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SCOP| Structural Classification of Proteins
| Structural Classification of ProteinsYou need to enable JavaScript to run this a【启航注暖】COP、EER、IPLV、NPLV、SCOP等 - 知乎
【启航注暖】COP、EER、IPLV、NPLV、SCOP等 - 知乎首发于【大锤注考】复习教材中知识点详解切换模式写文章登录/注册【启航注暖】COP、EER、IPLV、NPLV、SCOP等大锤助考注册公用设备工程师（暖通空调）性能系数COP(制冷)在规定工况下整台制冷机以同一单位表示的单位时间从低温物体中移去的热量与输入的能量之比。性能系数COP（制热）在规定工况下整台制冷机以同一单位表示的单位时间向高温物体中加入的热量与输入的能量之比。能效比EER 在规定工况下制冷量与总的输入功率之比。通常用来衡量半封闭、全封闭制冷压缩机和空调机的性能。部分负荷系数PLV用一个单一数值表示的空气调节用冷水机组的部分负荷效率指标，基于机组部分负荷的性能系数值，按机组在各种负荷下运行时间的加权因素计算而得。综合部分负荷性能系数IPLV基于机组部分负荷时的性能系数值,按机组在各种负荷条件下的累积负荷百分比进行加权计算获得的表示空气调节用冷水机组部分负荷效率的单一数值。非标准部分负荷性能系数NPLV 用一个单一数值表示的空气调节用冷水机组的部分负荷效率指标，基于规范规定的NPLV工况下机组部分负荷的性能系数值，按机组在特定负荷下运行时间的加权因素，通过公式计算而得。电冷源综合制冷性能系数SCOP设计工况下,电驱动的制冷系统的制冷量与制冷机、冷却水泵及冷却塔净输入能量之比。e全年综合性能系数ACOP水(地）源热泵机组在额定制冷工况和额定制热工况下满负荷运行时的能效，与多个典型城市的办公建筑按制冷、制热时间比例进行加权而来的全年性能系数。ACOP=056EER+0.44COP。EER为水(地）源热泵机组在额定制冷工况下满负荷运行时的能效。COP为水（地)源热泵机组在额定制热工况下满负荷运行时的能效。制冷季节能源消耗效率SEER制冷季节期间，空调器进行制冷运行时从室内除去的热量总和与消耗电量的总和之比。SEER应用于变频空调就标准(GB 21455-2008)。全年能源消耗效率(APF) 空调器在制冷季节和制热季节期间，从室内空气中除去的冷量与送人室内的热量的总和与同期间内消耗电量的总和之比。APF应用于变频空调新标准(GB 21455-2013)。APF考核的是全年的能耗水平，对空调性能的评估更加全面。制热季节能源消耗效率HSPF制热季节期间，空调器进行热泵制热运行时，送入室内的热量总和与消耗电量的总和之比。发布于 2021-04-14 14:53制冷与低温技术注册暖通暖通赞同 151 条评论分享喜欢收藏申请转载文章被以下专栏收录【大锤注考】复习教材中知识点详解对注册暖通《三版教材》中的疑难点进行深
SCOPe: Structural Classification of Proteins — extended. Release 2.08 (updated 2023-01-06, stable release September 2021)
SCOPe: Structural Classification of Proteins — extended. Release 2.08 (updated 2023-01-06, stable release September 2021)
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About
Welcome to SCOPe!
SCOPe (Structural Classification of
Proteins — extended) is a database developed
at the Berkeley Lab and UC Berkeley to extend the development and
maintenance of SCOP.
SCOP was conceived at the MRC Laboratory of Molecular Biology, and developed in collaboration with researchers in Berkeley.
Work on SCOP (version 1) concluded in June
2009 with the release of SCOP 1.75.
SCOPe classifies many newer structures
through a combination of automation and manual curation,
and corrects some errors in SCOP,
aiming to have the same accuracy as the hand-curated
SCOP releases.
SCOPe also
incorporates and updates the Astral database.
About SCOPe
Stats & Prior Releases
News
2023-01-06:
New pdb entries were added in a periodic update;
for more info on these updates, see the
online documentation.
2022-01-07: We published a paper describing the new features in SCOPe 2.08-stable. [PDF].
2021-09-20: SCOPe 2.08-stable has been released, with nearly 20,000 new pdb entries added since the last stable release. Important features include genetic variant search tools and annotations of structural heterogeneity and repeat units. Click either the About or Stats & History links for more details on what's new!
2018-11-30:
We published a paper describing updates to SCOPe, focusing on our findings from classifying large structures. [PDF].
Classes in SCOPe 2.08:
a: All alpha proteins [46456] (290 folds)
b: All beta proteins [48724] (180 folds)
c: Alpha and beta proteins (a/b) [51349] (148 folds)
d: Alpha and beta proteins (a+b) [53931] (396 folds)
e: Multi-domain proteins (alpha and beta) [56572] (74 folds)
f: Membrane and cell surface proteins and peptides [56835] (69 folds)
g: Small proteins [56992] (100 folds)
h: Coiled coil proteins [57942] (7 folds)
i: Low resolution protein structures [58117] (25 folds)
j: Peptides [58231] (151 folds)
k: Designed proteins [58788] (44 folds)
l: Artifacts [310555] (1 fold)
SCOPe: Structural Classification of Proteins — extended. Release 2.08 (updated 2023-01-06, stable release September 2021)
References:
Fox NK, Brenner SE, Chandonia JM. 2014.
