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Create Extended Structure from Residue Sequence
(Currently Proteins Only)

pdbUtilNight Create an Extended Structure
(Currently Proteins Only)

Frank Delaglio delaglio@nih.gov
Sequence File: Input file containing amino acid sequence for the protein structure to create. The input file can be in the form of an NMRPipe table with DATA SEQUENCE lines, a BMRB NMR-Star file with sequence information, or another PDB file. The sequence must contain only residues from the 20 common amino acids. Examples: ubiq_seq.tab and ubiq_seq.str

Alternatively, the input file can be a molecular specification in the DYNAMO GMC Record Format. Using this format provides a method to create multi-chain PDB files, to delete or add atoms, specify additional bonds, etc. Example: gmc_record.txt
Torsion File: Optional input file of one or more named torsions and their values. This provides a way to specify a particular backbone or sidechain torsions if desired. Example: ubiq_phipsi.txt
Reset Backbone Angles to Helix: if this option is selected, after the structure is created, the backbone angles will be reset to helical values. Otherwise, the structure produced will be a random coil. This reset option is ignored if a torsion file is specified above.

The Calculation results will be sent via Email.
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last update: Nov 2 2022