(PS)²: protein structure prediction server version 3.0

Abstract

Protein complexes are involved in many biological processes. Examining coupling between subunits of a complex would be useful to understand the molecular basis of protein function. Here, our updated (PS)2 web server predicts the three-dimensional structures of protein complexes based on comparative modeling; furthermore, this server examines the coupling between subunits of the predicted complex by combining structural and evolutionary considerations. The predicted complex structure could be indicated and visualized by Java-based 3D graphics viewers and the structural and evolutionary profiles are shown and compared chain-by-chain. For each subunit, considerations with or without the packing contribution of other subunits cause the differences in similarities between structural and evolutionary profiles, and these differences imply which form, complex or monomeric, is preferred in the biological condition for the subunit. We believe that the (PS)2 server would be a useful tool for biologists who are interested not only in the structures of protein complexes but also in the coupling between subunits of the complexes. The (PS)2 is freely available at http://ps2v3.life.nctu.edu.tw/.

BECN2 interacts with ATG14 through a metastable coiled‐coil to mediate autophagy

“…We first used CCBuilder to determine the register of parallel BECN2 CCD and ATG14 CCD sequences that results in optimal packing interactions at the CCD heterodimer interface. Next, we used the Protein Structure Prediction Server ((PS)) to calculate a pseudo‐atomic heterodimer model based on the amino acid sequences of each CCD and the best packing register obtained from CCBuilder. Interestingly, the BECN2:ATG14 CCD model is also curved, with a radius of curvature of 13 nm [Fig.…”

On the relationship between residue structural environment and sequence conservation in proteins

“…To sum up, the comparison of WCN 1 and WCN 2 with sequence‐estimated CS profiles may provide a potentially way to understand the evolutionary couplings between subunits of protein complexes as well as the relationship between protein and its ligands. In application, the protein structure prediction server (PS) version 3.0 combined structure prediction of protein complexes with the WCN–CS comparison to provide service that not only predicts the structures of dimeric complexes based on homology modelling but also gives a way to understand the evolutionary couplings between the subunits of the predicted protein complexes …”

In silico identification and characterization of antineoplastic asparaginase enzyme from endophytic bacteria

“…The three‐dimensional (3D) structure of a protein affects its shape, size, and function. For Three‐dimensional protein structure predictions, (PS)2‐v3: template‐based protein structure prediction server (http://ps2v3.life.nctu.edu.tw) was used. Ramachandran plot (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php) and the Z‐score calculated by protein structure analysis (ProSA) web (https://prosa.services.came.sbg.ac.at/prosa.php) were checked to measure the quality of the generated models.…”

“…For Three-dimensional protein structure predictions, (PS)2-v3: template-based protein structure prediction server (http://ps2v3.life.nctu. edu.tw) 29 was used. Ramachandran plot (http://mordred.…”