==============================================================================
US-align: universal structure alignment of monomeric and complex proteins
and nucleic acids
References:
- Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang
(2022) Nat Methods. 19(9), 1109-1115.
-
Chengxin Zhang, Anna Marie Pyle (2022) iScience. 25(10), 105218.
DISCLAIMER:
Permission to use, copy, modify, and distribute this program for
any purpose, with or without fee, is hereby granted, provided that
the notices on the head, the reference information, and this
copyright notice appear in all copies or substantial portions of
the Software. It is provided "as is" without express or implied
warranty.
*** updating history ****
2012/01/24: A C/C++ code of TM-align was constructed by J Yang
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'
2016/05/25: fixed a bug on PDB file reading
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
2018/07/27: Added the -byresi option for TM-score superposition without
re-alignment as in TMscore and TMscore -c
2018/08/07: Added the -dir option
2018/08/14: Added the -split option
2018/08/16: Added the -infmt1, -infmt2 options.
TMalign can now read .gz and .bz2 compressed files.
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).
2019/01/07: C Zhang added support for PDBx/mmCIF format.
2019/02/09: Fixed asymmetric alignment bug.
2019/03/17: Added the -cp option for circular permutation
2019/03/27: Added the -mirror option for mirror structure alignment
2019/04/25: The RNA-align algorithm was published by Bioinformatics
2019/07/24: Fixed bug in displaying matching residues.
Added GDT and MaxSub to TMscore program.
2019/08/18: Prevent excessive circular permutation alignment by -cp.
2020/05/19: Add back rasmol output
2020/12/12: Fixed bug in double precision coordinate mmcif alignment
2021/01/07: Fixed bug in TMscore -c
2021/05/29: Remove unnecessary depedency on malloc.h, which prevent
compilation on Mac OS
2021/08/17: Complete implementation of MMalign
2021/10/03: Support Windows
2022/02/27: Add -seq (-byresi 4 & 5) for TM-score superimposition guided by
sequence alignment.
2022/04/12: Support AlphaFold CIF
2022/05/11: Update -mm 4 output format
2022/05/24: Limited support for sequence order independent alignment
2022/05/30: Correct atom pair output for -mm 5
2022/06/07: Sequence order semi-independent alignment
2022/06/20: Sequentiality within SSE in sequence order semi-independent
alignment
2022/06/22: Fix infinite loop for mal-formatted PDB
2022/06/23: Fix -m for Windows. Add pymol plugin.
2022/06/26: Add -full option for -mm 2 and 4
2022/09/24: Support -TMscore for complex when the chain order is different
2023/06/09: Correct atom name justification in PDB file for standard amino
acids and nucleotides
2023/12/13: Refine chain assignment for -TMscore >=6 for large complex
2023/12/22: Forbid chain assignment refinment for -chainmap
2024/03/04: -chain1 and -chain2 option
2024/03/19: chain mapping for trimer -TMscore
2024/05/10: better handling of alternative location indicator, e.g., 5e1n
2024/06/02: implement -mm 4 -se
2024/07/05: implement -do
2024/07/30: implement -se -byresi 6 7
=========================
How to install US-align
To compile the program in your Linux computer, simply enter
make
or
g++ -static -O3 -ffast-math -lm -o USalign USalign.cpp
The '-static' flag should be removed on Mac OS, which does not support
building static executables.
USalign compiled on Linux, Mac OS and Linux Subsystem for Windows (WSL2) on
Windows 10 onwards can read both uncompressed files and gz compressed
files, provided that the "gunzip" command is available. On the other hand, due
to the lack of POSIX support on Windows, US-align natively compiled on Windows
without WSL2 cannot parse gz compressed files.
US-align is known to be compilable by g++ version 4.8.5 or later, clang++
version 12.0.5 or later and mingw-w64 version 9.3 or later.
=====================
How to use US-align
You can run the program without arguments to obtain a brief instruction
./USalign structure1.pdb structure2.pdb
A full list of available options can be explored by:
./USalign -h