Nucleic Acids Research 42:D304-309. doi: 10.1093/nar/gkt1240.
Chandonia JM, Guan L, Lin S, Yu C, Fox NK, Brenner SE. 2022.
Nucleic Acids Research 50:D553–559. doi: 10.1093/nar/gkab1054.
(citing information)
Copyright © 1994-2023 The SCOP
and SCOPe
authors
scope@compbio.berkeley.edu
SCOP2
SCOP2
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Structural Classification of Proteins 2
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November,2019
A new version of SCOP is available from it's original site. It provides the most significant update in coverage since SCOP version 1.75
SCOP version 2...
January,2014
SCOP2 prototype article in NAR is published
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Welcome to SCOP2 prototype
Citation
Antonina Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha, Alexey Murzin,
SCOP2 prototype: a new approach to
protein structure mining (2014) Nucl. Acid Res., 42 (D1): D310-D314. [PDF]
Description
SCOP2 prototype was a beta version of Structural classification of proteins (SCOP) used for the development of the current version of the classification that is available from it's original SCOP site.
Quick introduction on how to browse, search and download
SCOP2 prototype offers two different ways for accessing data:
SCOP2-browser, that allows navigation through the SCOP2 classification in a traditional way by browsing pages displaying the node information, and
SCOP2-graph, which is a graph-based web tool for display and navigation through the SCOP2 prototype classification.
Both tools provide search of SCOP2 prototype data by free text, node names, IDs, tags and keywords, as well as external identifiers associated with them, e.g. PDB and UniProt.
SCOP2 prototype data can also be retrieved via REST
interface or downloaded from the
SCOP2 Download page.
For more information visit the About page.
Web browser compatibility check
To test whether your web browser and its settings are suitable to view
SCOP2-graph and to visualize protein structures using Jmol applet click
here.
Information about the release
This release contains a fraction of protein structure data. We introduced the prototype to our users to seek for a comprehensive feedback.
.
SCOP2 - 2016-12
© 2016 MRC Laboratory of Molecular Biology
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Database Profile
SCOP
General information
URL:
http://scop.mrc-lmb.cam.ac.uk
Full name:
Structural Classification of Proteins
Description:
Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
Year founded:
1995
Last update:
Version:
Accessibility:
Manual:
Accessible
Real time :
Checking...
Country/Region:
United Kingdom
Classification & Tag
Data type:
Protein
Data object:
Animal
Database category:
Structure
Major species:
Homo sapiens
Mus musculus
Zea mays
Keywords:
protein structure
Contact information
University/Institution:
MRC Laboratory of Molecular Biology, Francis Crick Avenue
Address:
MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
City:
Province/State:
Country/Region:
United Kingdom
Contact name (PI/Team):
Alexey G. Murzin
Contact email (PI/Helpdesk):
agm@mrc-lmb.cam.ac.uk
Publications
31724711
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures. [PMID: 31724711]
Andreeva A, Kulesha E, Gough J, Murzin AG.
Abstract
The Structural Classification of Proteins (SCOP) database is a classification of protein domains organised according to their evolutionary and structural relationships. We report a major effort to increase the coverage of structural data, aiming to provide classification of almost all domain superfamilies with representatives in the PDB. We have also improved the database schema, provided a new API and modernised the web interface. This is by far the most significant update in coverage since SCOP 1.75 and builds on the advances in schema from the SCOP 2 prototype. The database is accessible from http://scop.mrc-lmb.cam.ac.uk.
Nucleic Acids Res. 2020:48(D1)
| 125 Citations (from Europe
PMC, 2024-03-02)
11752311
SCOP database in 2002: refinements accommodate structural genomics. [PMID: 11752311]
Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG.
Abstract
The SCOP (Structural Classification of Proteins) database is a comprehensive ordering of all proteins of known structure, according to their evolutionary and structural relationships. Protein domains in SCOP are grouped into species and hierarchically classified into families, superfamilies, folds and classes. Recently, we introduced a new set of features with the aim of standardizing access to the database, and providing a solid basis to manage the increasing number of experimental structures expected from structural genomics projects. These features include: a new set of identifiers, which uniquely identify each entry in the hierarchy; a compact representation of protein domain classification; a new set of parseable files, which fully describe all domains in SCOP and the hierarchy itself. These new features are reflected in the ASTRAL compendium. The SCOP search engine has also been updated, and a set of links to external resources added at the level of domain entries. SCOP can be accessed at http://scop.mrc-lmb.cam.ac.uk/scop.
Nucleic Acids Res. 2002:30(1)
| 256 Citations (from Europe
PMC, 2024-03-02)
7723011
SCOP: a structural classification of proteins database for the investigation of sequences and structures. [PMID: 7723011]
Murzin AG, Brenner SE, Hubbard T, Chothia C.
Abstract
To facilitate understanding of, and access to, the information available for protein structures, we have constructed the Structural Classification of Proteins (scop) database. This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure. It also provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references. Two search facilities are available. The homology search permits users to enter a sequence and obtain a list of any structures to which it has significant levels of sequence similarity. The key word search finds, for a word entered by the user, matches from both the text of the scop database and the headers of Brookhaven Protein Databank structure files. The database is freely accessible on World Wide Web (WWW) with an entry point to URL http: parallel scop.mrc-lmb.cam.ac.uk magnitude of scop.
