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
- Candidate structures of a multi-domain protein are generated by ZDOCK from individual domain structures.
- Domain-domain interface residues of each domain are predicted by the algorithm used in PreDom:Interface.
- 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.
- Candidate structures are sorted by DINE score that is a linear sum of docking score, interface score and end-to-end distance score.
Sample PDB file (glucosamine 6-phosphate synthase)
Sample FASTA sequence
>gi|253797503|ref|YP_003030504.1| hypothetical protein TBMG_00576 [Mycobacterium tuberculosis KZN 1435] MKLFDDRGDAGRQLAQRLAQLSGKAVVVLGLPRGGVPVAFEVAKSLQAPLDVLVVRKLGVPFQPELAFGA IGEDGVRVLNDDVVRGTHLDAAAMDAVERKQLIELQRRAERFRRGRDRIPLTGRIAVIVDDGIATGATAK AACQVARAHGADKVVLAVPIGPDDIVARFAGYADEVVCLATPALFFAVGQGYRNFTQTSDDEVVAFLDRA HRDFAEAGAIDAAADPPLRDEEVQVVAGPVPVAGHLTVPEKPRGIVVFAHGSGSSRHSIRNRYVAEVLTG AGFATLLFDLLTPEEERNRANVFDIELLASRLIDVTGWLATQPDTASLPVGYFGASTGAGAALVAAADPR VNVRAVVSRGGRPDLAGDSLGSVVAPTLLIVGGRDQVVLELNQRAQAVIPGKCQLTVVPGATHLFEEPGT LEQVAKLACDWFIDHLCGPGPSG