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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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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 ...
Victor B. Strelets, Hwa A. Lim
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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 ...
Erik, Verschueren +5 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
B C, Orcutt, W C, Barker
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Databases of Protein–Protein Interactions and Complexes
2009In the current understanding, translation of genomic sequences into proteins is the most important path for realization of genome information. In exercising their intended function, proteins work together through various forms of direct (physical) or indirect interaction mechanisms.
Hong Sain, Ooi +5 more
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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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Protein Function Database as a Deductive and Object-Oriented Database
1991This paper describes an experiment on a knowledge base approach to molecular biological databases, especially focusing on a protein function database.
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Software and Databases for Protein–Protein Docking
Protein-protein interactions (PPIs) provide valuable insights for understanding the principles of biological systems and for elucidating causes of incurable diseases. One of the techniques used for computational prediction of PPIs is protein-protein docking calculations, and a variety of software has been developed.Małgorzata, Jarończyk +2 more
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