J Mol Biol. 1995:247(4)
| 3659 Citations (from Europe
PMC, 2024-03-02)
Ranking
All databases:
85/5981
(98.596%)
Structure:
12/839
(98.689%)
85
Total Rank
4,037
Citations
139.207
z-index
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Protein
Structure
protein structure
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Record metadata
Created on: 2020-11-07
Curated by:
Lin Liu [2021-03-23]
Chang Liu [2020-11-23]
Chang Liu [2020-11-07]
SCOP
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SCOP: Structural Classification of Proteins
: Structural Classification of ProteinsStructural Classification of Proteins
Welcome to SCOP: Structural Classification of
Proteins.1.75 release (June 2009)
38221 PDB Entries. 1 Literature Reference.
110800 Domains.
(excluding nucleic acids and theoretical models).
Folds, superfamilies, and families statistics
here.
New folds
superfamilies
families.
List of obsolete entries and their replacements.
Authors. Alexey G. Murzin,
John-Marc Chandonia,
Antonina Andreeva,
Dave Howorth,
Loredana Lo Conte,
Bartlett G. Ailey,
Steven E. Brenner,
Tim J. P. Hubbard, and Cyrus Chothia.
scop@mrc-lmb.cam.ac.uk
Reference:
Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995).
SCOP: a structural classification
of proteins database for the investigation of sequences and
structures. J. Mol. Biol. 247, 536-540. [PDF]
Recent changes are described in: Lo Conte L., Brenner S. E., Hubbard T.J.P., Chothia C., Murzin A. (2002). SCOP database in 2002: refinements accommodate
structural genomics. Nucl. Acid Res. 30(1), 264-267. [PDF],
Andreeva A., Howorth D., Brenner S.E., Hubbard T.J.P., Chothia C.,
Murzin A.G. (2004). SCOP database in 2004: refinements integrate structure
and sequence family data.
Nucl. Acid Res. 32:D226-D229. [PDF], and
Andreeva A., Howorth D., Chandonia J.-M., Brenner S.E., Hubbard T.J.P.,
Chothia C., Murzin A.G. (2007). Data growth and its impact on the
SCOP database: new developments.
Nucl. Acid Res. advance access, doi:10.1093/nar/gkm993.
[PDF].
The new Structural Classification of Proteins database is now available at http://scop.mrc-lmb.cam.ac.uk/
Access methods
Enter SCOP at the
top of the hierarchy
Keyword search of
SCOP entries
SCOP parseable files (MRC site)
All
SCOP releases and reclassified entry history (MRC site)
pre-SCOP - preview of the next release
SCOP domain sequences and pdb-style coordinate
files
(ASTRAL)
Hidden Markov Model library for SCOP superfamilies
(SUPERFAMILY)
Structural alignments for proteins with non-trivial
relationships
(SISYPHUS)
Online resources of potential interest to
SCOP users
SCOP
mirrors
around the world may speed your access.
News
SCOP has been updated to include many
PDB entries released before 23 February 2009.
See folds, superfamilies, and families
statistics.
This release no longer classifies all PDB structures released
before a certain date. The process of classification of new entries
has been changed. For more information please visit
pre-SCOP - a preview of the next
release.
This release is similar in appearance to the previous release, so the
generic release notes from that release still
apply. Please read the notes; they contain more detailed explanations and examples
of SCOP features.
Previous releases' news.
Synopsis
Nearly all proteins have structural similarities with other
proteins and, in some of these cases, share a common evolutionary
origin. The SCOP database,
created by manual inspection and
abetted by a battery of automated methods, aims to provide a detailed
and comprehensive description of the structural and evolutionary
relationships between all proteins whose structure is known. As such,
it provides a broad survey of all known protein folds, detailed
information about the close relatives of any particular protein,
and a framework for future research and classification.
A more detailed
description
of the database is available. Help on using
the database may be obtained on any screen by pressing the question
mark button.
Online resources of
potential interest to scop users
Structural similarity search of SCOP using
SSM
Combinatorial Extension
(CE)
method for structural comparison
PALI pairwise and multiple alignments of SCOP families
SUPFAM structure/sequence relationships
Stuctural similarity search of
SCOP using
3dSearch
Stuctural alignment of SCOP sequences (database + server)
PINTS - Patterns In Non-homologous Tertiary Structures
Sequence similarity search of SCOP using
FPS
Universal Protein Resource (UniProt)
Pfam database of protein
families and HMMs
Integrated resource for protein families (InterPro)
CATH
structural classification
Dali structural comparison
and FSSP structural classification
PDB at a Glance
3Dee Protein Domain Definitions
Protein Data Bank (PDB)
Macromolecular Structure Database (EBI)
Nucleic Acid Database (NDB)
Swiss-Model
Macromolecular Motions Database
The PRESAGE Database
for Structural Genomics
Genome Census
Function assignment and metabolic models
Licensing information for commercial users
(MRC site)
Glossary of terms used in the fold classification
References related to fold classification
methods and fold definitions
Copyright
© 1994-2009 The scop authors /
scop@mrc-lmb.cam.ac.uk
(MRC-CPE,
MRC-LMB).
June 2009
SCOP 1.75: Structural Classification of Proteins — extended
SCOP 1.75: Structural Classification of Proteins — extended
Toggle navigation
Browse
Stats & History
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Searching
About
SCOP 1.75 data
Starting with SCOPe version 2.01, data from all versions of
SCOPe, SCOP, and Astral since 1.55 are stored
in a relational database.
To download a copy of the MySQL database released with stable
SCOPe 2.01 (sql.bz2 format),
click here (309.2 MB).
Documentation for our schema is available
here.
