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Biological database of proteins
The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their
Structural Classification of Proteins database
Structural_Classification_of_Proteins_database
Three-dimensional arrangement of atoms in an amino acid-chain molecule
Structural Classification of Proteins database. A related concept is protein topology. Proteins are not static objects, but rather populate ensembles of conformational
Protein_structure
schemes are: CATH database Structural Classification of Proteins database (SCOP) Both classification schemes are based on a hierarchy of fold types. At the
List_of_proteins
Categories of protein tertiary structure
classification databases (SCOP and CATH). All-α proteins are a class of structural domains in which the secondary structure is composed entirely of α-helices
Protein_fold_class
Self-stable region of a protein's chain that folds independently from the rest
motif Structural biology Structural Classification of Proteins (SCOP) CATH Protein Structure Classification database Sequence motif Structural motif George
Protein_domain
until 2010 was the Structural Classification of Proteins database (or SCOP). Over the years SCOP has supported the development of computational tools
Centre for Protein Engineering
Centre_for_Protein_Engineering
Grouping of proteins
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry
Protein_superfamily
SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences
Superfamily_database
wider family. For example, in the Structural Classification of Proteins database classification system, members of a subfamily share the same interaction
Protein_subfamily
Group of evolutionarily-related proteins
level of classification are protein superfamilies, which group distantly related proteins, often based on their structural similarity. Next are protein families
Protein_family
Families of Structurally Similar Proteins or FSSP is a database of structurally superimposed proteins generated using the "Distance-matrix ALIgnment" (DALI)
Families of Structurally Similar Proteins database
Families_of_Structurally_Similar_Proteins_database
Method of protein structure prediction
past three years have similar structural folds to ones already in the PDB. The Structural Classification of Proteins database (SCOP) provides a detailed
Threading_(protein_sequence)
Database of protein domains structures
The CATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships
CATH_database
Biomolecule consisting of chains of amino acid residues
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions
Protein
Bioinformatics subfield
Data Bank Structural Classification of Proteins database STING Molecular modelling List of software for molecular mechanics modeling Protein structure
Structural_bioinformatics
could be as many as 500,000 unique human proteins The Pfam (proteins families) database link The Worldwide Protein Data Bank (wwPDB) link and the related
List_of_biological_databases
Artificial intelligence program by DeepMind
Evolutionary Classification of Protein Domains database (ECOD) assigns ECOD classifications to all SwissProt proteins in AFDB. isoform.io is a database of AlphaFold2-generated
AlphaFold
Type of common three-dimensional structure in chain-like biological molecules
of protein families and domains SCOP Structural classification of Proteins CATH Class Architecture Topology Homology FSSP FSSP PASS2 PASS2 - Protein Alignments
Structural_motif
Protein structural motif
with extracting structural thermodynamics since there are always numerous other structural features present in whole proteins. Also proteins are inherently
Beta_sheet
Evolutionary Classification of Protein Domains (ECOD) is a biological database that classifies protein domains available from the Protein Data Bank. The
Evolutionary Classification of Protein Domains
Evolutionary_Classification_of_Protein_Domains
Type of biological prediction
kinds of structural features found in proteins. Descriptions of such terms may be found at the CATH Web site, the Structural Classification of Proteins (SCOP)
Protein_structure_prediction
Technique used for determining crystal structures and identifying mineral compounds
encyclopedia of proteins and other molecules RNABase HIC-Up database of PDB ligands Archived 2020-08-08 at the Wayback Machine Structural Classification of Proteins
X-ray_crystallography
Classification of membrane proteins including ion channels
system for membrane transport proteins, including ion channels. The upper level of classification and a few examples of proteins with known 3D structure: 1
Transporter Classification Database
Transporter_Classification_Database
Type of membrane protein that is permanently attached to the biological membrane
IMPs are transmembrane proteins. IMPs comprise a significant fraction of the proteins encoded in an organism's genome. Proteins that cross the membrane
Integral_membrane_protein
American biologist and academic
(1995). "SCOP: A structural classification of proteins database for the investigation of sequences and structures" (PDF). Journal of Molecular Biology
Steven_E._Brenner
Aligning molecular sequences using sequence and structural information
