ArchDB
Names
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ArchDB
metasource: Fairsharing.org
version: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
ArchDB14
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:29.705867
archdb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:29.705867
Names
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ArchDB
metasource: Fairsharing.orgversion: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
ArchDB14
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:29.705867
archdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:29.705867
Names
More detailed information about this field from each metasource.
ArchDB
metasource: Fairsharing.orgversion: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
ArchDB14
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:29.705867
archdb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:29.705867
ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.
Description
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ArchDB is a compilation of structural classifications of loops extracted from known protein structures. The structural classification is based on the geometry and conformation of the loop. The geometry is defined by four internal variables and the type of regular flanking secondary structures, resulting in 10 different loop types. Loops in ArchDB have been classified using an improved version (Espadaler et al.) of the original ArchType program published in 1997 by Oliva et al.
metasource: Fairsharing.orgversion: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
ArchDB (http://sbi.imim.es/archdb) is a relational database of classified structural motifs, consisting of one loop plus its bracing secondary structures. Motifs have been classified using an improved version[1] of ArchType[2], an automated loop classification program. ArchType has been successfully applied to the SCOP95 set from SCOP 1.65 release[3]. The previous non-redundant classification[1], based on the SCOP40 set, has also been updated. Currently, the SCOP90-based classification contains 46894 motifs clustered into 2029 classes and 5111 subclasses, and the SCOP40-based classification contains 24356 motifs clustered into 1221 classes and 3575 subclasses. In addition, a manually curated classification of a subset of kinase proteins, ArchKI, has been included[4]. Functional annotations concerning residues found within clustered motifs has been incorporated into ArchDB, such as small ligand contacts (within 6.0 Ã…) and PDB SITE and ACTSITE records[5]. SCOP domain classification and protein functional descriptors such as EC numbers[6] and GO terms[7] are also reported. Subclasses displaying conserved functional or structural annotations (above 75%) are reported.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Structural classification of loops extracted from known protein structures.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:29.705867
Webpage:
http://sbi.imim.es/archdbWebpage
More detailed information about this field from each metasource.
http://sbi.imim.es/archdb
metasource: Fairsharing.orgversion: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
http://sbi.imim.es/archdb/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:29.705867
Publications:
Publications
More detailed information about this field from each metasource.
ArchDB: automated protein loop classification as a tool for structural genomics
PMID: 14681390
metasource: Fairsharing.org
version: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
ArchDB 2014: structural classification of loops in proteins
PMID: 24265221
metasource: Fairsharing.org
version: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:29.705867
http://dx.doi.org/10.1093/nar/gkt1189
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
ArchDB: automated protein loop classification as a tool for structural genomics
PMID: 14681390
metasource: Fairsharing.org
version: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
ArchDB 2014: structural classification of loops in proteins
PMID: 24265221
metasource: Fairsharing.org
version: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:29.705867
http://dx.doi.org/10.1093/nar/gkt1189
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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ArchDB: automated protein loop classification as a tool for structural genomics
PubMed citations: 25.
25 articles citing: ArchDB: automated protein loop classification as a tool for structural genomics
Using feature optimization-based support vector machine method to recognize the β-hairpin motifs in enzymes. PMID:28855832
Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02. PMID:26782814
ArchDB 2014: structural classification of loops in proteins. PMID:24265221
Evolution of protein indels in plants, animals and fungi. PMID:23826714
How long is a piece of loop? PMID:23638343
The importance of slow motions for protein functional loops. PMID:22314977
Near-native protein loop sampling using nonparametric density estimation accommodating sparcity. PMID:22028638
Models to Approximate the Motions of Protein Loops. PMID:21031141
BriX: a database of protein building blocks for structural analysis, modeling and design. PMID:20972210
Template-based protein structure modeling. PMID:20835794
FragKB: structural and literature annotation resource of conserved peptide fragments and residues. PMID:20305778
Modeling of loops in proteins: a multi-method approach. PMID:20149252
Mining protein loops using a structural alphabet and statistical exceptionality. PMID:20132552
Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB). PMID:20066127
Template-based protein modeling: recent methodological advances. PMID:19929829
Multi-constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility. PMID:19194863
ProSeg: a database of local structures of protein segments. PMID:18931918
Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins. PMID:18578882
Prediction of the beta-hairpins in proteins using support vector machine. PMID:18071887
Clustering protein environments for function prediction: finding PROSITE motifs in 3D. PMID:17570144
"Pinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence. PMID:17426380
A supersecondary structure library and search algorithm for modeling loops in protein structures. PMID:16617149
Optimization of the GB/SA solvation model for predicting the structure of surface loops in proteins. PMID:16471897
Comparative modelling of protein structure and its impact on microbial cell factories. PMID:15989691
Large-scale conformational dynamics of the HIV-1 integrase core domain and its catalytic loop mutants. PMID:15731379 -
ArchDB 2014: structural classification of loops in proteins
PubMed citations: 15.
15 articles citing: ArchDB 2014: structural classification of loops in proteins
Benchmarking the Accuracy of AlphaFold 2 in Loop Structure Prediction. PMID:35883541
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. PMID:35438789
On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction. PMID:33937764
On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures. PMID:29028891
Using feature optimization-based support vector machine method to recognize the β-hairpin motifs in enzymes. PMID:28855832
Extension of the classical classification of β-turns. PMID:27627963
Known unknowns of cardiolipin signaling: The best is yet to come. PMID:27498292
Using Local States To Drive the Sampling of Global Conformations in Proteins. PMID:26808351
Engineered Domain Swapping as an On/Off Switch for Protein Function. PMID:26496687
Cardiolipin Interactions with Proteins. PMID:26300339
Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures. PMID:26252221
Conformational sampling and structure prediction of multiple interacting loops in soluble and β-barrel membrane proteins using multi-loop distance-guided chain-growth Monte Carlo method. PMID:25861965
Protein structure annotation resources. PMID:25502191
The Protein Data Bank archive as an open data resource. PMID:25062767
NMR structure of the S-linked glycopeptide sublancin 168. PMID:24405370 - http://dx.doi.org/10.1093/nar/gkt1189
Tags:
Tags
More detailed information about this field from each metasource.
classification
metasource: Fairsharing.org
version: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
secondary protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein structure
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein structural motifs and surfaces
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:29.705867
Tags
More detailed information about this field from each metasource.
classification
metasource: Fairsharing.orgversion: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
secondary protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: ArchDB; ArchDB; DOI: https://doi.org/10.25504/FAIRsharing.tp9z4q; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:08 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein structure
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein structural motifs and surfaces
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:29.705867
classification protein secondary protein structure structure protein structure protein structural motifs and surfaces
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