(ER diagrams were autogenerated using
SchemaSpy.)
Note that we have removed the astral_seq_blast* tables from the download, since these tables are so large. They are available on request.
Since SCOP release 1.55, the
SCOP classification has
been distributed in the form of a
set of sequences, coordinates, and parseable files, all based on a
new set of identifiers.For an account of these changes, file
formats, file contents and meaning, see the Lo Conte et al (2002)
and Chandonia et al (2004) references on the
Help > References
page.
SCOP parseable files for stable release 1.75:
dir.des.scop.txt (5.8 MB)
dir.cla.scop.txt (10.5 MB)
dir.hie.scop.txt (2.8 MB)
dir.com.scop.txt (4.2 MB)
Parseable files for previous stable releases of SCOP
:
dir.des.scop(e).txt: 1.73, 1.71, 1.69, 1.67, 1.65, 1.63, 1.61, 1.59, 1.57, 1.55dir.cla.scop(e).txt: 1.73, 1.71, 1.69, 1.67, 1.65, 1.63, 1.61, 1.59, 1.57, 1.55dir.hie.scop(e).txt: 1.73, 1.71, 1.69, 1.67, 1.65, 1.63, 1.61, 1.59, 1.57, 1.55dir.com.scop(e).txt: 1.73, 1.71, 1.69, 1.67, 1.65, 1.63
Astral data
The Astral
compendium is a collection of software and databases, partially
derived from SCOP(e), that aid research
into protein structure and evolution. These data are available on the
Downloads > Astral Sequences & Subsets page.
Free Software
Past
(PDB Archival Snapshot Toolkit):
Perl tools to efficiently store and archive multiple datestamped
snapshots of the PDB.
Version 1.42, released 29 July 2021, is needed to mirror
the "PDB format-like file" bundles for large PDB structures, and includes a fix to
the PDB's search URL.
XML2RAF:
Perl software to create RAF maps
from PDB XML files, used to build
Astral 1.73 and above.
Version 1.02, released 22 January 2015, ignores incorrectly
formatted PDB entries with multi-letter chain identifiers.
MakeRAF: Java software to create
RAF maps from
PDB files is
included in the
StrBio Java
class libraries.
As of Astral 1.73,
this software has been deprecated and replaced by
XML2RAF.
Parseable files for very old releases of
SCOP
(without stable identifiers):
dir.dom.scop.txt: 1.53, 1.50, 1.48, 1.41, 1.37, 1.35
Old sequence libraries
Brenner S. E., Chothia C., Hubbard T. (1998) Assessing
sequence comparison methods with reliable structurally
identified distant evolutionary relationships. Proc. Natl.
Acad. Sci. USA 95, 6073-6078.
sdqib40-1.35.seg.fa,
sdqib90-1.35.seg.fa
Park, S., Karplus, K., Barrett, C., Hughey, R., Haussler, D.,
Hubbard, T. and Chothia, C. (1998) Sequence comparisons
using multiple sequences detect three times as many remote
homologues as pairwise methods. J. Mol. Biol. 284 (4),
1201-1210.
PDB40D-J
Teichmann, S. A., Park, J. and Chothia, C. (1998)
Structural assignments to the Mycoplasma genitalium
proteins show extensive gene duplications and domain
rearrangements. Proc. Natl. Acad. Sci USA 95,
14658-14663.
PDB95D-T
SCOP: Structural Classification of Proteins and ASTRAL. Release 1.75 (June 2009)
Copyright © 1994-2009 The SCOP
and Astral authors
scop@mrc-lmb.cam.ac.uk and
astral@compbio.berkeley.edu
SCOP 1.75: Structural Classification of Proteins — extended
SCOP 1.75: Structural Classification of Proteins — extended
Toggle navigation
Browse
Stats & History
Downloads
ASTRAL Sequences & Subsets
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Help
Online Documentation
References
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Searching
About
SCOP 1.75 help
Overview
Structural Classification of Proteins — extended (SCOPe) is a database of protein structural
relationships that extends the SCOP
database. SCOP is a (mostly) manually
curated ordering of domains from the majority of proteins of known
structure in a hierarchy according to structural and evolutionary
relationships. Development of SCOP (version 1) concluded with SCOP 1.75, released in June 2009. SCOPe extends the SCOP database, using a combination of
manual curation and rigorously validated automated
methods to classify many newer PDB structures.
Our goal in implementing
automation is to extend SCOPe to include structures that can be
classified in the SCOP
hierarchy, without sacrificing the reliability of the database
that was developed through years of expert curation.
SCOPe also incorporates and updates the
Astral compendium. Astral provides several databases and tools
to aid in the analysis of the protein structures classified in
SCOP, particularly through the use
of their sequences. Here is a link to more
info about Astral. New releases
of Astral are derived from SCOPe.
The SCOPe website provides
integrated access to data found in all releases of
the SCOP and
Astral databases that feature
stable identifiers.
The SCOP hierarchy
Applies to: SCOP version 1.55 through current releaseReference: 5
Part of the SCOP (version 1) hierarchy
By analogy with taxonomy, SCOP was
created as a hierarchy of several levels where the fundamental unit
of classification is a domain in the experimentally determined
protein structure. Starting at the bottom, the hierarchy of
SCOP domains comprises the following levels:
Species representing a distinct protein sequence and its
naturally occurring or artificially created variants.