construct a database known as FSSP (Fold classification based on Structure-Structure alignment of Proteins, or Families of Structurally Similar Proteins) in which
Structural_alignment
Type of secondary structure of proteins
classifying proteins by their dominant fold, the Structural Classification of Proteins database maintains a large category specifically for all-α proteins. Hemoglobin
Alpha_helix
Protein without a fixed 3D structure
multi-domain proteins. They are sometimes considered as a separate class of proteins along with globular, fibrous and membrane proteins. IDPs are a very
Intrinsically disordered proteins
Intrinsically_disordered_proteins
Three-dimensional shape of a protein
coil structure. Hence, proteins may be classified by the structures they hold. Databases of proteins which use such a classification include SCOP and CATH
Protein_tertiary_structure
Study of the structure of every protein in a genome
repository for protein sequence and structural information UniProt: provides sequence and functional information Structural Classification of Proteins (SCOP Classifications):
Structural_genomics
Proteins that are part of, or interact with, biological membranes
Membrane proteins are common proteins that are part of, or interact with, biological membranes. Membrane proteins fall into several broad categories depending
Membrane_protein
including other tools. SCOP the Structural Classification of Proteins [2] a detailed and comprehensive description of the structural and evolutionary relationships
Protein_structure_database
Protein family
Activities) proteins (more commonly referred to as "triple-A ATPases") are a large group of protein family sharing a common conserved module of approximately
AAA_proteins
English biochemist (1942–2019)
and Tim Hubbard to create the Structural Classification of Proteins database (SCOP), a periodic table for all known protein structures. With Julian Gough
Cyrus_Chothia
Online molecular biology database
an online database for peptidases (also known as proteases, proteinases and proteolytic enzymes) and their inhibitors. The classification scheme for
MEROPS
Database of protein families, domains and functional sites
InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied
InterPro
Protein emerging once on each face of a lipid bilayer
several model organisms. Bitopic proteins in OPM database "Single-pass membrane protein". UniProt. Membrane Structural Biology: With Biochemical and Biophysical
Single-pass_membrane_protein
This list of protein subcellular localisation prediction tools includes software, databases, and web services that are used for protein subcellular localization
List of protein subcellular localization prediction tools
List_of_protein_subcellular_localization_prediction_tools
Enzyme database
CAZy is a database of Carbohydrate-Active enZYmes (CAZymes). The database contains a classification and associated information about enzymes involved
CAZy
Non-soluble proteins with elongated or sheet-like structures
fibrous proteins or scleroproteins are one of the three main classifications of protein structure (alongside globular and membrane proteins). Fibrous
Fibrous_protein
database via the Protein Data Bank, which often provides a hyperlink to the molmovdb entry for proteins found in both databases. The database includes a web-based
Database_of_Molecular_Motions
Type of beta barrel protein domain structure
30% of the all-beta proteins annotated in the Structural Classification of Proteins (SCOP) database. The basic jelly roll structure consists of eight
Jelly_roll_fold
of the APC superfamily and consists of proteins from bacteria and archaea. These proteins are of various sizes and topologies. For example, CstA of E
Peptide transporter carbon starvation family
Peptide_transporter_carbon_starvation_family
Biological database
The database of three-dimensional interacting domains (3did) is a biological database containing a catalogue of protein-protein interactions for which
3did
Number and arrangement of multiple folded protein subunits in a multi-subunit complex
numbers of subunits. In contrast to the first three levels of protein structure, not all proteins will have a quaternary structure since some proteins function
Protein_quaternary_structure
Physical interactions and constructions between multiple proteins
Furthermore, members of the skeletal muscle lipid droplet-associated proteins family associate with other proteins, as activator of adipose triglyceride
Protein–protein_interaction
Online biodatabase of proteins
Membranome database provides structural and functional information about more than 6000 single-pass (bitopic) transmembrane proteins from Homo sapiens
Membranome_database
of structurally-characterized Prx group members) to search sequence databases. Searches of PREX for Prxs of interest can be conducted using protein annotation
Peroxiredoxin classification index
Peroxiredoxin_classification_index
Biological database
Retrieval of Interacting Genes/Proteins, previously Search Tool for Recurring Instances of Neighbouring Genes) is a biological database and web resource of known
STRING
globular proteins by their concave surfaces; and zinc-finger proteins, which regulate the expression of genes by binding DNA. Tandem repeat proteins frequently
Protein_tandem_repeats
