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Building scientific ML for molecular discovery
🎯
Building scientific ML for molecular discovery

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@SmartChemDesign @cayleypy @LigandPro

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SergeiNikolenko/README.md

Sergei A. Nikolenko

Staff scientific ML engineer and computational chemistry lead building practical AI systems for molecular discovery.

My work spans molecular docking, protein-ligand modeling, generative molecular design, ADMET/QSAR, chemical LLMs, spectra workflows, scientific benchmarks, and reproducible Python/HPC infrastructure.

Portfolio · LinkedIn · ORCID · Kaggle

Selected public work

  • Matcha — multi-stage Riemannian flow matching for physically valid molecular docking.
  • HEDGEHOG — stage-based evaluation for generative molecular design.
  • Bento — reproducible protein-ligand docking benchmark and HPC workflows.
  • SynthLadder — chemistry benchmark and evaluation package for agentic LLMs.
  • posecheck-fast — high-throughput docking pose validation.
  • Burrete — macOS molecular previews and Quick Look tooling.

Focus

  • AI-driven drug discovery and molecular modeling
  • Scientific ML benchmarks, reproducible pipelines, and research infrastructure
  • Chemical LLMs, tool-enabled evaluation, and structured scientific workflows
  • Product-grade research tooling for computational chemistry teams

Collaboration

Open to research and engineering collaborations in computational chemistry, molecular modeling, drug discovery AI, chemical LLMs, molecular spectra, and scientific software infrastructure.

Pinned Loading

  1. Burrete Burrete Public

    macOS menu bar app and Quick Look extension for molecular previews: Mol* 3D, fast XYZ, xyzrender SVG, and RDKit grids.

    JavaScript 25

  2. LigandPro/Matcha LigandPro/Matcha Public

    Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.

    Python 29 3

  3. LigandPro/hedgehog LigandPro/hedgehog Public

    Stage-based evaluation pipeline for generative molecular design: filters, retrosynthesis checks, docking, pose validation, reports, CLI/TUI.

    Python 11 2

  4. LigandPro/Bento LigandPro/Bento Public

    UV-first benchmark for protein-ligand docking with reproducible annotation, pocket similarity, and HPC workflows.

    Jupyter Notebook 12

  5. LigandPro/posecheck-fast LigandPro/posecheck-fast Public

    High-throughput docking pose validation: symmetry-corrected RMSD and lightweight PoseBusters-style distance/clash filters.

    Python 6 1

  6. SynthLadder SynthLadder Public

    Synthesis-focused chemistry benchmark and evaluation package for agentic LLMs across reaction understanding, retrosynthesis, and route planning tasks.

    Python 3