My software notes

October 11, 2011

[web server] protein structural analysis

Filed under: servers — kpwu @ 7:00 pm
Tags: ,

PDBsum provides service that users can upload their calculated structures for analysis including ramachandran plot, sequence+secondary structural element, etc. The figure below is an example. For self-generated structures, users need to click the link “generate” to upload your PDB files. To know the structural information of published biomolecules at Protein Data Bank, just type the pdb access to get the details.

After a short waiting (to this example, i just waited 10 minutes to get analysis done), an email sent from PDBsum provide users to look the details of the submitted structure. I clicked link at the left down corner to see the information of sequence and location of secondary structures. Other analysis including topology, SAS search and rama plot are also available for self-uploaded structures.

Another web server called “POLYVIEW 2D” also provides similar service. Users can look at the structural information of published structures deposited at PDB or upload their own structures (in PDB format) to draw either single or ensemble views. Two snapshots are shown below.

NOTE. POLYVIEW-3D, another service provided by the same team is an useful web server to generate pictures of target biomolecules without opening the molecular viewers on your own computers. It is very convenient for me when I am away from lab and wanna to see some snapshots of proteins. Highly recommended.

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3 Comments »

  1. […] click this post “[web server] protein structural analysis” to read new […]

    Pingback by PDBSum announces topology diagrams for protein domains « My software notes — November 4, 2011 @ 6:20 pm | Reply

  2. thanks for sharing this useful information with us…ROC Software

    Comment by Sethuraman R — June 11, 2014 @ 11:31 pm | Reply


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