http://wiki.cathdb.info/
2026-03-13T23:48:32+00:00CATH
http://wiki.cathdb.info/
http://wiki.cathdb.info/lib/exe/fetch.php?media=wiki:dokuwiki.svgtext/html2008-09-19T13:11:50+00:00Anonymous (anonymous@undisclosed.example.com)alpha_beta_plait
http://wiki.cathdb.info/doku.php?id=glossary:alpha_beta_plait&rev=1221829910&do=diff
Alpha-beta plaittext/html2015-08-17T17:59:41+00:00Anonymous (anonymous@undisclosed.example.com)alpha_hairpin
http://wiki.cathdb.info/doku.php?id=glossary:alpha_hairpin&rev=1439834381&do=diff
Alpha Hairpin
This motif comprises two
sequential alpha helices linked by a coil, which lie adjacent in space
and run approximately antiparallel. See also hairpin.
The example shown is the central domain in a rRNA methyltransferase (CATH domain ID 1o9gA02).text/html2008-09-17T07:49:13+00:00Anonymous (anonymous@undisclosed.example.com)alpha_helix
http://wiki.cathdb.info/doku.php?id=glossary:alpha_helix&rev=1221637753&do=diff
Alpha Helix
The alpha helix is the most abundant type of secondary structure in proteins and has been extensively documented.
In brief, alpha helices are formed from stretches of consecutive amino acid residues
with phi and psi angle pairs which correspond to the bottom left quadrant of thetext/html2015-08-17T17:56:46+00:00Anonymous (anonymous@undisclosed.example.com)antiparallel_beta_sheets
http://wiki.cathdb.info/doku.php?id=glossary:antiparallel_beta_sheets&rev=1439834206&do=diff
Antiparallel Beta Sheets
This is a beta-pleated sheet in which adjacent beta strands in the structure point
in opposite directions, for example amino-terminal to carboxy-terminal, carboxy-terminal
to amino-terminal, amino-terminal to carboxy-terminal, etc. Such sheets have narrowly
spaced hydrogen bond pairs that alternate with widely spaced pairs. In each residue the main
chain -NH and -CO groups point in the same direction, but which alternates
with successive residues.text/html2008-08-13T15:48:12+00:00Anonymous (anonymous@undisclosed.example.com)architecture
http://wiki.cathdb.info/doku.php?id=glossary:architecture&rev=1218642492&do=diff
Architecture
This describes the overall shape of the domain structure as determined by the orientations of the secondary structures but ignores the connectivity between the secondary structures. It is currently assigned manually using a simple description of the secondary structure arrangement e.g. barrel or 3-layer sandwich. Reference is made to the literature for well-known architectures (e.g the beta-propellor or alpha four helix bundle).text/html2008-08-13T12:09:41+00:00Anonymous (anonymous@undisclosed.example.com)atom
http://wiki.cathdb.info/doku.php?id=glossary:atom&rev=1218629381&do=diff
Domain Sequence (ATOM) file
The Domain Sequence (ATOM) file stores the FASTA sequence for a particular protein based on the atoms as seen in the solved crystal or NMR protein structure.text/html2008-09-19T08:08:45+00:00Anonymous (anonymous@undisclosed.example.com)beta_alpha_beta_motif
http://wiki.cathdb.info/doku.php?id=glossary:beta_alpha_beta_motif&rev=1221811725&do=diff
Beta-Alpha-Beta Motif
This motif comprises a beta strand-loop-helix-loop-strand arrangment,
with the strands lying parallel and hydrogen-bonded to the helix. The
alpha helix packs against the beta strands and thus buries the hydrophobic
side chains in these strands. The
joining loops regions in the motif can vary in length from one residue to more
than 100 residues. 99% of these motifs are right handed.text/html2008-08-06T14:56:06+00:00Anonymous (anonymous@undisclosed.example.com)beta_arch
http://wiki.cathdb.info/doku.php?id=glossary:beta_arch&rev=1218034566&do=diff
Beta Arch
This describes the motif formed by two sequentially adjacent
beta strands connected by a coil, which are antiparallel, but lie
in different sheets, usually in a beta-sandwich architecture.text/html2008-08-11T08:54:41+00:00Anonymous (anonymous@undisclosed.example.com)beta_barrel
http://wiki.cathdb.info/doku.php?id=glossary:beta_barrel&rev=1218444881&do=diff