Protein grouping together similar sequences of essentially the
same functions that either originate from different biological
species or represent different isoforms within the same species
Family containing proteins with similar sequences but
typically distinct functions
Superfamily bridging together protein families with common
functional and structural features inferred to be from a common
evolutionary ancestor.
Levels above Superfamily are classified based on structual
features and similarity, and do not imply homology:
Folds grouping structurally similar superfamilies.
Classes based mainly on secondary structure content and organization.
Only the first seven classes are true classes. Because
traditionally the aim of SCOP has been
to classify every residue in the PDB, the remaining classes were
maintained as placeholders to keep track of portions of a PDB
structure that were not appropriate to include
in SCOP. The SCOPe
automated classification methods do not currently add entries to
classes other than the first seven.
The multi-domain class is a special class. It contains chains with
multiple domains that haven't been observed in a different context.
Changes to SCOP(e) design and
size
Applies to: SCOP version 1.55 through current releaseReferences: 1-5,8
The figure below shows the number of structures in the PDB and
SCOP(e) at the time of
each SCOP(e) release. Extended
horizontal lines start at the freeze date for
each SCOP(e) release and show the
number of PDB entries available on that date. (The "freeze date"
is the last date for PDB entries to be released and still classified
in a given SCOP(e) release. Prior to
SCOP 1.73, all protein structures available on
the freeze date were manually classified.)
Timeline of SCOP(e)
releases
The figure below, adapted from
[3],
illustrates how SCOP(e)
has changed over the years. The length of the vertical line for
each release is proportional to the number of entries classified. The angle
of the blue baseline between releases reflects the degree of
divergence from comprehensive and fully manually curated
releases. The angle is based on the percentage of PDB entries on the
freeze date that were not classified in the release, and the extent
to which entries were manually classified.
Changes
to SCOP(e)
design and size
Note that since releases beyond SCOP
1.71 are not comprehensive, not all structurally characterized
protein families and folds from the PDB are classified in these
releases. Therefore, we caution against using later releases
to (for example) analyze the rate at which new folds are being
discovered.
Stable identifiers
Applies to: SCOP version 1.55 through current releaseReference: 8
The SCOPe database continues to
support the same style of stable identifiers in use
since SCOP 1.55. Identifiers are
provided as an unambiguous way to link to each
a SCOP or
SCOPe entry and are stable
across releases. See the sections
on citing and linking
to SCOPe
and SCOP using stable identifiers.
sccs. SCOP(e) concise
classification string. This is a dot notation used to
concisely describe a SCOP(e) class,
fold, superfamily, and family. For example, a.39.1.1
references the "Calbindin D9K" family, where "a" represents
the class, "39" represents the fold, "1" represents the
superfamily, and the last "1" represents the family.
sunid. SCOP(e) unique
identifier. This is simply a number that may be used to
reference any entry in the SCOP(e)
hierarchy, from root to leaves (Fold, Superfamily, Family,
etc.).
sid. Stable domain identifier. A 7-character sid
consists of "d" followed by the 4-character PDB ID of the file
of origin, the PDB chain ID ('_' if none, '.' if multiple as
is the case in genetic domains), and a single character
(usually an integer) if
needed to specify the domain uniquely ('_' if not). Sids are
currently all lower case, even when the chain letter is
upper case. Example
sids include d4akea1, d9hvpa_, and d1cph.1.
Both sunids and sccs identifiers are expected to remain stable
across releases, except in cases where the classification changes
substantially. For example, when nodes in the hierarchy
(e.g. Superfamilies) are merged or split due to new evidence
of evolutionary relationships, corresponding identifiers become
obsolete and new sunids are introduced. If a domain is split,
or the boundaries change substantially, new sid(s) and sunid(s) are
assigned.
A history of changes between all consecutive SCOP(e) releases is available under the
Stats & History tab, and a history
of changes to each individual entry is shown at the bottom
of the page describing that entry.
Astral documentation
Applies to: SCOP version 1.55 through current releaseReferences: 11-13
The primary sources of Astral documention
are the three references cited above and listed on the Help > References page. The Astral
compendium is a collection of software and databases, partially
derived from SCOP(e), that aid research
into protein structure and evolution.
Astral provides sequences and
coordinate files for all SCOP(e) domains,
as well as sequences for all PDB chains
that are classified in SCOP(e).
Chemically modified amino acids are translated back to the original
sequence, and sequences are curated to eliminate errors resulting
from the automated parsing of PDB
files. Because the majority of sequences in the PDB are very similar to others, Astral provides representative subsets of
proteins that span the set of classified protein structures or
domains while alleviating bias toward well-studied proteins. The
highest quality representative in each subset is chosen using AEROSPACI scores, which provide a numeric
estimate of the quality and precision of crystallographically
determined structures.
The figure below, taken from the
2004 NAR paper, gives a brief overview
of how Astral is created. New releases
of Astral are derived from SCOPe domain definitions.
Data flow in ASTRAL
Data flow in Astral: Primary
data sources are shown in green. Primary
Astral databases are shown in light
yellow. Less commonly used resources are shown in darker
yellow. Resources added more recently are outlined in light
blue/grey. Using the
RAF maps, four complete sequence sets are created for every
domain in the first seven classes of
the SCOP(e) database. Two sets (the
genetic domain
sets) include the genetic domain sequences described in the 2002
NAR paper, and the other two (the
original-style sequence sets) use the prior
method of splitting each multi-chain domain into multiple
sequences. For each of these methodologies, one complete sequence
set is derived from sequences in the
PDB
ATOM records, and
another from sequences in the SEQRES
records. The SEQRES sets (for both
genetic domain and original-style methods) are used to derive
representative subsets. Each set is fully compared against
itself using BLAST, and subsets are
created using three similarity criteria and various thresholds.
