{"id":13958595,"url":"https://github.com/pylelab/USalign","last_synced_at":"2025-07-21T00:31:21.130Z","repository":{"id":38220435,"uuid":"411298622","full_name":"pylelab/USalign","owner":"pylelab","description":"Universal Structure Alignment of Monomeric and Complex Structure of Nucleic Acids and Proteins","archived":false,"fork":false,"pushed_at":"2025-04-22T03:46:39.000Z","size":733,"stargazers_count":135,"open_issues_count":2,"forks_count":27,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-22T06:09:21.135Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://zhanggroup.org/US-align/","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pylelab.png","metadata":{"files":{"readme":"readme.txt","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-09-28T13:43:16.000Z","updated_at":"2025-04-22T03:46:43.000Z","dependencies_parsed_at":"2023-12-13T05:20:19.960Z","dependency_job_id":"9c28cf19-bb6c-42f4-a01d-f3bf6de3daa7","html_url":"https://github.com/pylelab/USalign","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/pylelab/USalign","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pylelab%2FUSalign","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pylelab%2FUSalign/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pylelab%2FUSalign/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pylelab%2FUSalign/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pylelab","download_url":"https://codeload.github.com/pylelab/USalign/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pylelab%2FUSalign/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266221261,"owners_count":23894965,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-08-08T13:01:45.749Z","updated_at":"2025-07-21T00:31:21.123Z","avatar_url":"https://github.com/pylelab.png","language":"C++","funding_links":[],"categories":["蛋白质结构"],"sub_categories":["网络服务_其他"],"readme":"==============================================================================\n   US-align: universal structure alignment of monomeric and complex proteins\n   and nucleic acids\n\n   References:\n   * Chengxin Zhang, Morgan Shine, Anna Marie Pyle, Yang Zhang\n     (2022) Nat Methods. 19(9), 1109-1115.\n   * Chengxin Zhang, Anna Marie Pyle (2022) iScience. 25(10), 105218.\n\n   DISCLAIMER:\n     Permission to use, copy, modify, and distribute this program for \n     any purpose, with or without fee, is hereby granted, provided that\n     the notices on the head, the reference information, and this\n     copyright notice appear in all copies or substantial portions of \n     the Software. It is provided \"as is\" without express or implied \n     warranty.\n\n   *************** updating history ********************************\n   2012/01/24: A C/C++ code of TM-align was constructed by J Yang\n   2016/05/21: Several updates of this program were made by J Wu, including\n              (1) fixed several compiling bugs\n              (2) made I/O of C/C++ version consistent with the Fortran version\n              (3) added outputs including full-atom and ligand structures\n              (4) added options of '-i', '-I' and '-m'\n   2016/05/25: fixed a bug on PDB file reading\n   2018/06/04: Several updates were made by C Zhang, including\n              (1) Fixed bug in reading PDB files with negative residue index,\n                  at the expense of the '-o' option now only being able to\n                  output superposed structure instead of full rasmol script.\n              (2) Implemented the fTM-align algorithm (by the '-fast' option)\n                  as described in R Dong, S Pan, Z Peng, Y Zhang, J Yang\n                  (2018) Nucleic acids research. gky430.\n              (3) Included option to perform TM-align against a whole \n                  folder of PDB files. A full list of options not available\n                  in the Fortran version can be explored by TMalign -h\n   2018/07/27: Added the -byresi option for TM-score superposition without\n               re-alignment as in TMscore and TMscore -c\n   2018/08/07: Added the -dir option\n   2018/08/14: Added the -split option\n   2018/08/16: Added the -infmt1, -infmt2 options.\n               TMalign can now read .gz and .bz2 compressed files.\n   2018/10/20: C Zhang and S Gong updated the RNA alignment part of\n               the program. Changes include:\n              (1) new d0 calculation for RNA.