Beta Barrel
In some instances large anti-parallel (or parallel) sheets can roll up
completely to join edges and form a cylinder or closed 'barrel', in which the
first strand is hydrogen bonded to the last. The strands form
the 'staves' of the barrel.The example shown is porin (pdb code 2por)).text/html2008-09-17T09:08:47+00:00Anonymous (anonymous@undisclosed.example.com)beta_bulges
http://wiki.cathdb.info/doku.php?id=glossary:beta_bulges&rev=1221642527&do=diff
Beta Bulges
Beta bulges are regions of irregularity in a beta sheet, where the
normal pattern of hydrogen bonding is disrupted, e.g. by the insertion of
an extra residue. A bulge usually involves two or more residues in
the bulged strand, opposite a single residue in the adjacent strand.
These irregularities have been identified and classified
automatically. In all, five types of beta-bulge were identified:
classic, G1, wide, bent and special. Bulges were found to occur
frequently in protein…text/html2008-09-18T14:04:33+00:00Anonymous (anonymous@undisclosed.example.com)beta_hairpin
http://wiki.cathdb.info/doku.php?id=glossary:beta_hairpin&rev=1221746673&do=diff
Beta Hairpin
The simplest type of up-down antiparallel beta-sheet topology whereby two adjacent antiparallel strands are joined by a loop. This motif occurs very frequently in nature and can be observed in many different beta-sheet structures.
The example given below is the epidermal growth factor-like domain of heregulin-alpha (CATH domain ID 1hreA00).text/html2008-09-17T09:31:29+00:00Anonymous (anonymous@undisclosed.example.com)beta_helix
http://wiki.cathdb.info/doku.php?id=glossary:beta_helix&rev=1221643889&do=diff
Beta Helix
In this mainly beta fold, the polypeptide chain is wound into a large right-handed coil (or super helix).
There are two different types of beta helix, one with two beta sheets, and one with three beta
sheets. In our classification scheme we describe these as 2-solenoid and 3-solenoid betatext/html2008-09-18T14:18:21+00:00Anonymous (anonymous@undisclosed.example.com)beta_meander
http://wiki.cathdb.info/doku.php?id=glossary:beta_meander&rev=1221747501&do=diff
Beta Meander
This is a simple 'up-and-down' beta sheet motif with three strands, which is characterised
by (+1, +1) connectivities. A large sheet may comprise sequential meanders to form the
up-down beta barrel.
Referencestext/html2008-09-17T11:00:32+00:00Anonymous (anonymous@undisclosed.example.com)beta_prism
http://wiki.cathdb.info/doku.php?id=glossary:beta_prism&rev=1221649232&do=diff
Beta Prism
The beta prism is a fold with three internal repeats, each being an antiparallel beta
sheet with (+1, +1, -3) connectivity. The three sheets are arranged like the faces of
a triangular prism, with internal pseudo-threefold symmetry (Shimizu and Morikawa, 1996). There are two types of prism: the orthogonal prism,
in which the strands are perpendicular to the prism axis; and the aligned prism,
in which the strands are parallel to the prism axis.text/html2008-09-17T11:05:19+00:00Anonymous (anonymous@undisclosed.example.com)beta_propellor
http://wiki.cathdb.info/doku.php?id=glossary:beta_propellor&rev=1221649519&do=diff
Beta Propellor
This fold comprises 4, 6, 7 or 8 antiparallel beta sheets with a radial arrangement in space, giving the overall structure the appearance of a propellor. The beta sheets
pack face to face, and form a closed structure, in which each beta sheet packs against
two neighbours. The sheets have a mean twist and orientation that depends on the
number of beta sheets that form the propellor. The beta sheets have the same topology,
i.e. the propellor blades are structurally similar units (f…text/html2008-09-17T11:06:31+00:00Anonymous (anonymous@undisclosed.example.com)beta_sandwich
http://wiki.cathdb.info/doku.php?id=glossary:beta_sandwich&rev=1221649591&do=diff
Beta Sandwich
This protein architecture comprises two beta sheets that pack together, face-to-face, in a layered arrangement.