Biological database
full-length proteins. The database consists of position-specific score matrices and serves as resource for protein annotation such as identification of conserved
Conserved_Domain_Database
(April 1995). "SCOP: a structural classification of proteins database for the investigation of sequences and structures". Journal of Molecular Biology. 247
Myelin oligodendrocyte glycoprotein
Myelin_oligodendrocyte_glycoprotein
Specific genus of RNA viruses
serotypes. As with influenza viruses, a dual classification system is used based on two proteins on the surface of the virus. The glycoprotein VP7 defines
Rotavirus
Use of bioinformatic methods to correlate proteins with biofunctions
more well conserved than protein sequence, structural similarity is a good indicator of similar function in two or more proteins. Many programs have been
Protein_function_prediction
Glycoprotein spike on a viral capsid or viral envelope
called spike protein, formerly known as E2) is the largest of the four major structural proteins found in coronaviruses. The spike protein assembles into
Coronavirus_spike_protein
Protein family
A.72) is a member of the APC superfamily of secondary carriers. Proteins of the KUP/HAK/KT family include the KUP (TrkD) protein of E. coli and homologues
Potassium_uptake_permease
Professor of Bioinformatics at King's College London
(1995). "SCOP: A structural classification of proteins database for the investigation of sequences and structures" (PDF). Journal of Molecular Biology
Tim_Hubbard
Predicted proteins
hypothetical proteins, make up an estimated 20% to 40% of proteins encoded in each newly sequenced genome. The real evidences for the hypothetical protein functioning
Hypothetical_protein
Database of protein structures
Orientations of Proteins in Membranes (OPM) database provides spatial positions of membrane protein structures with respect to the lipid bilayer. Positions of the
Orientations of Proteins in Membranes database
Orientations_of_Proteins_in_Membranes_database
Class of enzymes
smaller range of structures. In fact, according to the Structural Classification of Proteins database, only three different folds have been observed for
Glycosyltransferase
Database and web server for analyzing knots in protein structures
the analysis page. The server can also search the AlphaKnot database for proteins structurally or sequentially similar to the analysed model and display
AlphaKnot
Bioinformatics database
information in the Structural Classification of Proteins (SCOP) database, the metabolic pathways database of the Kyoto Encyclopedia of Genes and Genomes
MANET_database
Small structural protein motif found mostly in transcriptional proteins
protein followed soon thereafter by the Krüppel factor in Drosophila. It often appears as a metal-binding domain in multi-domain proteins. Proteins that
Zinc_finger
database that contains beta barrel (β-barrel) outer membrane proteins from Gram-negative bacteria. Such proteins are responsible for a broad range of
OMPdb
Study of how proteins move and change shape
molecular biology, proteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly
Protein_dynamics
Class of cell surface receptors coupled to G-protein-associated intracellular signaling
receptors, serpentine receptors, and G protein-linked receptors (GPLR), form a large group of evolutionarily related proteins that are cell surface receptors
G_protein-coupled_receptor
Tertiary structure prediction tool for protein sequence
derived from either Structural Classification of Proteins database (SCOP) or the Protein Data Bank (PDB) depending on the source of the detected template
Phyre
from the N-terminus of the coat protein. Autotransporter proteins are outer membrane or secreted proteins found in a broad variety of Gram-negative bacteria
Asparagine_peptide_lyase
terminology; the Structural Classification of Proteins (SCOP) database describes these proteins using the term "alpha alpha superhelix". The CATH database uses the
Alpha_solenoid
Protein structure
molecules in the barrel calyx. Examples of the family include retinol binding proteins (RBPs) and major urinary proteins (Mups). RBP binds and transports retinol
Beta_barrel
Class of proteins
Membrane fusion proteins (not to be confused with chimeric or fusion proteins) are proteins that cause fusion of biological membranes. Membrane fusion
Membrane_fusion_protein
Species of virus
weight, the other 78% being structural proteins. Structurally, the virus is constructed from 7 different structural proteins. The capsid has icosahedral
Wound_tumor_virus
Protein that regulates the rate of DNA transcription
Rooman M (September 1996). "Structural classification of HTH DNA-binding domains and protein-DNA interaction modes". Journal of Molecular Biology. 262 (2):
Transcription_factor
Family of DNA sequences found in prokaryotic organisms
the proteins Cas6e and Cas6f respectively, recognise stem-loops created by the pairing of identical repeats that flank the crRNA. These Cas proteins cleave
CRISPR
Complex lasso proteins (also called pierced lasso bundles or tadpoles) are proteins in which a covalent loop (portion of the backbone closed with a covalent
Complex_lasso_proteins
Visual representation of allowable protein conformations
