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(PS)2 specifications


Unique identifier OMICS_08386
Name (PS)2
Interface Web user interface
Restrictions to use None
Input data Protein sequences
Input format FASTA
Output data The predicted structures are visualized in PNG format generated by the MolScript and Raster3D packages. A user can download the predicted structure coordinates in the PDB format.
Output format PNG, PDB
Programming languages Perl, PHP
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes


  • person_outline Chih-Chieh Chen

Publications for (PS)2

(PS)2 citations


Homology Modeling and Virtual Screening to Discover Potent Inhibitors Targeting the Imidazole Glycerophosphate Dehydratase Protein in Staphylococcus xylosus

PMCID: 5686052
PMID: 29177138
DOI: 10.3389/fchem.2017.00098
call_split See protocol

[…] et al., ), which revealed suitable templates for the homology modeling. Target sequences of the IGPD protein were constructed based on the build homology models using Discovery Studio (version 3.0), (PS)2-v2: protein structure prediction server (Chen et al., , ), as well as MODELLER (Webb and Sali, ). The needle pairwise sequence alignment was used to calculate sequence similarity (Li et al., ). S […]


Predicted Cold Shock Proteins from the Extremophilic Bacterium Deinococcus maricopensis and Related Deinococcus Species

PMCID: 5624153
PMID: 29098004
DOI: 10.1155/2017/5231424

[…] er. The result of PSIPRED, as shown in , has good confidence and contains 5 beta-strands, which are expected among Csps [, ].The modeling of the likely tertiary structure of Dm-Csp1, as predicted by (PS)2-v2, used a known Csp from Bacillus caldolyticus (PDB #1C9O) as a template. The B. caldolyticus Csp crystal structure used as a template is 66 amino acids in length and shares 61.76% sequence iden […]


Predictive characterization of hypothetical proteins in Staphylococcus aureus NCTC 8325

PMCID: 5267966
PMID: 28149057
DOI: 10.6026/97320630012209

[…] protein sequence []. Researchers frequently use Pfam and CDD-BLAST together to characterize parts of the protein involved in binding capability [,,].Tertiary structure predictions were completed by (PS)2, which is an automatic homology modeling server uses a protein sequence in pair-wise and multiple alignments though unions of PSI-BLAST, integrated molecular pathway level analysis, and multiple […]


Surgical Management of the Primary Tumor in Stage IV Colorectal Cancer: A Confirmatory Retrospective Cohort Study

PMCID: 4860801
PMID: 27162543
DOI: 10.7150/jca.14717
call_split See protocol

[…] clinical & demographic variables: age (<65 vs. ≥65), gender, major comorbid illness (as per Charlson comorbidity index), secondary cancer, Eastern Cooperative Oncology Group performance status [ECOG PS] (<2 vs. ≥2), cancer center, and smoking; laboratory values: albumin (≥36 vs. <36 g/l), bilirubin (≥26 vs. <26 um/l), alkaline phosphatase (≥120 vs. <120 U/l), sodium level (≤135 mEq/l vs. >135 mEq […]


Ketide Synthase (KS) Domain Prediction and Analysis of Iterative Type II PKS Gene in Marine Sponge Associated Actinobacteria Producing Biosurfactants and Antimicrobial Agents

Front Microbiol
PMCID: 4751271
PMID: 26903957
DOI: 10.3389/fmicb.2016.00063

[…] rget and template, the two KS proteins structures can be reliable and they adopt similar structure. The secondary structures of type II PKS and ketosynthase domains of 3D models were created using a (PS)2 is an automated homology modeling server (). The (PS)2 combines PSI-BLAST, IMPALA, and T-Coffee in both template selection and target-template alignment. The final three dimensional structures we […]


Burkholderia pseudomallei type III secreted protein BipC: role in actin modulation and translocation activities required for the bacterial intracellular lifecycle

PMCID: 5180589
PMID: 28028452
DOI: 10.7717/peerj.2532

[…] the hits obtained shared low sequence identity with only approximately 30% within a small coverage in the sequence. Since there were no potential structural template, the web servers’ pDomThreader, (PS)2-v2, and RaptorX were therefore used for protein fold recognition in order to further identify the potential template for structural modeling.From pDomThreader analysis, 1wp1B01 was identified as […]


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(PS)2 institution(s)
Institute of Bioinformatics, National Chiao Tung University, Taiwan, China; Department of Biological Science and Technology, National Chiao Tung University, Taiwan, China; Core Facility for Structural Bioinformatics, National Chiao Tung University, Taiwan, China
(PS)2 funding source(s)
This work was supported by National Science Council.

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