Representatives are chosen according to
AEROSPACI scores.
PDB chain sequence sets
are derived from the SEQRES records
of every PDB chain in
SCOP(e);
selected subsets are created at 90-100% ID thresholds.
PDB-style files are derived
from the RAF maps and SCOP(e) domain
definitions. At each new release
of Astral, all non-redundant sequences
from each SCOP(e) family and superfamily
are aligned using
MAFFT.
A hidden Markov model (HMM) is
created from the multiple sequence alignment for each family and
superfamily using
HMMER.
These HMMs, and
BLAST, are used to predict domains in
the sequences of newly released PDB
entries on a weekly basis. HMMs from
the
Pfam-A database are also
used to predict domains in regions of the sequences not identified
by HMMs derived
from Astral. Unassigned regions of at
least 20 consecutive residues are also predicted to be potential
domains.
Documentation describing more recent updates (since the 2004 paper)
can be found in the release notes, which are linked from the
Downloads > Astral Sequences & Subsets page.
Searching SCOP and SCOPe
Applies to: SCOP version 1.55 through current releaseReference: 8
The website search bar at the top of each page supports keyword search,
as well as searches
by a number of different SCOP(e) identifiers.
View
the Search examples page for
further details on the syntax, as well as many examples.
Domain visualization
Thumbnails for d4akea1
Applies to: SCOP version 1.55 through current releaseReference: 1
Thumbnails were generated for each domain using
PyMOL,
based on a viewing angle for each protein calculated using
OVOP
(Sverud O, MacCallum RM. 2003. Towards optimal views of proteins.
Bioinformatics 19(7): 882-888 [PubMed]).
On the SCOPe website page showing
information about each domain, thumbnails are displayed showing
the domain in isolation, in the context of its chain, and in the
context of its PDB structure. Links to other domains in the same
chain, and in the same PDB structure,
are below the corresponding thumbnail. To preview
thumbnails from these other domains and get tool tip text with a
short description, mouse over the links to the other
domains. The figure to the right shows the thumbnails generated
for the domain d4akea1.
Domain pages also include a JavaScript-based viewer that allows
users to view and rotate domains in 3D without installing additional software.
The 3D visualization domain visualization tool was built using
JSmol,
a Javascript-based viewer created by the Jmol project.
How to link to SCOP and SCOPe nodes
Applies to: SCOP version 1.55 through current releaseReferences: 1,8
Because the SCOPe website is based on
different technology from the
older SCOP websites, old search paths
(e.g., those using the search.cgi engine) are deprecated. URLs in
the older style will be redirected approprately, so all old links to
the Berkeley SCOP mirror should still
work, including links to retrieve data that used to be on
the Astral website (e.g., getseqs.cgi,
spaci.cgi). We also support old-style links to all versions
of SCOP with stable identifiers; for
example, http://scop.berkeley.edu/scop/
links to SCOP 1.75, the last release of SCOP
(version 1),
while
http://scop.berkeley.edu/scop-1.67/
links to
SCOP version 1.67.
When making new links to SCOP or
SCOPe data on this
website, please use the new link formats below:
To link to a node the current release, use any
stable identifier (sunid,
sid or sccs).
The link formats are:
http://scop.berkeley.edu/sunid=xxxxx
http://scop.berkeley.edu/sid=xxxxx
http://scop.berkeley.edu/sccs=xxxxx
Linking by sunid is preferred because it is faster
(sunid is a number, e.g. 46456; sids and sccs are both alphanumeric).
Note that if the identifier you are linking to has become obsolete
in the current release, the last release in which the identifier
appears is shown, along with an explanation.
To link to a node in a particular SCOP
or SCOPe
release, use the version number and sunid. The link format is:
http://scop.berkeley.edu/sunid=xxxxx&ver=yyyy
(versions are alphanumeric; e.g., 1.55 or 2.01).
You can also use this style of linking to link to nodes
by sid or by sccs.
To link to the root of a particular SCOP
or SCOPe
release, use the version number. The link format is:
http://scop.berkeley.edu/ver=yyyy
(versions are alphanumeric; e.g., 1.55 or 2.01).
To link to information we have on a PDB
file, use its PDB code. The link
format is:
http://scop.berkeley.edu/pdb/code=xxxx
We plan for this link format to remain stable for all future
versions of SCOPe
unless there is a major change
to the classification, even if we make changes to our
underlying website technology.
How to cite SCOP and SCOPe entries
Applies to: SCOP version 1.55 through current releaseReferences: 1,8
In the interest of scientific reproducibility, when you publish a manuscript
or give a talk about data you obtained from SCOP
or SCOPe, it's crucial to
unambiguously refer to the data you used. Using these citation
conventions will provide all the information needed for other researchers to
accurately download the same data that you are working with.
For related help, see the section on
stable identifiers.