\n              (2) secondary structure assignment for RNA.\n              (3) automatic detection of molecule type (protein vs RNA).\n   2019/01/07: C Zhang added support for PDBx/mmCIF format.\n   2019/02/09: Fixed asymmetric alignment bug.\n   2019/03/17: Added the -cp option for circular permutation\n   2019/03/27: Added the -mirror option for mirror structure alignment\n   2019/04/25: The RNA-align algorithm was published by Bioinformatics\n   2019/07/24: Fixed bug in displaying matching residues.\n               Added GDT and MaxSub to TMscore program.\n   2019/08/18: Prevent excessive circular permutation alignment by -cp.\n   2020/05/19: Add back rasmol output\n   2020/12/12: Fixed bug in double precision coordinate mmcif alignment\n   2021/01/07: Fixed bug in TMscore -c\n   2021/05/29: Remove unnecessary depedency on malloc.h, which prevent\n               compilation on Mac OS\n   2021/08/17: Complete implementation of MMalign\n   2021/10/03: Support Windows\n   2022/02/27: Add -seq (-byresi 4 \u0026 5) for TM-score superimposition guided by\n               sequence alignment.\n   2022/04/12: Support AlphaFold CIF\n   2022/05/11: Update -mm 4 output format\n   2022/05/24: Limited support for sequence order independent alignment\n   2022/05/30: Correct atom pair output for -mm 5\n   2022/06/07: Sequence order semi-independent alignment\n   2022/06/20: Sequentiality within SSE in sequence order semi-independent\n               alignment\n   2022/06/22: Fix infinite loop for mal-formatted PDB\n   2022/06/23: Fix -m for Windows. Add pymol plugin.\n   2022/06/26: Add -full option for -mm 2 and 4\n   2022/09/24: Support -TMscore for complex when the chain order is different\n   2023/06/09: Correct atom name justification in PDB file for standard amino\n               acids and nucleotides\n   2023/12/13: Refine chain assignment for -TMscore \u003e=6 for large complex\n   2023/12/22: Forbid chain assignment refinment for -chainmap\n   2024/03/04: -chain1 and -chain2 option\n   2024/03/19: chain mapping for trimer -TMscore\n   2024/05/10: better handling of alternative location indicator, e.g., 5e1n\n   2024/06/02: implement -mm 4 -se\n   2024/07/05: implement -do\n   2024/07/30: implement -se -byresi 6 7\n   2024/10/30: set default for -ter and -split\n   2024/11/08: -chimerax\n===============================================================================\n\n=========================\n How to install US-align\n=========================\nTo compile the program in your Linux computer, simply enter\n\n    make\n\nor\n\n    g++ -static -O3 -ffast-math -lm -o USalign USalign.cpp\n\nThe '-static' flag should be removed on Mac OS, which does not support\nbuilding static executables. Compilation takes just a few seconds.\n\nUSalign compiled on Linux, Mac OS and Linux Subsystem for Windows (WSL2) on\nWindows 10 onwards can read both uncompressed files and gz compressed\nfiles, provided that the \"gunzip\" command is available. On the other hand, due\nto the lack of POSIX support on Windows, US-align natively compiled on Windows\nwithout WSL2 cannot parse gz compressed files.\n\nUS-align is known to be compilable by g++ version 4.8.5 or later, clang++\nversion 12.0.5 or later and mingw-w64 version 9.3 or later.\n\nIt is also possible to install using package managers.\n\nIf you are using Homebrew, run the following command.\nThe executable is supposed to work on MacOS (x86_64, arm64) and Linux (x86_64).\n\n```shell\nbrew install brewsci/bio/usalign\n```\n\nIf you are using conda, run the following command.\nThe executable is supposed to work on Linux (x86_64, aarch64) and MacOS (x86_64, arm64).\n\n```shell\nconda install -c bioconda usalign\n```\n\nThe Homebrew and conda packages may not have the most recent version of US-align.\n\n=====================\n How to use US-align\n=====================\nYou can run the program without arguments to obtain a brief instruction\n\n    ./USalign structure1.pdb structure2.pdb\n\nA full list of available options can be explored by:\n\n    ./USalign -h\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpylelab%2FUSalign","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpylelab%2FUSalign","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpylelab%2FUSalign/lists"}