Protein Design Solutions (PDS) is building hydration-aware AI for protein design. We reveal how water responds to protein surfaces—in context—showing physical behavior that sequence and static structure alone can miss.
PDS helps teams decide which related candidates deserve experimental resources by adding context-dependent hydration information to protein-engineering workflows.
Rank closely related antibody and protein variants before experimental testing.
Identify context-dependent hydration patterns that conventional amino-acid scales can miss.
Add interpretable hydration information to existing protein-engineering workflows.
PDS uses custom enhanced-sampling molecular simulations and statistical thermodynamics to measure hydration signals that cannot be inferred reliably from sequence or a static structure alone. Protein hydration depends in nontrivial ways on local chemistry and surface topography, and its most informative signatures appear in rare, collective low-density fluctuations of water.
The underlying approach was pioneered by PDS co-founder Nicholas Rego, PhD, and collaborators in Prof. Amish Patel’s lab at the University of Pennsylvania. Through a completed NSF SBIR Phase I, PDS extended that work into a proprietary, first-of-its-kind dataset of residue-level protein hydration behavior and trained fast models that make those expensive calculations usable at protein-design scale.
These hydration-aware models produce interpretable, residue-level signals that can help scientists rank variants, understand why closely related proteins behave differently, and design better-behaved proteins.
Co-founder
Nicholas Rego, PhD, co-founded Protein Design Solutions to translate fundamental protein biophysics into practical tools for protein design. He developed the core hydration methodology during his doctoral and postdoctoral research at the University of Pennsylvania with Prof. Amish Patel, then led its translation through NSF I-Corps and received an NSF Phase I SBIR.
Co-founder
Amish J. Patel, PhD, is a co-founder of Protein Design Solutions and Professor of Chemical and Biomolecular Engineering at the University of Pennsylvania. The Patel Group uses statistical mechanics, liquid-state theory, molecular modeling, and atomistic simulation to study solvation, hydrophobicity, and protein interactions. This research helped establish the scientific foundation for PDS’s hydration-aware approach.
PDS is seeking biologics and protein-engineering teams interested in hydration-aware variant ranking and validation studies.