KineticDB: a database of protein folding kinetics

KineticDB: a database of protein folding kinetics

We propose here KineticDB, a systematically compiled database of protein folding kinetics, which contains about 90 unique proteins. The main goal of the KineticDB is to provide users with a diverse set of protein folding rates determined experimentally. The search for determinants of protein folding is still in progress, aimed at obtaining a new understanding of the folding process. Comparison ...

A simple theory of protein folding kinetics

We present a simple model of protein folding dynamics that captures key qualitative elements recently seen in all-atom simulations. The goals of this theory are to serve as a simple formalism for gaining deeper insight into the physical properties seen in detailed simulations as well as to serve as a model to easily compare why these simulations suggest a different kinetic mechanism than previo...

Cooperativity in protein-folding kinetics.

How does a protein find its native state without a globally exhaustive search? We propose the "HZ" (hydrophobic zipper) hypothesis: hydrophobic contacts act as constraints that bring other contacts into spatial proximity, which then further constrain and zip up the next contacts, etc. In contrast to helix-coil cooperativity, HZ-heteropolymer collapse cooperativity is driven by nonlocal interact...

PFD: a database for the investigation of protein folding kinetics and stability

We have developed a new database that collects all protein folding data into a single, easily accessible public resource. The Protein Folding Database (PFD) contains annotated structural, methodological, kinetic and thermodynamic data for more than 50 proteins, from 39 families. A user-friendly web interface has been developed that allows powerful searching, browsing and information retrieval, ...

Statistical Analysis of Protein Folding Kinetics