The connections between the strands in the sheet differ between beta sandwiches with different
topologies.
The example given here is beta-2-microglobulin (CATH domain ID 2hlaB00).text/html2015-09-15T14:53:41+00:00Anonymous (anonymous@undisclosed.example.com)beta_sheet
http://wiki.cathdb.info/doku.php?id=glossary:beta_sheet&rev=1442328821&do=diff
Beta Sheet
The beta sheet is a major secondary structural element in globular proteins. These structures are formed from beta strands and are in an almost fully extended conformation with psi,phi bond angle pairs in the wide allowed region in the upper left-hand
corner of thetext/html2008-08-06T11:17:56+00:00Anonymous (anonymous@undisclosed.example.com)beta_strand
http://wiki.cathdb.info/doku.php?id=glossary:beta_strand&rev=1218021476&do=diff
Beta Strand
A beta strand describes a single length of polypeptide chain that forms part of a
beta sheet.text/html2008-09-17T11:39:41+00:00Anonymous (anonymous@undisclosed.example.com)beta_trefoil
http://wiki.cathdb.info/doku.php?id=glossary:beta_trefoil&rev=1221651581&do=diff
Beta Trefoil
This architecture is formed from a capped beta barrel with an internal pseudo threefold symmetry.
The examples shown below are the agglutinin domain (CATH domain ID 1jlxA01), and acidic fibroblast growth factor (FGF-1) (CATH domain ID 1afcA00).text/html2008-09-17T11:41:25+00:00Anonymous (anonymous@undisclosed.example.com)beta_turn
http://wiki.cathdb.info/doku.php?id=glossary:beta_turn&rev=1221651685&do=diff
Beta Turn
A beta turn occurs where the polypeptide chain makes a sharp reversal by 180 degrees
within 4 residues. A turn is defined by 4 consecutive residues (i to i+3) if the C-alpha(i)
to C-alpha(i+3) distance is less than 7 angstroms, and if the central two residues are
not helical. There is often atext/html2008-08-11T09:34:50+00:00Anonymous (anonymous@undisclosed.example.com)class
http://wiki.cathdb.info/doku.php?id=glossary:class&rev=1218447290&do=diff
Class
This is the highest level of classification and is derived from the gross secondary structure
content. There are 4 classes defined in the CATH classification.
* Mainly Alpha
* Mainly Beta
* Alpha Beta
* Few Secondary Structures.text/html2008-09-16T08:06:12+00:00Anonymous (anonymous@undisclosed.example.com)combs
http://wiki.cathdb.info/doku.php?id=glossary:combs&rev=1221552372&do=diff
COMBS file
When dealing with the amino acid sequence for a given CATH domain (or PDB chain), it is important to differentiate between the amino acid sequence as defined by the ATOM records and the sequence as defined by the SEQRES records in the PDB file (they are not necessarily the same). We resolve this issue by using an internal NW algorithm to align the SEQRES and ATOM sequences to provide the 'full' amino acid sequence (called COMBS).text/html2008-09-19T10:31:18+00:00Anonymous (anonymous@undisclosed.example.com)crossover
http://wiki.cathdb.info/doku.php?id=glossary:crossover&rev=1221820278&do=diff
Crossover
This is a term used to describe one possible type of backbone connection observed between
beta strands in which the chain loops around to re-enter the sheet on the opposite end. For beta sheet connectivity, cross over connections are denoted by nx,
where n denotes how many strands it moves over in the sheet and in which direction.
