Structural alignment software

! NAME

! Description

| Topology-independent superposition of RNA/DNA 3D structures and structure-based sequence alignment

| Superposition of two arbitrary RNA/DNA 3D structure fragments & 3D motif identification

| Fast and accurate protein structure alignment and visualisation

| Protein structure repository with visualisation and structural analytics tools

| MAtching Molecular Models Obtained from Theory

| CE

| Combinatorial Extension

| CE-MC

| Combinatorial Extension-Monte Carlo

| Distance Matrix Alignment

| TM-align

| TM-score based protein structure alignment

|Multiple protein structure alignment based on TM-align

|Cα

|Multi

|No

|[http://yanglab.nankai.edu.cn/mTM-align/ server and download]

|R. Dong, Z. Peng, Y. Zhang & J. Yang

|2018

| Vector Alignment Search Tool

| PrISM

| Protein Informatics Systems for Modeling

| Molecular Operating Environment. Extensive platform for protein and protein-ligand structure modelling.

| Sequential Structure Alignment Program

| SARF2

| Spatial ARrangements of Backbone Fragments

|NA

| STAMP

|STructural Alignment of Multiple Proteins

| Multiple Alignment by Secondary Structure

| SCALI

| Structural Core ALIgnment of proteins

| NA

| SSM

| Secondary Structure Matching

| Structural Homology by Environment-Based Alignment

| LGA{{cite journal |author=Zemla A |year=2003 |title=LGA: A method for finding 3D similarities in protein structures |journal=Nucleic Acids Research |volume=31 |issue=13 |pages=3370–3374 |pmid=12824330 |pmc=168977 |doi=10.1093/nar/gkg571}}

| Local-Global Alignment, and Global Distance Test (GDT-TS) structure similarity measure

| Partial Order Structure Alignment

| PyMOL

| "super" command does sequence-independent 3D alignment

| Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists

| deconSTRUCT

| Database search on substructural level and pairwise alignment.

| MArkovian TRAnsition of protein Structure

| MAMMOTH-mult

| MAMMOTH-based multiple structure alignment

| NA

| PRIDE

| PRobability of IDEntity

| FAST Alignment and Search Tool

| C-BOP

| Coordinate-Based Organization of Proteins

| Protein least-squares Fitting

| TOPOFIT

| Alignment as a superimposition of common volumes at a topomax point

| MUltiple STructural AligNment AlGorithm

| URMS

| Unit-vector RMSD

| Hierarchical protein structure superposition

| LOCK 2

| Improvements over LOCK

| Consistency Based Alignment

| TetraDA

| Tetrahedral Decomposition Alignment

| STRucture based Alignment Program

| LOVOALIGN

| Low Order Value Optimization methods for Structural Alignment

| Genetic Algorithm for Non-sequential, Gapped protein STructure Alignment

| GANGSTA+

| Combinatorial algorithm for nonsequential and gapped structural alignment

| MatAlign{{cite journal|last=Aung|first=Zeyar|author2=Kian-Lee Tan |title=MatAlign: Precise protein structure comparison by matrix alignment|journal=Journal of Bioinformatics and Computational Biology|date=Dec 2006|volume=4|issue=6|pmid=17245810|pages=1197–216|doi=10.1142/s0219720006002417}}

| Protein Structure Comparison by Matrix Alignment

| Fast structure alignment using Voronoi contacts

| EXPRESSO

| Fast Multiple Structural Alignment using T-Coffee and Sap

| Cα Align

| YAKUSA

| Internal Coordinates and BLAST type algorithm

| Conformation-based alphabet alignments

| CLEPAPS

| Conformation-based alphabet alignments

| Torsion Angle ALIgnment

| MolCom

| NA

| NA

| FlexProt

| Flexible Alignment of Protein Structures

| Multiple Alignment of Protein Structures

| CTSS

| Protein Structure Alignment Using Local Geometrical Features

| NA

| Matt

| Multiple Alignment with Translations and Twists

| Protein structure alignment and visualization of structural similarities; alignment of multiprotein complexes

| SSGS

| Secondary Structure Guided Superimposition

| Comparison of protein structures by growing neighborhood alignments

| UCSF Chimera

| see MatchMaker tool and "matchmaker" command

| Fast aLignment Algorithm for finding Structural Homology of proteins

| RAPIDO

| Rapid Alignment of Protein structures In the presence of Domain mOvements

| Structural Alignment based on Differential Geometrical Encoding

| ProCKSI

| Protein (Structure) Comparison, Knowledge, Similarity and Information

| Structure similarity search Aided by Ramachandran Sequential Transformation

| Cα

| Fr-TM-align

| Fragment-TM-score based protein structure alignment

| Comparing topological models of protein structures enhanced with ligand information

| TOPS++FATCAT

| Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists derived from TOPS+ String Model

