Protein design by provable algorithms

OSPREY: protein design with ensembles, flexibility, and provable algorithms.

UNLABELLED We have developed a suite of protein redesign algorithms that improves realistic in silico modeling of proteins. These algorithms are based on three characteristics that make them unique: (1) improved flexibility of the protein backbone, protein side-chains, and ligand to accurately capture the conformational changes that are induced by mutations to the protein sequence; (2) modeling...

Algorithms for protein design.

Computational structure-based protein design programs are becoming an increasingly important tool in molecular biology. These programs compute protein sequences that are predicted to fold to a target structure and perform a desired function. The success of a program's predictions largely relies on two components: first, the input biophysical model, and second, the algorithm that computes the be...

On Provable Security for Digital Signature Algorithms

Provable algorithms for parallel generalized sweep scheduling

We present provably efficient parallel algorithms for sweep scheduling, which is a commonly used technique in Radiation Transport problems, and involves inverting an operator by iteratively sweeping across a mesh from multiple directions. Each sweep involves solving the operator locally at each cell. However, each direction induces a partial order in which this computation can proceed. On a dis...

Provable Algorithms for Machine Learning Problems

Modern machine learning algorithms can extract useful information from text, images and videos. All these applications involve solving NP-hard problems in average case using heuristics. What properties of the input allow it to be solved efficiently? Theoretically analyzing the heuristics is often very challenging. Few results were known. This thesis takes a different approach: we identify natur...