+1x denotes a crossover connection between nearest neighbours, +2x
denotes a crossover connection that misses one intervening strand in the sheet, and so o…text/html2008-09-19T10:33:58+00:00Anonymous (anonymous@undisclosed.example.com)domain
http://wiki.cathdb.info/doku.php?id=glossary:domain&rev=1221820438&do=diff
Domain
Domains are regions of contiguous polypeptide chain that have been described as
compact, local, and semi-independent units. Within a protein, domains can be anything
from independant globular units joined only by a flexible length of polypeptide
chain, to units which have a very extensive interface. There are a number of algorithms that have been developed to detect domains automatically, some of which have been incorporated into the CATH update protocol. Many domains, however, still hav…text/html2008-08-13T10:03:49+00:00Anonymous (anonymous@undisclosed.example.com)dssp
http://wiki.cathdb.info/doku.php?id=glossary:dssp&rev=1218621829&do=diff
DSSP
The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. The abbreviation DSSP stands for Define Secondary Structure of Proteins.
DSSP recognizes eight types of secondary structure (each identified by its own symbol), depending on the pattern of hydrogen bonds. The 310 helix, alpha helix and pi helix are symbolized as G, H and I, respectively and the algorithm can also recognise bet…text/html2008-08-13T12:13:46+00:00Anonymous (anonymous@undisclosed.example.com)dsspwide
http://wiki.cathdb.info/doku.php?id=glossary:dsspwide&rev=1218629626&do=diff
DSSP
The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic-resolution coordinates of the protein. The abbreviation DSSP stands for Define Secondary Structure of Proteins.
DSSP recognizes eight types of secondary structure (each identified by its own symbol), depending on the pattern of hydrogen bonds. The 310 helix, alpha helix and pi helix are symbolized as G, H and I, respectively and the algorithm can also recognise bet…text/html2008-09-17T07:51:28+00:00Anonymous (anonymous@undisclosed.example.com)ef_hand
http://wiki.cathdb.info/doku.php?id=glossary:ef_hand&rev=1221637888&do=diff
EF Hand
This is a helix-loop-helix, calcium-binding motif, in which two helices pack
together at an angle of approximately 90 degrees, separated by a loop region, where
calcium binds. The 'EF' notation for the motif resulted from the structure of parvalbumin, in which the 'E' and 'F' helices were originally identified to form this calcium-binding motif.
The example shown is a human psoriasin (PDB code 1psr).text/html2008-09-17T07:52:54+00:00Anonymous (anonymous@undisclosed.example.com)four_helix_bundle
http://wiki.cathdb.info/doku.php?id=glossary:four_helix_bundle&rev=1221637974&do=diff
Four Helix Bundle
Four helix bundles are a common structural motif or architecture
that has been extensively documented. They can be observed both independently and as components of larger folding units. The motif comprises four helices
packed together in a variety of different ways, forming a hydrophobic core. In the most common
bundles, the helices that are adjacent in the amino acid sequence are also adjacent in the
three dimensional structure, forming the so-called up-down-up-down four he…text/html2008-08-13T14:31:00+00:00Anonymous (anonymous@undisclosed.example.com)gcf
http://wiki.cathdb.info/doku.php?id=glossary:gcf&rev=1218637860&do=diff
GenBank Correspondence file
Result of performing a sequence alignment between the PDB's SEQRES records and ATOM records on a per chain basis and this is used as the basis of a lot of calculations in CATH including generating sequence files.text/html2008-08-13T13:58:12+00:00Anonymous (anonymous@undisclosed.example.com)grath
http://wiki.cathdb.info/doku.php?id=glossary:grath&rev=1218635892&do=diff
GRATH files
Grath is a graph-based structure comparison algorithm. It rapidly, and accurately, matches a novel structure against a library of domain structures already classified in CATH to find the most similar ones. GRATH uses a measure of similarity that details the geometric information, number of secondary structures and number of residues within secondary structures, that any two protein structures share.text/html2008-09-18T13:50:23+00:00Anonymous (anonymous@undisclosed.example.com)greek_key
http://wiki.cathdb.info/doku.php?id=glossary:greek_key&rev=1221745823&do=diff
Greek Key
This is a four-stranded beta sheet motif which is characterised by +3, -1, -1
connectivities in a two-dimensional schematic diagram of a protein structure, as shown here. The diagram on the left shows an N-type Greek key motif, whilst on the right is a C-type Greek key.text/html2008-08-11T10:57:27+00:00Anonymous (anonymous@undisclosed.example.com)hairpin
http://wiki.cathdb.info/doku.php?id=glossary:hairpin&rev=1218452247&do=diff
Hairpin
This is a term used to describe a motif of two sequential secondary structures joined
by a loop which folds back on itself to form a 'hairpin' structure. e.g.
