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. 2010 Jul;38(Web Server issue):W450-6.
doi: 10.1093/nar/gkq328. Epub 2010 Apr 30.

ConPlex: a server for the evolutionary conservation analysis of protein complex structures

Yoon Sup Choi  1 , Seong Kyu Han, Jinho Kim, Jae-Seong Yang, Jouhyun Jeon, Sung Ho Ryu, Sanguk Kim
Affiliations

ConPlex: a server for the evolutionary conservation analysis of protein complex structures

Yoon Sup Choi et al. Nucleic Acids Res. 2010 Jul.

Abstract

Evolutionary conservation analyses are important for the identification of protein-protein interactions. For protein complex structures, sequence conservation has been applied to determine protein oligomerization states, to characterize native interfaces from non-specific crystal contacts, and to discriminate near-native structures from docking artifacts. However, a user-friendly web-based service for evolutionary conservation analysis of protein complexes has not been available. Therefore, we developed ConPlex (http://sbi.postech.ac.kr/ConPlex/) a web application that enables evolutionary conservation analyses of protein interactions within protein quaternary structures. Users provide protein complex structures; ConPlex automatically identifies protein interfaces and carries out evolutionary conservation analyses for the interface regions. Moreover, ConPlex allows the results of the residue-specific conservation analysis to be displayed on the protein complex structure and provides several options to customize the display output to fit each user's needs. We believe that ConPlex offers a convenient platform to analyze protein complex structures based on evolutionary conservation of protein-protein interface residues.

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Figures

Figure 1.
Figure 1.
A flow chart of the ConPlex calculation processes.
Figure 2.
Figure 2.
ConPlex Server outputs formats. (A) The main output page of ConPlex. (B) Conservation scores of interface, ROS, core and rim residues of the protein complex structure. (C) Intermediate calculation results, including homologous sequences, multiple sequence alignment and residue-specific conservation scores. (D) Visualization script for structure viewer programs. (E) Color-coded sequence conservation analyses of the primary amino-acid sequence. (F) List of the interface residues and their conservation scores.
Figure 3.
Figure 3.
Display options for complex structure analysis. Rho–RhoGAP complex (PDB id: 1TX4) is used as example. (A) Default display format. Users have the option to toggle conservation colors (B), interface residues (C), and each chain in structures with two binding partners (D). (E) Users can rotate and enlarge/reduce the structure in the display. (F) Clicking a residue in sequence window will highlight the corresponding residue on the structure with a yellow outline.
See this image and copyright information in PMC

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