seen with proline; it has been used in the classification of motifs and more recently for designing proteins. While the Ramachandran plot has been a textbook
Ramachandran_plot
Metabolic disease involving abnormal deposited amyloid proteins
forms, 14 are grouped as systemic forms, and three proteins can identify as either. These proteins can become irregular due to genetic effects, as well
Amyloidosis
disordered regions in proteins that undergo a disorder-to-order transition upon binding to their partners. MoRFs are implicated in protein-protein interactions
Molecular_recognition_feature
Self-stabilizing region of a protein that binds to specific DNA sequences
[citation needed] Many proteins involved in the regulation of gene expression contain DNA-binding domains. For example, proteins that regulate transcription
DNA-binding_domain
caudovirales and Bacillota can be found in the Transporter Classification Database. One characteristic member of the Hol44 family is oenophage fOg44 (Lys44; TC#
Hol44_family
Protein family
Mitochondrial carriers are also classified in the Transporter Classification Database. The Mitochondrial Carrier (MC) Superfamily has been expanded to
Mitochondrial_carrier
Protein family
interact with cytoskeletal proteins and therefore play a cell structural role. Some of the currently characterized members of the AE family can be found
Anion_exchanger_family
Class of enzymes which break glycosidic bonds via hydrolysis
different families. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The database provides a series of regularly updated
Glycoside_hydrolase
Type of protein
RNA-binding proteins (often abbreviated as RBPs) are proteins that bind to the double or single stranded RNA in cells and participate in forming ribonucleoprotein
RNA-binding_protein
Cytoskeletal structure
Branchiostoma. Intermediate filaments are composed of a family of related proteins sharing common structural and sequence features. Initially designated 'intermediate'
Intermediate_filament
Protein family
these proteins is available in the Transporter Classification Database. Homologues are found in a variety of Gram-positive and Gram-negative bacteria. Clostridioides
Clostridial_Cytotoxin_family
biological membrane occupied by the protein. Several databases provide experimentally determined topologies of membrane proteins. They include Uniprot, TOPDB
Membrane_topology
Protein domain
protein kinase domain is a structurally conserved protein domain containing the catalytic function of protein kinases. Protein kinases are a group of
Protein_kinase_domain
Database of histone sequences
searching method to a group of proteins containing the histone fold motif in the early-mid-1990. The first version of the Histone Database was released in 1995
Histone_Database
Species of virus
functions of the virus are the L-P protein complex. These two proteins are required for the production of all of the proteins utilized by the rabies virus and
Rabies_virus
Family of transport proteins
resistance-associated macrophage proteins (Nramps), also known as metal ion (Mn2+-iron) transporters (TC# 2.A.55), are a family of metal transport proteins found throughout
Natural resistance-associated macrophage protein
Natural_resistance-associated_macrophage_protein
Protein-coding gene in humans
encodes the protein phakinin ("beaded filament structural protein 2") in humans. More than 99% of the vertebrate ocular lens consists of terminally differentiated
BFSP2
Database of biological information
problem, as many databases must store the same information, e.g. protein structure databases also contain the sequence of the proteins they cover, their
Biological_database
Arrangement of amino acid sequence
relationship between proteins whereby the proteins have a changed order of amino acids in their peptide sequence. The result is a protein structure with different
Circular permutation in proteins
Circular_permutation_in_proteins
Infectious agent that replicates in cells
consisting of (i) genetic material, i.e., long molecules of DNA or RNA that encode the structure of the proteins by which the virus acts; (ii) a protein coat
Virus
Method of analyzing transmission electron microscopy imagery
from TEM images of particulate samples, typically proteins or other large biological entities such as viruses. Individual images of stained or unstained
Single_particle_analysis
Polish-American structural biologist (born 1946)
biophysicist, a specialist in structural biology and protein crystallography. He is a Harrison Distinguished Professor of Molecular Physiology and Biological
Wladek_Minor
Organisation of viruses into a taxonomic system
defined by the presence of a protein of a certain structural family. Baltimore classification (first defined in 1971) is a classification system that places
Virus_classification
Protein helix–loop–helix motif
The EF hand is a helix–loop–helix structural domain or motif found in a large family of calcium-binding proteins. The EF-hand motif contains a helix–loop–helix
EF_hand
Database of protein families
of its wide coverage of proteins and sensible naming conventions. It is used by experimental biologists researching specific proteins, by structural biologists
Pfam
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