beta hairpin, alpha hairpin.text/html2008-08-06T11:17:56+00:00Anonymous (anonymous@undisclosed.example.com)helix
http://wiki.cathdb.info/doku.php?id=glossary:helix&rev=1218021476&do=diff
Helix
A helix is formed by a polypeptide chain with repeating phi and psi angles.
Its geometry is defined by the number of residues per turn, and the rise per residue.
In principle the polypeptide chain can form right and left handed helices with
a range of pitches.text/html2008-09-19T10:36:47+00:00Anonymous (anonymous@undisclosed.example.com)homologous_superfamily
http://wiki.cathdb.info/doku.php?id=glossary:homologous_superfamily&rev=1221820607&do=diff
Homologous Superfamily
This level of the CATH hierarchy groups together protein domains which are thought to share a common ancestor and can therefore be described as homologous. Similarities are identified either by high sequence identity or structure comparison usingtext/html2008-09-19T10:38:10+00:00Anonymous (anonymous@undisclosed.example.com)hydrogen_bond
http://wiki.cathdb.info/doku.php?id=glossary:hydrogen_bond&rev=1221820690&do=diff
Hydrogen Bond
A hydrogen bond is a polar interaction between two electronegative atoms, a donor and an
acceptor. In proteins hydrogen bonds involving the main chain oxygen and amide are critical
in forming the secondary structures. The polar side chains also form hydrogen bonds.
Energetically it is important to satisfy all hydrogen bond donors and acceptors.
In proteins more than 90% of side chain atoms are 'satisfied' by forming
hydrogen bonds to protein atoms or solvent.text/html2008-09-19T12:46:09+00:00Anonymous (anonymous@undisclosed.example.com)ig_domain
http://wiki.cathdb.info/doku.php?id=glossary:ig_domain&rev=1221828369&do=diff
Immunoglobulin domain
The immunoglobulin (Ig) domain is found in a wide variety of proteins, in particular those involved in the immune response. This includes immunoglobulin molecules themselves (antibodies), T cell and B cell receptors, major histocompatibility (MHC) proteins (including beta-2-microglobulin), Fc receptors, as well as the CD4 and CD8 co-receptors.text/html2015-08-17T21:17:26+00:00Anonymous (anonymous@undisclosed.example.com)index
http://wiki.cathdb.info/doku.php?id=glossary:index&rev=1439846246&do=diff
Glossary
Here is a list of terms and definitions for CATH and structural biology in general.
Click on the item of interest to get further information.
Alpha Helix
Beta Sheet
Mixed Structure
Structural Terms
Classification Terms
Other Miscellaneous Termstext/html2008-09-19T08:05:24+00:00Anonymous (anonymous@undisclosed.example.com)jelly_roll
http://wiki.cathdb.info/doku.php?id=glossary:jelly_roll&rev=1221811524&do=diff
Jelly Roll
This is a fold topology that classically consists of four
Greek key motifs that adopt an eight-stranded beta sandwich structure. In this fold the hydrogen bonding
pattern between adjacent strands is broken in two places, and as a consequence the
structure comprises two four-stranded beta sheets. Both sheets are purely antiparallel,
with strands adjacent in sequence appearing in different sheets with the exception of the
fourth and fifth strands, which are in the same sheet. This…text/html2008-09-19T10:39:46+00:00Anonymous (anonymous@undisclosed.example.com)loop
http://wiki.cathdb.info/doku.php?id=glossary:loop&rev=1221820786&do=diff
Loop
A protein loop is any stretch of non-regular polypeptide chain connecting
secondary structures.