When citing a particular SCOPe
or SCOP entry, we recommend the
following conventions, depending on the level of the entry cited:
Class: Use the complete SCOP(e)
version number, full name of the class, and
sunid. Examples:
SCOPe 2.03-stable Class a: All alpha proteins [46456]
SCOP 1.67 Class c: Alpha and beta proteins (a/b) [51349]
Fold, Superfamily, or Family: Use the complete SCOP(e)
version number, sccs,
full name, and sunid. Examples:
SCOPe 2.03-2013-12-12 Fold b.1: Immunoglobulin-like beta-sandwich [48725]
SCOPe 2.03-stable Family c.2.1.1: Alcohol dehydrogenase-like, C-terminal domain [51736]
Protein or Species: Use the complete SCOP(e)
version number, full
name, sunid, and sccs. Examples:
SCOPe 2.03-stable Protein Adenylate kinase [52554] (sccs
c.37.1.1)
SCOP 1.75 Species: Baker's yeast (Saccharomyces
cerevisiae) [TaxId: 4932] [56639] (sccs e.5.1.1)
Domain. Use the complete SCOP(e)
version number, sid, sunid, and sccs. Examples:
SCOPe 2.03-stable d1p0ca2 [87639] (sccs c.2.1.1)
SCOPe 2.03-2013-12-12 d4cadj2 [229759] (sccs b.1.1.0)
Publications using SCOP,
Astral
or SCOPe data should also
cite the appropriate references given on the Help > References page rather than just referring to the website.
Parseable files
Applies to: SCOP version 1.55 through current releaseReference: 8
Parseable files have been provided for each SCOP(e) release,
available from the Downloads > Parseable Files & Software page. Each
of these files has a header, starting with the '#' character,
which includes release, version, and copyright information.
The list below shows the four parseable formats for SCOP(e)
data. For information on downloading and parsing Astral subsets and
RAF sequence maps, see the Astral help.
dir.des.scop(e).txt. - Descriptions for each node
in the SCOP(e) hierarchy.
46457 cf a.1 - Globin-like
113449 px a.1.1.1 d1ux8a_ 1ux8 A:
^1 ^2 ^3 ^4 ^5
Five tab-delimited columns:
sunid
level: cl - class; cf - fold; sf
- superfamily; fa - family; dm - protein; sp - species; px -
domain
sccs
sid or "-"
description
dir.cla.scop(e).txt - Full classification for each
domain.
d1ux8a_ 1ux8 A: a.1.1.1 113449 cl=46456,cf=46457,sf=46458,fa=46459,dm=46460,sp=116748,px=113449
2gtld1 2gtl D:8-147 a.1.1.2 135658 cl=46456,cf=46457,sf=46458,fa=46463,dm=116758,sp=116759,px=135658
d1cph.1 1cph B:,A: g.1.1.1 43831 cl=56992,cf=56993,sf=56994,fa=56995,dm=56996,sp=56997,px=43831
^1 ^2 ^3 ^4 ^5 ^6
Six tab-delimited columns:
sid
PDB ID
description
sccs
sunid
sunids of ancestor nodes in comma-delimited list, in
the format "level=sunid". For level codes, see
description for dir.des.scop(e).txt.
dir.hie.scop(e).txt - Children and parents for
each node
0 - 46456,48724,51349,53931,56572,56835,56992,57942,58117,58231,58788
46457 46456 46458,46548
^1 ^2 ^3
Three tab-delimited columns:
sunid
parent's sunid or "-"
comma-separated list of children's sunids or "-"
dir.com.scop(e).txt - Human and machine-annotated
comments
100067 ! complexed with cyn, hem, xe
63437 ! SQ Q10784
164742 ! automated match to d1s56b_ ! complexed with cyn, hem, na; mutant
^1 ^2 ^3
Two or more "!"-delimited columns:
sunid
first comment
additional comments (one per column)
Plans for future website development
We are continuing to upgrade the website. Planned features include
more sophisticated search functionality (including searches by
sequence and by structure), use of AJAX
to avoid full page reloads, and a SCOPe
tree browser for more efficient display of results. We also plan to
allow downloads of additional derived data (e.g., sequence sets and
HMMs) for different clades in the
tree.
Further help
The primary sources of documentation are the papers listed on
the Help > References page.
Please report bugs and usability issues to us at
scope@compbio.berkeley.edu.
About SCOP and SCOPe
Overview
The SCOP hierarchy
Changes to SCOP(e) design and size
Stable identifiers
Astral documentation
Using the SCOPe website
Searching SCOP and SCOPe
Domain visualization
How to link to SCOP and SCOPe nodes
How to cite SCOP and SCOPe entries
Parseable files
Plans for future website development
More Resources
Further help
back to top
SCOP: Structural Classification of Proteins and ASTRAL. Release 1.75 (June 2009)
Copyright © 1994-2009 The SCOP
and Astral authors
scop@mrc-lmb.cam.ac.uk and
astral@compbio.berkeley.edu
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Home
Database
Database Profile
SCOPe
General information
URL:
http://scop.berkeley.edu/
Full name:
Structural Classification of Proteins-extended
Description:
A database of protein structural relationships that extends the SCOP database
Year founded:
2014
Last update:
2022-02-10
Version:
v2.05
Accessibility:
Manual:
Accessible
Real time :
Checking...
Country/Region:
United States
Classification & Tag
Data type:
Protein
Data object:
NA
Database category:
Structure
Major species:
NA
Keywords:
protein structural relationship
Contact information
University/Institution:
Lawrence Berkeley National Laboratory
Address:
Berkeley,CA 94720,USA
City:
Berkeley
Province/State:
CA
Country/Region:
United States
Contact name (PI/Team):
Steven E. Brenner
Contact email (PI/Helpdesk):
scope@compbio.berkeley.edu
Publications
34850923
SCOPe: improvements to the structural classification of proteins - extended database to facilitate variant interpretation and machine learning. [PMID: 34850923]
Chandonia JM, Guan L, Lin S, Yu C, Fox NK, Brenner SE.
