Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin

Identification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41-0.71 for eight intraprotein interaction examples, and 0.07-0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three-dimensional protein structure data are available.

Studies on terrestrial interface processes in arid areas, China

In the present paper, we have elucidated the importance of energy and water cycling in arid areas to investigate global climate and local economics. Then, we were concerned with the physical arguments as how to stratify the soil, and the stability of the numerical scheme in the mathematical model for predicting temperature variation and water motion. Furthermore, we discuss the methods to estimate evaporation in arid areas. Numerical simulation of energy and water cycling at the Acsu Observatory, CAS, Xinjiang province and Shapuotou Observatory, CAS, Ningxia Province are conducted as case studies. The results show that the laws of terrestrial processes are rather typical in these arid areas. Planting drought-endurable trees can alleviate unfavourable conditions to a certain extent. (C) 1997 Academic Press Limited.