Empirical parameters for estimating protein-protein binding energies: number of short- and long-distance atom-atom contacts.
The number of atom-atom contacts in long distance can fit to the experimental binding energies in a dataset containing 151 experimental data with the correlation coefficient about 0.68. Based on this factor, a set of distance-dependent empirical potentials for various types of short-distance (2.4 A-5 A) contacts was obtained by guided fitting, i.e. a set of two parameters fitting. Incorporation of these short-distance potentials improved the correlation coefficients to 0.881.
Li
Yong Chao
YC
Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Zeng
Zong-Hao
ZH
D030562:Databases, Protein; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D013223:Statistics as Topic; D013816:Thermodynamics
D011506:Proteins