Physics and physical chemistry are an important thread in computational protein design,
complementary to knowledge-based tools. They provide molecular mechanics scoring …

Proteins are the workhorse of life. They are the building infrastructure of living systems; they
are the most efficient molecular machines known, and their enzymatic activity is still …

We describe methods for physics-based protein design and some recent applications from
our work. We present the physical interpretation of a MC simulation in sequence space and …

Understanding natural protein evolution and designing novel proteins are motivating interest
in development of high-throughput methods to explore large sequence spaces. In this work …

Motivation Despite many successes, de novo protein design is not yet a solved problem as
its success rate remains low. The low success rate is largely because we do not yet have an …

With over 270 unique occurrences in the human genome, peptide-recognizing PDZ domains
play a central role in modulating polarization, signaling, and trafficking pathways. Mutations …

This chapter describes two computational methods for PDZ–peptide binding: high-
throughput computational protein design (CPD) and a medium-throughput approach …

New Computational Methods to Predict Cancer Resistance Mutations and Design D-Peptide
Therapeutics Page 1 i v New Computational Methods to Predict Cancer Resistance …

We describe methods and software for physics-based protein design. The folded state
energy combines molecular mechanics with Generalized Born solvent. Sequence and …