N-BIO BINDS

Predict 3D structure of multi-domain protein

PreDom:Structure predicts 3D structure of multi-domain protein from 3D structure of each domain.

  • If whole 3D structure of a homologus multi-domain protein to the query protein is available, PreDom:Structure predicts the whole 3D structure of the query protein by homology modeling using MODELLER
  • Otherwise, PreDom:Structure predicts the 3D structure of each domain by homology modeling. If two 3D structures of domains in the query protein can be obtained, PreDom:Structure predicts their relative orientation as follows
    1. Candidate structures of a multi-domain protein are generated by ZDOCK from individual domain structures.
    2. Domain-domain interface residues of each domain are predicted by the algorithm used in PreDom:Interface.
    3. The distance between the C-terminus of first domain and the N-terminus of second domain is estimated using the number of residues in the domain linker.
    4. Candidate structures are sorted by DINE score that is a linear sum of docking score, interface score and end-to-end distance score.

Input type:
Amino acid sequence
in FASTA format:
FASTA format file:
domain 1 PDB format file: chain:
domain 2 PDB format file: chain:
domain 3 PDB format file: chain:
domain 4 PDB format file: chain:
domain 5 PDB format file: chain:
domain 6 PDB format file: chain:
domain 7 PDB format file: chain:
domain 8 PDB format file: chain:
domain 9 PDB format file: chain:
domain 10 PDB format file: chain:
Whole amino acid sequence
Amino acid sequence
in FASTA format:
FASTA format file:
Parameters for DINE
KIP method Threshold of sequence identity: % Threshold of sequence coverage: % Threshold of BLAST E-value:
IP method Threshold of IP score: Threshold of residue contact: Å Minimum size of interface: aa.
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Sample PDB file (glucosamine 6-phosphate synthase)

  • glutaminase (N-terminal) domain: 1xff.pdb (chain A)
  • isomerase (C-terminal) domain: 1moq.pdb (chain A)

Sample FASTA sequence 

>gi|253797503|ref|YP_003030504.1| hypothetical protein TBMG_00576 [Mycobacterium tuberculosis KZN 1435]
MKLFDDRGDAGRQLAQRLAQLSGKAVVVLGLPRGGVPVAFEVAKSLQAPLDVLVVRKLGVPFQPELAFGA
IGEDGVRVLNDDVVRGTHLDAAAMDAVERKQLIELQRRAERFRRGRDRIPLTGRIAVIVDDGIATGATAK
AACQVARAHGADKVVLAVPIGPDDIVARFAGYADEVVCLATPALFFAVGQGYRNFTQTSDDEVVAFLDRA
HRDFAEAGAIDAAADPPLRDEEVQVVAGPVPVAGHLTVPEKPRGIVVFAHGSGSSRHSIRNRYVAEVLTG
AGFATLLFDLLTPEEERNRANVFDIELLASRLIDVTGWLATQPDTASLPVGYFGASTGAGAALVAAADPR
VNVRAVVSRGGRPDLAGDSLGSVVAPTLLIVGGRDQVVLELNQRAQAVIPGKCQLTVVPGATHLFEEPGT
LEQVAKLACDWFIDHLCGPGPSG