●I-TASSER ●D-I-TASSER ●I-TASSER-MTD ●C-I-TASSER ●CR-I-TASSER ●QUARK ●C-QUARK ●D-QUARK ●DRfold ●DRfold2 ●DeepFoldRNA ●RNArefine ●LOMETS ●MUSTER ●CEthreader ●SEGMER ●DeepFold ●FoldDesign ●COFACTOR ●COACH ●MetaGO ●TripletGO ●ATGO ●IonCom ●FG-MD ●ModRefiner ●REMO ●DEMO ●DEMO-EM ●PPLM ●DMFold ●SPRING ●COTH ●Threpp ●PEPPI ●BSpred ●ANGLOR ●EDock ●BSP-SLIM ●SAXSTER ●FUpred ●ThreaDom ●ThreaDomEx ●EvoDesign ●BindProf ●BindProfX ●SSIPe ●GPCR-I-TASSER ●MAGELLAN ●ResQ ●STRUM ●DeepTherm ●DAMpred ●TCRfinder

●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●TM-search ●Ouroboros ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●DeepMSA2 ●rMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER ●PRING ●SMP

●BioLiP ●HPmod ●E. coli ●UniBioMap ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●ProteinConform ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

• 2026/03/28: Fix -mm 1 asymmetric alignment bug where oligomer alignment output depends occasionally on input file order
• 2024/11/08: Add -chimerax for UCSF ChimeraX format output
• 2024/10/30: Set default for -ter and -split based on -mm output
• 2024/07/30: Allow using -se with -byresi 6 7
• 2024/07/05: Add -do to output distances for aligned residue pairs
• 2024/06/02: Allow using -mm 4 with -se
• 2024/05/10: better handling of alternative location indicator, e.g., 5e1n
• 2024/03/19: chain mapping for trimer -TMscore
• 2024/03/04: Add -chain1 and -chain2 options to specify chains to align
• 2023/12/22: Forbid chain assignment refinment for -chainmap
• 2023/12/13: Refine chain assignment for -TMscore >=6 for large complex
• 2023/06/09: Correct atom name justification in PDB file for standard amino acids and nucleotides
• 2022/09/24: Support -TMscore for complex when the chain order is different
• 2022/06/26: Add -full option for -mm 2 and 4 to show chain level alignment
• 2022/06/23: Fix -m for Windows. Add pymol plugin
• 2022/06/22: Fix infinite loop for mal-formatted PDB
• 2022/06/20: Ensure sequentiality within SSE in sequence order semi-independent alignment
• 2022/06/07: Sequence order semi-independent alignment
• 2022/05/30: Correct atom pair output for -mm 5
• 2022/05/24: Limited support for sequence order independent alignment
• 2022/05/11: Update -mm 4 output format
• 2022/04/12: Support AlphaFold CIF
• 2022/02/27: Add -seq (-byresi 4 & 5) for TM-score superimposition guided by sequence alignment
• 2021/10/03: Support Windows
• 2021/08/17: Complete implementation of MMalign for oligomer alignment
• 2021/05/29: Remove unnecessary depedency on malloc.h, which prevent compilation on Mac OS
• 2021/01/07: Fixed bug in TMscore -c for TM-score superposition between two oligomers
• 2020/12/12: Fixed bug in double precision coordinate mmcif alignment
• 2020/05/19: Add back rasmol output by -rasmol
• 2019/08/18: Prevent excessive circular permutation alignment by -cp
• 2019/07/24: Fixed bug in displaying matching residues. Added GDT and MaxSub to TMscore program.
• 2019/04/25: The RNA-align algorithm was published by Bioinformatics
• 2019/03/27: Added the -mirror option for mirror structure alignment
• 2019/03/17: Added the -cp option for circular permutation
• 2019/02/09: Fixed asymmetric alignment bug where the output result is occasionally dependent on the order of input files.
• 2019/01/07: C Zhang added support for PDBx/mmCIF format
• 2018/10/20: C Zhang and S Gong updated the RNA alignment part of the program. Changes include: (1) new d0 calculation for RNA. (2) secondary structure assignment for RNA. (3) automatic detection of molecule type (protein vs RNA).
• 2018/08/16: Added the -infmt1, -infmt2 options. TMalign can now read .gz and .bz2 compressed files.
• 2018/08/14: Added the -split option to split input structure by chain or by model
• 2018/08/07: Added the -dir option for all-against-all alignment within a folder
• 2018/07/27: Added the -byresi option for TM-score superposition without re-alignment as in TMscore and TMscore -c
• 2018/06/04: Several updates were made by C Zhang, including (1) Fixed bug in reading PDB files with negative residue index, at the expense of the '-o' option now only being able to output superposed structure instead of full rasmol script. (2) Implemented the fTM-align algorithm (by the '-fast' option) as described in R Dong, S Pan, Z Peng, Y Zhang, J Yang (2018) Nucleic acids research. gky430. (3) Included option to perform TM-align against a whole folder of PDB files. A full list of options not available in the Fortran version can be explored by TMalign -h
• 2016/05/25: fixed a bug on PDB file reading
• 2016/05/21: Several updates of this program were made by J Wu, including (1) fixed several compiling bugs (2) made I/O of C/C++ version consistent with the Fortran version (3) added outputs including full-atom and ligand structures (4) added options of '-i', '-I' and '-m'
• 2012/01/24: A C/C++ code of TM-align was constructed by J Yang