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The (PS)2 version 3.0 is an updated server which provides new functions for complex protein structure prediction and calculating both sequence conservation and packing density profiles. The packing density of each residue is estimated by weighted contact number (WCN), a structure-derived property equal to the number of contact residues weighted by the square of the reciprocal distances between contacting pairs. Our previous studies have related WCN to protein thermal fluctuation (1), and related WCN to site-specific evolutionary rate (2,3). Moreover, WCN have been applied both to the prediction of catalytic residues (4) and to estimate the degree of coupling between the subunits in a protein complex through comparison of WCN and conservation profiles (5). However, currently there is not yet a web server available for comparison between packing density profile obtained from the predicted 3D structure and sequence conservation profile obtained from query sequence. Here, we implement these functions to the updated server, referred to as (PS)2 v.3. his server accepts protein sequence in FASTA format and tries to builds homologous 3D structures using (PS)2 methodology (6,7). Our previous (PS)2 server has been running more than five years, and was accessed more than 5000 times per year as well as cited over 100 times. Now the updated (PS)2 server supports protein complex structure prediction. The predicted tertiary complex structure with their packing density and conservation profiles are visualized by a Java-based 3D graphics viewer.


1) Lin CP, Huang SW, Lai YL, Yen SC, Shih CH, Lu CH, et al. Deriving protein dynamical properties from weighted protein contact number. Proteins 2008;72:929-35.

2) Shih CH, Chang CM, Lin YS, Lo WC, Hwang JK. Evolutionary information hidden in a single protein structure. Proteins 2012;80:1647-57.

3) Yeh SW, Liu JW, Yu SH, Shih CH, Hwang JK, Echave J. Site-specific structural constraints on protein sequence evolutionary divergence: Local packing density versus solvent exposure. Molecular biology and evolution 2014;31:135-9.

4) Huang SW, Yu SH, Shih CH, Guan HW, Huang TT, Hwang JK. On the relationship between catalytic residues and their protein contact number. Current protein & peptide science 2011;12:574-9.

5) Chang CM, Huang YW, Shih CH and Hwang JK: On the relationship between the sequence conservation and the packing density profiles of the protein complexes. Proteins 2013, 81, 1192-1199.

6) Chen CC, Hwang JK and Yang JM: (PS)2-v2: template-based protein structure prediction server. BMC Bioinformatics 2009, 10, 366.

7) Chen CC, Hwang JK and Yang JM: (PS)2: protein structure prediction server. Nucleic Acids Research 2006, 34, W152-W157.

Huang TT, Hwang JK, Chen CH, Chu CS, Lee CW, Chen CC. (PS)2: protein structure prediction server version 3.0. Nucleic Acids Res. 2015, gkv454.
Last updated Apr 7, 2015 (56547 complex templates)