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ArchDB: automated protein loop classification as a tool for structural genomics
2004
Nucleic Acids Research
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The annotation of protein function has become a crucial problem with the advent of sequence and structural genomics initiatives. ...
Here we present ArchDB, a classi®cation database of structural motifs, consisting of one loop plus its bracing secondary structures. ...
IMPROVED LOOP CLASSIFICATION PROTOCOL The current version of ArchDB is based on a list of protein domains derived from SCOP 40 on release 1.61 of SCOP (12) . ...
doi:10.1093/nar/gkh002
pmid:14681390
pmcid:PMC308737
fatcat:iwv56qkqjrcp7beml6nfnwimky
Protein Structure Annotation Resources
[chapter]
2014
Msphere
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Since the 3-D structure of proteins are ultimately responsible for most actions in the cell, this review will focus on protein structure annotation resources that aim to explain a ...
A key reason three-dimensional (3-D) protein structures are annotated with supporting or derived information is to understand the molecular basis of protein function. ...
The ArchDB classification database classifies loops extracted from structures in the PDB archive (42) . ...
doi:10.1007/978-1-4939-2230-7_1
pmid:25502191
pmcid:PMC5586544
fatcat:n4wrlx7rtvfy7mya7w457ppwca
Comparative modelling of protein structure and its impact on microbial cell factories
2005
Microbial Cell Factories
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This review is intended to serve as a guide for the biologist who has no special expertise and who is not involved in the determination of protein structure. ...
Comparative modeling is becoming an increasingly helpful technique in microbial cell factories as the knowledge of the three-dimensional structure of a protein would be an invaluable aid to solve problems ...
ii) the conformation of a loop is influenced by the core stem regions that span the loop as well as by the structure of rest of the protein that encircles the loop. ...
doi:10.1186/1475-2859-4-20
pmid:15989691
pmcid:PMC1183243
fatcat:j7ti552ebzgztgjkrigcrtr3ya
Template-Based Protein Modeling: Recent Methodological Advances
2010
Current Topics in Medicinal Chemistry
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structure prediction, model building, loop building, side-chain prediction and model quality assessment. ...
The latest advances and progress in computational power have helped to solve this problem to a considerable extent; however, predicting accurate three-dimensional structure of proteins has always been ...
Fold recognition methods, generally suggested for automatic prediction of protein structure, can also be used as a tool for identifying remote homologues. ...
doi:10.2174/156802610790232314
pmid:19929829
pmcid:PMC5943704
fatcat:ads473bjenclhkrkdh72kbcb3u
Structural Protein Function Prediction - A Comprehensive Review
2015
International Journal of Modern Education and Computer Science
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The aim was to provide a recent and comprehensive review of protein structure related topics: function aspects, structural classification, databases, tools and methods. ...
The large amounts of available protein structures emerges the need for computational methods for protein function prediction. ...
Recently, a structural classification of loops in proteins (ArchDB) [14] and an evolutionary classification of protein domains (ECOD) [15] are presented. ...
doi:10.5815/ijmecs.2015.10.07
fatcat:xvvm2j7zjranhngr2eqpx7jf4y
Local Protein Structures
2007
Current Bioinformatics
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In addition, a classification of the backbone conformation limited to 3 states (the classical repetitive secondary structures and coils) does not precisely describe the protein structures, because it fails ...
and the loops. ...
The clustering procedure was then improved and fully automated resulting in ArchDB database [219] . In addition, updates enabled the inclusion of clusters for many long loops. ...
doi:10.2174/157489307781662105
fatcat:wosaroff5jhcnojc7zlozpvd5e
On the use of direct-coupling analysis with a reduced alphabet of amino acids combined with super-secondary structure motifs for protein fold prediction
2021
NAR Genomics and Bioinformatics
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As a result of a compressed alphabet, the number of sequences required for the multiple sequence alignment is reduced. ...
Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. ...
ArchDB is a structural classification of sMotifs, formed by clusters of similar structures. ...
doi:10.1093/nargab/lqab027
pmid:33937764
pmcid:PMC8061457
fatcat:ippjdib6svfznjiidfucywn3u4
Application of Models for Biomolecular Structure and Interactions to Understand and Influence Biological Function
2011
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Ein Teil dieser Arbeit beschäftigt sich mit der Untersuchung von Proteininteraktionen, wobei als Methoden für die Modellierung von Protein-Protein-Wechselwirkungen (POEM) und für die Protein-Liganden-Wechselwirkung ...
Dazu wurde ein in silico Alanin-Scanning-Protokoll entwickelt, welches experimentelle Verfahren zur Untersuchung wichtiger Interaktionen in der Protein-Protein-Kontaktfläche ergänzt. ...
Thank also to my colleague Konstantin, it was a pleasure to be in the office with him, to Simon for his kind help in the Zuzammenfassung, and to Priya for the good advice with the references and of course ...
doi:10.5445/ir/1000025036
fatcat:qojmj4dhd5cdflkenvmdpptpku