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2015
The scientific community's major conceptual notion of structural biology has recently shifted in emphasis from the classical structure-function paradigm due to the emergence of intrinsically disordered proteins (IDPs). As opposed to their folded cousins, these proteins are defined by the lack of a stable 3D fold and a high degree of inherent structural
VÁRADI, Mihály, Tompa, Peter
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The scientific community's major conceptual notion of structural biology has recently shifted in emphasis from the classical structure-function paradigm due to the emergence of intrinsically disordered proteins (IDPs). As opposed to their folded cousins, these proteins are defined by the lack of a stable 3D fold and a high degree of inherent structural
VÁRADI, Mihály, Tompa, Peter
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Molecular Biotechnology, 2009
Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses, and schematic diagrams relating to its 3D structure and biological function.
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Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses, and schematic diagrams relating to its 3D structure and biological function.
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2009
Protein sequence databases do not contain just the sequence of the protein itself but also annotation that reflects our knowledge of its function and contributing residues. In this chapter, we will discuss various public protein sequence databases, with a focus on those that are generally applicable.
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Protein sequence databases do not contain just the sequence of the protein itself but also annotation that reflects our knowledge of its function and contributing residues. In this chapter, we will discuss various public protein sequence databases, with a focus on those that are generally applicable.
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Protein-Protein Interaction Databases
2015Years of meticulous curation of scientific literature and increasingly reliable computational predictions have resulted in creation of vast databases of protein interaction data. Over the years, these repositories have become a basic framework in which experiments are analyzed and new directions of research are explored.
Szklarczyk, Damian, Jensen, Lars Juhl
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Threading a database of protein cores
Proteins: Structure, Function, and Bioinformatics, 1995AbstractWe present an analysis of 10 blind predictions prepared for a recent conference, “Critical Assessment of Techniques for Protein Structure Prediction.”1 The sequences of these proteins are not detectably similar to those of any protein in the structure database then available, but we attempted, by a threading method, to recognize similarity to ...
Madej, T. +2 more
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1990
Publisher Summary Researchers at the National Biomedical Research Foundation (NBRF) have maintained the Protein Sequence Database since the early 1960s. The database has become truly international with the recent establishment of PIR-International, an association of protein sequence data collection centers including NBRF, the Martinsried Institute ...
David G. George +2 more
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Publisher Summary Researchers at the National Biomedical Research Foundation (NBRF) have maintained the Protein Sequence Database since the early 1960s. The database has become truly international with the recent establishment of PIR-International, an association of protein sequence data collection centers including NBRF, the Martinsried Institute ...
David G. George +2 more
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Databases and Protein Structures
2018Bioinformatics databases contain biological data from scientific experiments most importantly DNA and protein sequences and protein structures. Databases of published literature, computational analysis of primary data, and metadata are also important. Primary and secondary databases refer to the type and source of stored data.
Lisbeth Elvira de Vries +1 more
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Searching the protein sequence database
Bulletin of Mathematical Biology, 1984As the volume of protein sequence data grows, rapid methods for searching the protein sequence database become of primary importance. Rigorous comparison of sequences is obtained with the well-known dynamic programming algorithms. However, these algorithms are not rapid enough to use for routinely searching the entire database. In this paper we discuss
Bruce C. Orcutt, Winona C. Barker
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Compression of protein sequence databases
Bioinformatics, 1995We have created an algorithm for compressing a PIR database to assist individual researchers and software developers who utilize sequence database information but may not have huge storage space. The resulting compact databank contains compressed PIR information and an interface written in C which allows fast direct access to the stored information ...
Hwa A. Lim, Victor B. Strelets
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Protein design with fragment databases
Current Opinion in Structural Biology, 2011Structure-based computational methods are popular tools for designing proteins and interactions between proteins because they provide the necessary insight and details required for rational engineering. Here, we first argue that large-scale databases of fragments contain a discrete but complete set of building blocks that can be used to design ...
Peter Vanhee +8 more
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