience with high‑performance computing and/or cloud‑based simulation environments
Demonstrated ability to work collaboratively in cross‑functional team environments
Experience with force field parameterization for non‑standard nucleotide analogs, including QM‑derived charge fitting (RESP, AM1‑BCC) and torsion parameter development
Familiarity with quantum chemical methods (DFT, ab initio) for electronic structure analysis of modified nucleotides and their impact on duplex stability and reactivity
Understanding of how chemical modifications influence oligonucleotide secondary structure, folding, and conformational dynamics, including modification‑dependent effects on duplex geometry and protein recognition
Experience with machine learning approaches for molecular property prediction, including graph neural networks, molecular language models, or transformer‑based architectures applied to chemical or biopolymer data
Familiarity with molecular representations for modified oligonucleotides (HELM, extended SMILES, or similar macromolecular encoding schemes)
Knowledge of oligonucleotide‑specific ADME properties, including nuclease‑mediated metabolism, plasma protein binding of phosphorothioate backbones, and endosomal escape
Track record of peer‑reviewed publications demonstrating expertise in computational chemistry applied to nucleic acids or modified biopolymers
Deep understanding of nucleic acid structure and chemistry, including familiarity with common therapeutic modifications (2’‑OMe, 2’‑F, 2’‑MOE, LNA/cET, phosphorothioate, GalNAc conjugates)
Experience designing computational workflows that integrate with automated experimental platforms and high‑throughput screening
Proficiency in Rust or other systems‑level languages for performance‑critical scientific computing is a plus

Benefits

Comp & perks

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Perform molecular dynamics simulations of chemically modified oligonucleotide duplexes and single‑stranded species to characterize the structural and thermodynamic consequences of sugar, backbone, and base modifications
Apply free energy methods (FEP, thermodynamic integration, MM/PBSA, MM/GBSA) to predict modification‑dependent binding affinities, duplex stability, and protein–oligonucleotide interactions
Develop and validate force field parameters for novel nucleotide analogs using quantum mechanical calculations, enabling rapid computational evaluation of new chemistries emerging from the medicinal chemistry team
Build and apply cheminformatics descriptors and QSAR/QSPR models adapted for chemically modified oligonucleotides, moving beyond sequence‑only representations to capture the full chemical diversity of the modification space
Collaborate with medicinal chemists and biologists to integrate computational predictions with experimental SAR data, contributing to the identification of optimal modification patterns for on‑target potency, selectivity, metabolic stability, and safety
Contribute to reusable computational workflows, data assets, and modeling platforms that support cross‑program learning and integration with the team’s unified machine learning models
Present findings to cross‑functional teams and contribute to scientific strategy discussions, publications, and patent applications 🎯 Requirements
PhD in computational chemistry, physical chemistry, chemical physics, biophysics, or a closely related field
Demonstrated expertise in molecular dynamics simulation of nucleic acids or chemically modified biopolymers
Experience with free energy calculation methods applied to biomolecular systems
Proficiency in cheminformatics toolkits (RDKit, OpenEye, or equivalent) and/or commercial CADD platforms (Schrödinger, MOE)
Strong programming skills in Python, with experience in scientific computing libraries
Familiarity with machine learning and AI methods applied to molecular sciences, including experience with predictive modeling for molecular properties, chemical optimization, or structure–activity relationships
Excellent written and oral communication skills with ability to present complex computational results to diverse scientific audiences including medicinal chemists and biologists
Experience with high‑performance computing and/or cloud‑based simulation environments
Demonstrated ability to work collaboratively in cross‑functional team environments
Experience with force field parameterization for non‑standard nucleotide analogs, including QM‑derived charge fitting (RESP, AM1‑BCC) and torsion parameter development
Familiarity with quantum chemical methods (DFT, ab initio) for electronic structure analysis of modified nucleotides and their impact on duplex stability and reactivity
Understanding of how chemical modifications influence oligonucleotide secondary structure, folding, and conformational dynamics, including modification‑dependent effects on duplex geometry and protein recognition
Experience with machine learning approaches for molecular property prediction, including graph neural networks, molecular language models, or transformer‑based architectures applied to chemical or biopolymer data
Familiarity with molecular representations for modified oligonucleotides (HELM, extended SMILES, or similar macromolecular encoding schemes)
Knowledge of oligonucleotide‑specific ADME properties, including nuclease‑mediated metabolism, plasma protein binding of phosphorothioate backbones, and endosomal escape
Track record of peer‑reviewed publications demonstrating expertise in computational chemistry applied to nucleic acids or modified biopolymers
Deep understanding of nucleic acid structure and chemistry, including familiarity with common therapeutic modifications (2’‑OMe, 2’‑F, 2’‑MOE, LNA/cET, phosphorothioate, GalNAc conjugates)
Experience designing computational workflows that integrate with automated experimental platforms and high‑throughput screening
Proficiency in Rust or other systems‑level languages for performance‑critical scientific computing is a plus Apply Now 📊 Check your resume score for this job Improve your chances of getting an interview by checking your resume score before you apply. Check Resume Score 🌐 Worldwide Built by Lior Neu-ner. I'd love to hear your feedback — Get in touch via DM or support@remoterocketship.com Search Search Jobs by country Search jobs by city Search jobs by job title Search entry-level jobs Search junior-level jobs Search senior-level jobs Search jobs by tech stack Search jobs by contract type Search remote internships Search remote part-time jobs Remote jobs Anywhere in the World Companies Hiring Anywhere in the World Companies Hiring Sales People Anywhere in the World Companies Hiring Software Engineers Anywhere in the World Resources Advice Tips for finding remote jobs Interview questions and answers Resume examples Cover letter examples Post a job Affiliates Privacy policy Terms of service Job board SEO course AI Apply Copilot OpenClaw job finder Jobs by Country Remote jobs anywhere in the world (Worldwide remote jobs) Remote jobs United States Remote jobs Australia Remote jobs Brazil Remote jobs Canada Remote jobs France Remote jobs Ireland Remote jobs Germany Remote jobs Netherlands Remote jobs Spain Remote jobs UK Popular Jobs Remote data analyst jobs Remote customer support jobs Remote executive assistant jobs Remote marketing jobs Remote product designer jobs Remote product manager jobs Remote project manager jobs Remote recruiter jobs Remote sales jobs Remote software engineer jobs Jobs by Type Remote full-time jobs Remote part-time jobs Remote contract jobs Remote internship jobs Remote entry-level jobs Remote jobs with no experience required Remote junior jobs (1-3 years of experience) Digital nomad jobs Remote jobs with no degree required Freelance remote jobs Temporary remote jobs Remote jobs hiring now Stay at home mom jobs

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Hard Skills & Tools

Molecular Dynamics SimulationFree Energy Calculation MethodsForce Field ParameterizationQuantum Chemical MethodsComputational Workflow DesignPredictive ModelingHigh-Performance ComputingCheminformaticsNucleic Acid Structure and ChemistryMachine Learning Approaches

Soft Skills

Excellent Communication SkillsCollaborative Teamwork

Certifications

PhD in Computational Chemistry