Database Commons

a catalog of worldwide biological databases

Insights into protein folding rely increasingly on the synergy between experimental and theoretical approaches. Developing successful computational models requires access to experimental data of sufficient quantity and high quality. We compiled folding rate constants for what initially appeared to be 184 proteins from 15 published collections/web databases. To generate the highest confidence in the dataset, we verified the reported lnkf value and exact experimental construct and conditions from the original experimental report(s). The resulting comprehensive database of 126 verified entries, ACPro, will serve as a freely accessible resource (https://www.ats.amherst.edu/protein/) for the protein folding community to enable confident testing of predictive models. In addition, we provide a streamlined submission form for researchers to add new folding kinetics results, requiring specification of all the relevant experimental information according to the standards proposed in 2005 by the protein folding consortium organized by Plaxco. As the number and diversity of proteins whose folding kinetics are studied expands, our curated database will enable efficient and confident incorporation of new experimental results into a standardized collection. This database will support a more robust symbiosis between experiment and theory, leading ultimately to more rapid and accurate insights into protein folding, stability, and dynamics.

BACKGROUND: There are many different methods for estimating solvent accessible surface area for proteins in their unfolded states. In this article, we compare eight methods, assessing whether or not they lead to different estimates of total accessible surface area as well as their impact on relationships with thermodynamic variables.
FINDINGS: Our results demonstrate that most pairs of compared methods do result in different unfolded estimates of accessible surface area (only four pairs of methods do not yield significantly different estimates). However, we do not see a significant impact on the relationship between accessible surface area and thermodynamic parameters across the different methods.
CONCLUSIONS: We advocate the use of the Gong and Rose transition midpoint method for computing solvent accessible surface area due to its computational ease, physical basis, and performance in terms of relationships with thermodynamic parameters.