| Molecular Local Surface Alignment

| FASE

| Flexible Alignment of Secondary Structure Elements

| Protein Structural Alignment based on a vectorial Structure Representation

| STON

| NA

| Sequence-Structure Hybrid Method

| MAX-PAIRS

| NA

| Maximum likelihood superpositioning

| TABLEAUSearch

| Structural Search and Retrieval using a Tableau Representation of Protein Folding Patterns

| Tableau-based protein substructure search using quadratic programming

| ProSMoS

| Protein Structure Motif Search

| Energy-based multiple structural alignment of proteins

| MSVNS for MaxCMO

| A simple and fast heuristic for protein structure comparison

| Least Squares Root Mean Square deviation minimization by dynamic programming

| ProBiS{{cite journal |author1=Janez Konc |author2=Dušanka Janežič |title=ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment |journal=Bioinformatics |volume=26 |issue=9 |pages=1160–1168 |year=2010 | url= |doi=10.1093/bioinformatics/btq100 |pmid=20305268 |pmc=2859123}}

| Detection of Structurally Similar Protein Binding Sites by Local Structural Alignment

| Dynamics-based Alignment: superposing proteins by matching their collective movements

| SWAPSC

| Sliding Window Analysis Procedure for detecting Selective Constraints for analysing genetic data structured for a family or phylogenetic tree using constraints in protein-coding sequence alignments.

| Fast and accurate protein substructure searching with simulated annealing and GPUs

| RCSB PDB Protein Comparison Tool

| Provides CE, FATCAT, CE variation for Circular Permutations, Sequence Alignments

| Maximal common 3D motif; non-parametric; outputs pairwise correspondence; works also on small molecules

| EpitopeMatch

| discontinuous structure matching; induced fit consideration; flexible geometrical and physicochemical specificity definition; transplantation of similar spatial arrangements of amino acid residues

| Topology-independent 3D structure comparison

| Smolign

| Spatial motifs based protein structural alignment

| Comparing three-dimensional shape-density

| DEDAL

| DEscriptor Defined ALignment

| msTALI

| multiple sTructure ALIgnment

| multiple PB sequence alignment

| SAS-Pro

| Similtaneous Alignment and Superimposition of PROteins

| Match Index based structural alignment method

| SPalign

| Structure Pairwise alignment

| Fast Pairwise or Multiple Alignments using Gaussian Overlap

| DeepAlign{{cite journal|last=Wang|first=Sheng |author2=Jianzhu Ma |author3=Jian Peng |author4=Jinbo Xu|title=Protein structure alignment beyond spatial proximity|journal=Scientific Reports|date=March 2013|doi=10.1038/srep01448|pmid=23486213|volume=3|pages=1448 |pmc=3596798|bibcode=2013NatSR...3E1448W }}

| Protein structure alignment beyond spatial proximity (evolutionary information and hydrogen-bonding are taken into consideration)

| extension of DeepAlign

| TS-AMIR{{cite journal|last=Razmara|first=Jafar |author2=Safaai Deris |author3=Sepideh Parvizpour|title=TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison|journal=Algorithms for Molecular Biology|date=Feb 2012|volume=7|issue=4|pmid=22336468|doi=10.1186/1748-7188-7-4|pages=4|pmc=3298807 |doi-access=free }}

| A topology string alignment method for intensive rapid protein structure comparison

|MICAN can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments

| SPalignNS{{cite journal|last=Brown|first=P.|author2=Pullan W. |author3=Yang Y. |author4=Zhou Y. |title=Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic|journal=Bioinformatics|date=Oct 2015|pmid=26454279 |doi=10.1093/bioinformatics/btv580 |volume=32 |issue=3|pages=370–7|doi-access=free|hdl=10072/101971|hdl-access=free}}

| Structure Pairwise alignment Non-Sequential

| Fit3D{{cite journal|last=Kaiser|first=F.|author2=Eisold A. |author3=Bittrich S. |author4=Labudde D. |title=Fit3D: a web application for highly accurate screening of spatial resiudue patterns in protein structure data|journal=Bioinformatics|date=Oct 2015|pmid=26519504 |doi=10.1093/bioinformatics/btv637 |volume=32 |issue=5|pages=792–4|doi-access=free}}

| highly accurate screening for small structural motifs featuring definition of position-specific exchanges, detection of intra- and inter-molecular occurrences, definition of arbitrary atoms used for motif alignment

|Bayesian statistical inference of alignments based on information theory and compression.

| RCSB PDB strucmotif-search{{cite journal| author=Bittrich S, Burley SK, Rose AS| title=Real-time structural motif searching in proteins using an inverted index strategy. | journal=PLOS Comput Biol | year= 2020 | volume= 16 | issue= 12 | pages= e1008502 | pmid=33284792 | doi=10.1371/journal.pcbi.1008502 | pmc=7746303 | bibcode=2020PLSCB..16E8502B | doi-access=free }}

| Small structural motifs search that takes seconds to run on 180k or more structures, with nucleic acid & bioassembly support