Abstract
The Structural Classification of Proteins-extended (SCOPe, https://scop.berkeley.edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description of the structural and evolutionary relationships amongst the majority of proteins of known structure, along with resources for analyzing the protein structures and their sequences. Structures from the PDB are divided into domains and classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.08, we have developed search and display tools for analysis of genetic variants we mapped to structures classified in SCOPe. In order to improve the utility of SCOPe to automated methods such as deep learning classifiers that rely on multiple alignment of sequences of homologous proteins, we have introduced new machine-parseable annotations that indicate aberrant structures as well as domains that are distinguished by a smaller repeat unit. We also classified structures from 74 of the largest Pfam families not previously classified in SCOPe, and we improved our algorithm to remove N- and C-terminal cloning, expression and purification sequences from SCOPe domains. SCOPe 2.08-stable classifies 106 976 PDB entries (about 60% of PDB entries).
Nucleic Acids Res. 2022:50(D1)
| 22 Citations (from Europe
PMC, 2024-03-02)
30500919
SCOPe: classification of large macromolecular structures in the structural classification of proteins-extended database. [PMID: 30500919]
Chandonia JM, Fox NK, Brenner SE.
Abstract
The SCOPe (Structural Classification of Proteins-extended, https://scop.berkeley.edu) database hierarchically classifies domains from the majority of proteins of known structure according to their structural and evolutionary relationships. SCOPe also incorporates and updates the ASTRAL compendium, which provides multiple databases and tools to aid in the analysis of the sequences and structures of proteins classified in SCOPe. Protein structures are classified using a combination of manual curation and highly precise automated methods. In the current release of SCOPe, 2.07, we have focused our manual curation efforts on larger protein structures, including the spliceosome, proteasome and RNA polymerase I, as well as many other Pfam families that had not previously been classified. Domains from these large protein complexes are distinctive in several ways: novel non-globular folds are more common, and domains from previously observed protein families often have N- or C-terminal extensions that were disordered or not present in previous structures. The current monthly release update, SCOPe 2.07-2018-10-18, classifies 90 992 PDB entries (about two thirds of PDB entries).
Nucleic Acids Res. 2019:47(D1)
| 50 Citations (from Europe
PMC, 2024-03-02)
27914894
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins - extended Database. [PMID: 27914894]
Chandonia JM, Fox NK, Brenner SE.
Abstract
SCOPe (Structural Classification of Proteins-extended, http://scop.berkeley.edu) is a database of relationships between protein structures that extends the Structural Classification of Proteins (SCOP) database. SCOP is an expert-curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. SCOPe classifies the majority of protein structures released since SCOP development concluded in 2009, using a combination of manual curation and highly precise automated tools, aiming to have the same accuracy as fully hand-curated SCOP releases. SCOPe also incorporates and updates the ASTRAL compendium, which provides several databases and tools to aid in the analysis of the sequences and structures of proteins classified in SCOPe. SCOPe continues high-quality manual classification of new superfamilies, a key feature of SCOP. Artifacts such as expression tags are now separated into their own class, in order to distinguish them from the homology-based annotations in the remainder of the SCOPe hierarchy. SCOPe 2.06 contains 77,439 Protein Data Bank entries, double the 38,221 structures classified in SCOP.
J Mol Biol. 2017:429(3)
| 50 Citations (from Europe
PMC, 2024-03-02)
24304899
SCOPe: Structural Classification of Proteins--extended, integrating SCOP and ASTRAL data and classification of new structures. [PMID: 24304899]
Fox NK, Brenner SE, Chandonia JM.
Abstract
Structural Classification of Proteins-extended (SCOPe, http://scop.berkeley.edu) is a database of protein structural relationships that extends the SCOP database. SCOP is a manually curated ordering of domains from the majority of proteins of known structure in a hierarchy according to structural and evolutionary relationships. Development of the SCOP 1.x series concluded with SCOP 1.75. The ASTRAL compendium provides several databases and tools to aid in the analysis of the protein structures classified in SCOP, particularly through the use of their sequences. SCOPe extends version 1.75 of the SCOP database, using automated curation methods to classify many structures released since SCOP 1.75. We have rigorously benchmarked our automated methods to ensure that they are as accurate as manual curation, though there are many proteins to which our methods cannot be applied. SCOPe is also partially manually curated to correct some errors in SCOP. SCOPe aims to be backward compatible with SCOP, providing the same parseable files and a history of changes between all stable SCOP and SCOPe releases. SCOPe also incorporates and updates the ASTRAL database. The latest release of SCOPe, 2.03, contains 59 514 Protein Data Bank (PDB) entries, increasing the number of structures classified in SCOP by 55% and including more than 65% of the protein structures in the PDB.
Nucleic Acids Res. 2014:42(Database issue)
| 332 Citations (from Europe
PMC, 2024-03-02)
Ranking
All databases:
249/5981
(95.854%)
Structure:
23/839
(97.378%)
249
Total Rank
453
Citations
45.3
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Protein
Structure
protein structural relationship
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Cited by
Record metadata
Created on: 2015-06-20
Curated by:
Sicheng Luo [2022-05-10]
Lin Liu [2021-11-13]
Lina Ma [2018-06-11]
Yang Zhang [2018-01-28]
Lin Xia [2016-03-29]
Lin Xia [2015-11-23]
Lin Xia [2015-06-28]
SCOPe
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