Short loops commonly have little structure and are often found joining two adjacent beta strands . They are often referred to as reverse turns.
Long loops are often flexible and are able to adopt a number of different conformations, effectively making them invisible in x-ray crystal structures. These loops are likely to be involved in protein function and can switch from a 'open' conformatio…text/html2008-08-11T11:01:44+00:00Anonymous (anonymous@undisclosed.example.com)mixed_beta_sheet
http://wiki.cathdb.info/doku.php?id=glossary:mixed_beta_sheet&rev=1218452504&do=diff
Mixed Beta Sheet
A beta sheet which has both parallel and antiparallel strands.
Referencestext/html2008-08-11T11:02:19+00:00Anonymous (anonymous@undisclosed.example.com)motif
http://wiki.cathdb.info/doku.php?id=glossary:motif&rev=1218452539&do=diff
Motif
A commonly occuring substructure, usually comprising two to three secondary structures.text/html2008-09-19T10:40:58+00:00Anonymous (anonymous@undisclosed.example.com)omega_loop
http://wiki.cathdb.info/doku.php?id=glossary:omega_loop&rev=1221820858&do=diff
Omega Loop
An omega loop has been defined as a continous segment of polypeptide
chain that adopts a 'loop-shaped' conformation in three-dimensional space,
with a small distance between its segment termini. The main
chain of an idealized loop has the appearance of a Greek letter omega (hence the term
'omega loop').text/html2008-08-11T11:21:18+00:00Anonymous (anonymous@undisclosed.example.com)parallel_beta_sheets
http://wiki.cathdb.info/doku.php?id=glossary:parallel_beta_sheets&rev=1218453678&do=diff
Parallel Beta Sheets
This is a beta-pleated sheet in which successive beta strands all
lie parallel in three dimensions. Such sheets have evenly spaced
hydrogen bond pairs that lie at an angle to the beta strands.
Referencestext/html2008-08-13T10:15:01+00:00Anonymous (anonymous@undisclosed.example.com)pdb
http://wiki.cathdb.info/doku.php?id=glossary:pdb&rev=1218622501&do=diff
The Protein Data Bank
The Protein Data Bank (PDB) at Brookhaven National Laboratory, is a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules. These data are released into the public domain and can be accessed for free. PDB files include the coordinates of every atom identified when the structure was solved.text/html2008-09-19T10:44:55+00:00Anonymous (anonymous@undisclosed.example.com)ramachandran_plot
http://wiki.cathdb.info/doku.php?id=glossary:ramachandran_plot&rev=1221821095&do=diff
Ramachandran Plot
This is a diagram of the sterically allowed regions for a dipeptide unit in phi,psi
space. The conformation of the dipepetide is defined by 2 dihedral angles:
phi (the angle of rotation around the N-C-alpha bond in a peptide unit),
and psi (the angle of rotation around the
C-alpha-C' bond in a peptide unit). The plot indicates whether a given phi,psi
conformation is sterically allowed. A conformation is not allowed if atoms
approach closer than the sum of their van der Waals r…text/html2008-09-19T09:36:46+00:00Anonymous (anonymous@undisclosed.example.com)rossmann_fold
http://wiki.cathdb.info/doku.php?id=glossary:rossmann_fold&rev=1221817006&do=diff
Rossmann Fold
This fold is made up of three or more parallel beta strands linked by two alpha helices in the topological order beta-alpha-beta-alpha-beta. Two Rossmann folds, wound in opposite
directions create a dinucleotide binding unit found in many enzymes, specifically
in nucleotide binding proteins (hence its alternative name mononucleotide-bindingtext/html2008-08-13T13:57:05+00:00Anonymous (anonymous@undisclosed.example.com)sec
http://wiki.cathdb.info/doku.php?id=glossary:sec&rev=1218635825&do=diff
Sec files
This is a data file created by the inhouse algorithm secmake. This gives information on all the secondary structure elements present within a particular protein structure.
