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●D-I-TASSER ●DMFold ●LOMETS3 ●DeepMSA2 ●HPmod ●BioLiP2 ●US-align ●InterLabelGO ●StarFunc ●ShapeME

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D-I-TASSER download

D-I-TASSER Suite is a package of standalone programs for distance-assisted protein structure prediction. The user manual is at README.txt. Please contact Wei Zheng for any problems or questions. The D-I-TASSER Suite is free for academic and non-profit researchers.

D-I-TASSER benchmark datasets download:
D-I-TASSER Suite download:
D-I-TASSER library download:

D-I-TASSER third-party sequence library download:
  • uniclust30_2017_04: Uniclust30 HHblits style HMM sequence library (for D-I-TASSER, DeepMSA/DeepMS2).
  • uniref90: UniRef90 library (for D-I-TASSER, DeepMSA/DeepMS2).
  • metaclust: Metaclust library (for D-I-TASSER, DeepMSA/DeepMS2).
  • UniRef30_2022_02: UniRef30 HHblits style HMM sequence library (for D-I-TASSER, DeepMS2).
  • BFD: BFD HHblits style HMM sequence library (for D-I-TASSER, DeepMS2).
  • MGnify: MGnify library (for D-I-TASSER, DeepMS2).

    • D-I-TASSER non-redundant sequence library, sourced from JGIclust, TaraDB and MetaSourceDB metagenome databases with 50% sequence identity threshold, producted by Zhang Lab (for MSA construction). We recommand you download the D-I-TASSER Suite first, then use download_lib.py download this library.
  • JGI list
  • DB.fasta.aa
  • DB.fasta.aa.ssi
  • DB.fasta.ab
  • DB.fasta.ab.ssi
  • DB.fasta.ac
  • DB.fasta.ac.ssi
  • DB.fasta.ad
  • DB.fasta.ad.ssi

    • D-I-TASSER main library download:
  • CE: CEthreader library (for D-I-TASSER, LOMETS2/3 and CEthreader).
  • PDB: non-redundant protein structures from PDB (for D-I-TASSER, LOMETS2/3, MUSTER, CEthreader and SEGMER).
  • MTX: Sequence profiles from PSI-BLAST search (for D-I-TASSER, LOMETS2/3, MUSTER and SEGMER).
  • DEP : Depth-dependent structure profiles of templates (for D-I-TASSER, LOMETS2/3, MUSTER and SEGMER).
  • SIG: Residue environmental profiles of templates (for D-I-TASSER, LOMETS2/3).
  • CNT: Side-chain center contacts of templates (for D-I-TASSER, LOMETS2/3).
  • dotProfile: Sequence profiles from PSI-BLAST search (for D-I-TASSER, LOMETS2/3).
  • stride: Seven state secondary structure assignment (for D-I-TASSER, LOMETS2/3).
  • summary1: Sequence, secondary structure, solvent accessibilty, phi/psi angles (for D-I-TASSER, LOMETS2/3, MUSTER and SEGMER).
  • summary2: Training data for phi/psi prediction and contact prediction by SVM (for D-I-TASSER, LOMETS2/3, MUSTER and SEGMER).
  • Bfactor: B-factor values of templates (for B-factor profile prediction).
  • nr: Non-redundant NCBI sequence database (for secondary structure prediction etc).

    AlphaFold2 library used in D-I-TASSER (with AlphaFold2 distance) pipeline:
  • AlphaFold2 parameters.
  • PDB70 library.
  • MMCIF format coordinates.
  • PDB sequences.
  • Small BFD sequence database.
  • Uniprot sequence database.

    • Template library files needed for the COFACTOR and COACH programs. All libraries are weekly updated.
  • BioLiP: Ligand-protein binding database.

    Instruction on how to configure the D-I-TASSER libraries is available at README.txt

    References:
  • Wentao Ni, Qiqige Wuyun, Quancheng Liu, Yilin Pu, Wei Zheng, Lydia Freddolino. D-I-TASSER: A platform for single- and multi-domain protein structure and function predictions based on deep learning spatial restraints and knowledge-based potentials. In preparation.
  • Wei Zheng, Qiqige Wuyun, Peter L Freddolino, Yang Zhang. Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15. Proteins. 2023; 1-20. doi:10.1002/prot.26585.

    • Contact WeiZheng