Computational Science & Engineering

Clarity from complexity.
Protein dynamics, unraveled.

Unravel provides computational chemistry consulting and scientific software engineering, specializing in molecular dynamics simulations, HDX-MS analysis, and high-performance C++ data processing for life sciences research.

Alexander Patapoff

I am a computational scientist with five years of biopharma drug-discovery experience, building and scaling methods that connect structural insight with practical decisions.

My core work spans molecular dynamics simulations, HDX-MS workflows, and high-performance scientific software in C++ and Python.

I founded Unravel to bring deep scientific rigor and production-grade engineering to consulting engagements in computational biology.

What I Do

Molecular Dynamics: Custom simulation pipelines, enhanced sampling design, and analysis frameworks for biologically relevant systems.
Mass Spectrometry: Spectral deconvolution and HDX-MS extraction engines tuned for reproducibility and scale.
Scientific Software: Production C++ and Python tools from prototype through deployment and maintenance.
Consulting: Strategic guidance for computational workflows, architecture decisions, and team enablement.

Experience & Publications

Experience

2021–2026

Genentech (via Medasource)

Computational scientist supporting 4+ drug discovery campaigns. MD, HDX-MS, SBDD, FBDD.

Publications

2025

Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions

Walters BT, Patapoff A, Kiefer JA, Wu P, Wang W. J. Chem. Inf. Model. (2025)

2025

Targeting PTPN22 at Nonorthosteric Binding Sites—A Fragment Approach

Di Lello P, [...] Patapoff A, [...] Huard K. ACS Omega (2025)

2023

Delocalization of interacting directed polymers on a periodic substrate

Melkani A, Patapoff A, Paulose J. Phys. Rev. E (2023)

In prep

PAGE method — multimodal MS peak deconvolution

algebraic method for deconvolving overlapping MS peaks, with applications to HDX-MS and native MS.

In prep

OpenHDX-MS

Open-source software for HDX-MS data analysis.

Full CV available on request.

Testimonials

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Let's Talk

Interested in working together? Reach out and let’s discuss how Unravel can support your computational science needs.