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ArchDB: automated protein loop classification as a tool for structural genomics

J. Espadaler
2004 Nucleic Acids Research  
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]

Margaret J. Gabanyi, Helen M. Berman
2014 Msphere  
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

Nuria B Centeno, Joan Planas-Iglesias, Baldomero Oliva
2005 Microbial Cell Factories  
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

Pankaj Daga, Ronak Patel, Robert Doerksen
2010 Current Topics in Medicinal Chemistry  
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

Huda A. Maghawry, Mostafa G. M. Mostafa, Mohamed H. Abdul-Aziz, Tarek F. Gharib
2015 International Journal of Modern Education and Computer Science  
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

Bernard Offmann, Manoj Tyagi, Akexandre de Brevern
2007 Current Bioinformatics  
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

Bernat Anton, Mireia Besalú, Oriol Fornes, Jaume Bonet, Alexis Molina, Ruben Molina-Fernandez, Gemma De Las Cuevas, Narcis Fernandez-Fuentes, Baldo Oliva
2021 NAR Genomics and Bioinformatics  
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

Irene Meliciani
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