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Structural alignment

Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two…

Types of comparisons, Methods & RNA structural alignment

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Overview

Data produced by structural alignment

Types of comparisons

Algorithmic complexity

Representation of structures

Methods

Recent developments

RNA structural alignment

Software

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Map overview Semantic statistics

Structural alignment

Nodes74
Edges73
Triples127
Avg. degree1.97
Density0.027027
Components1

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Structural alignment

Top relations

related to Recent developments · 18
Structural alignment → As, CE, DALI, G-Losa, H-bond, Improvements, In, MAPPIS, MultiBind, Other, Others, ProBiS, The, The MultiBind, These, TM-align, Unlike, While G-Losa
related to Mammoth · 16
Structural alignment → All-against-all, C-alpha, E-value, Expectation, For, It, Local, MAMMOTH, MaxSub, Rather, SCOP, The, These, This, To, URMS
has method · 13
Structural alignment → Cα, Each, Foldseek, It, MUSCLE-3D, PDB, Protein Data Bank, Reseek, Structural, Such, The, This, To
related to SSAP · 12
Structural alignment → Architecture, CATH, CATH Protein Structure Classification, Class, Dynamic, Homology, Instead, It, Sequential Structure Alignment Program, SSAP, The SSAP, Topology
related to DALI · 10
Structural alignment → Because DALI, DALI, DALI's, Distance-matrix ALIgnment, In, Monte Carlo, Secondary, Submatrix, This, When
related to RNA structural alignment · 8
Structural alignment → Functionally, GSSUs, However, One, RNA, SETTER, Structural, The
related to Optimal solution · 7
Structural alignment → However, MaxSub, NP-complete, Strictly, The, These, Unfortunately
related to Data produced by structural alignment · 6
Structural alignment → CASP, GDT, Note, RMSD, The, This
related to Software · 6
Structural alignment → Choosing, Org, ProCKSI, Properties, Proteopedia, Structural Alignment Tools
related to Types of comparisons · 6
Structural alignment → Because, For, Only, Other, RMSD, When

Important terminology Word statistics

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Important terminology

alignment structural structures structure protein used similarity matrix proteins sequence two methods method superposition residues rna known input sequences dali

Entity relationships Subject–Predicate–Object triples

SubjectPredicateObjectConfidenceSrc
Structural alignmentis avaluable tool for the comparison of proteins with low sequence similarity0.90text
Structural alignmentis aset of residues that are considered equivalent between the structures0.90text
the global distance testinstance ofas well as other more sophisticated measures of structural similarity0.80text
the four-helix bundleinstance ofSuch algorithms have successfully identified canonical folds0.80text
secondary structure elementsinstance ofReducing the protein to a coarse metric0.80text
secondary structureinstance ofthe original definition of the CE method included only structural superpositions and inter-residue distances but has since been expanded to include local environmental properties0.80text
solvent exposureinstance ofthe original definition of the CE method included only structural superpositions and inter-residue distances but has since been expanded to include local environmental properties0.80text
hydrogen-bonding patternsinstance ofthe original definition of the CE method included only structural superpositions and inter-residue distances but has since been expanded to include local environmental properties0.80text
and dihedral angles.An alignment path is calculated as the optimal path through the similarity matrix by linearly progressing through the sequencesinstance ofthe original definition of the CE method included only structural superpositions and inter-residue distances but has since been expanded to include local environmental properties0.80text
extending the alignment with the next possible high-scoring AFP pairinstance ofthe original definition of the CE method included only structural superpositions and inter-residue distances but has since been expanded to include local environmental properties0.80text
SCOPinstance ofparticularly structures generated by ab initio structure prediction to structure families0.80text
because it emphasizes extracting a statistically reliable sub alignmentinstance ofparticularly structures generated by ab initio structure prediction to structure families0.80text

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