The number of secondary structures (as calculated by WOLF in the protein of interest is given, and then a list that, for each secondary structure, gives the following information:text/html2008-08-13T14:23:38+00:00Anonymous (anonymous@undisclosed.example.com)seqres
http://wiki.cathdb.info/doku.php?id=glossary:seqres&rev=1218637418&do=diff
SEQRES file
SEQRES records can be found as part of a protein structures PDB file and contains the amino acid or nucleic acid sequence of residues in each chain of the protein of interest.text/html2013-03-12T14:07:58+00:00Anonymous (anonymous@undisclosed.example.com)sift
http://wiki.cathdb.info/doku.php?id=glossary:sift&rev=1363097278&do=diff
SIFT Criteria
Structures in the PDB repository are of varying quality. In order to maintain accuracy when classifying and clustering protein domains, it is important only to include high quality structures. For this reason we have defined a strict set of criteria, called SIFT, to state whether or not a PDB chain can be accepted into CATH.text/html2008-09-19T10:27:03+00:00Anonymous (anonymous@undisclosed.example.com)split_beta_alpha_beta_motif
http://wiki.cathdb.info/doku.php?id=glossary:split_beta_alpha_beta_motif&rev=1221820023&do=diff
Split beta-alpha-beta motif
This motif is a beta-alpha-beta motif
in which the strands lie parallel in the same sheet, but are non-adjacent
and not hydrogen bonded together. The number of intervening strands is
usually small. These motifs are common in alpha-beta proteins with an
antiparallel sheet.text/html2008-09-19T10:54:13+00:00Anonymous (anonymous@undisclosed.example.com)ssap
http://wiki.cathdb.info/doku.php?id=glossary:ssap&rev=1221821653&do=diff
SSAP
Full name: Secondary Structure Alignment Program.
This secondary structure alignment program uses dynamic programming to align proteins by matching vectors between residues. For each residue in a protein, a local
structural environment is defined by a set of inter-atomic vectors. The method
matches residues by comparing these structural environments. An important aspect
of these environments is that because they are defined independently for each
residue, they are rotationally invariant, …text/html2008-09-19T10:41:39+00:00Anonymous (anonymous@undisclosed.example.com)superfold
http://wiki.cathdb.info/doku.php?id=glossary:superfold&rev=1221820899&do=diff
Superfold
A superfold is defined as a protein fold which has been observed in three or more
non-homologous proteins. There are nine superfolds which have been identified so far, including the beta trefoil and the jelly roll .
Referencestext/html2008-11-19T15:54:00+00:00Anonymous (anonymous@undisclosed.example.com)topology
http://wiki.cathdb.info/doku.php?id=glossary:topology&rev=1227110040&do=diff
Topology (Fold Group)
This level of the CATH hierarchy describes structures that are grouped according to whether they share the same topology or fold in the core of the domain, that is, if they share the same overall shape and connectivity of the secondary structures in the domain core. Domains in the same fold group may have different structural decorations to the common core.text/html2008-08-13T12:57:50+00:00Anonymous (anonymous@undisclosed.example.com)wolf
http://wiki.cathdb.info/doku.php?id=glossary:wolf&rev=1218632270&do=diff
WOLF file
This is a data file created by WOLF, a modified version of the DSSP algorithm, which, unlike DSSP, includes the positioning of C-beta atoms in its output.
CATH-Gene3D is a Global Biodata Core Resource Learn more...
CATH-Gene3D is a Global Biodata Core Resource Learn more...