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PDB Utility Servers

pdbUtilDay PDB Utility Servers

Contact:
Yang Shen     shenyang@nih.gov

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Add Protons to an Existing PDB Structure

(Currently for Proteins Only) Given an existing PDB structure with heavy atoms, this server will create a new version of the PDB which includes H atoms. The advanced options can also be used to help resolve steric clashes.

Server: https://spin.niddk.nih.gov/bax-apps/nmrserver/pdbutil/sa.html

Calculate Hydrogen Bonds for an Existing PDB Structure

Given an existing PDB structure with hydrogen atoms, this server calculates hydrogen bonds between acceptors and donors in the structure.

Server: https://spin.niddk.nih.gov/bax-apps/nmrserver/pdbutil/hbond.html

Create a PDB File Extended Structure from Amino Acid Sequence

(Proteins Only) Given amino acid sequence information, this server creates a PDB file with identical backbone angles for all residues.

Server: https://spin.niddk.nih.gov/bax-apps/nmrserver/pdbutil/ext.html

Coordinate Alignment of Related Structures in a PDB File

This server reads a PDB file with multiple structures, and performs an atomic coordinate alignment so that each structure is overlayed with the first one.

Server: https://spin.niddk.nih.gov/bax-apps/nmrserver/pdbutil/ov.html

Rotations and Translations of a PDB File

This server reads a PDB file and performs one or more rotations or translations of the atomic coordinates.

Server: https://spin.niddk.nih.gov/bax-apps/nmrserver/pdbutil/trans.html

List and Graph Secondary Structure Information

(Proteins Only) This server reads a PDB file, and tabulates and graphs information about the backbone and sidechain torsions, hydrogen bonds, and secondary structure. It also returns simple estimates of the mass, solvent-accessible surface area, volume, and radius of gyration.

Server: https://spin.niddk.nih.gov/bax-apps/nmrserver/pdbutil/ss.html

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last updated: Oct 30 2022