CATH – a hierarchic classification of protein domain structures.

"... Traditionally, proteins have been viewed as a construct based on elements of secondary structure and their arrangement in three-dimensional space. In a departure from this perspective we show that protein structures can be modelled as network systems that exhibit small-world, single-scale, and to so ..."

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Traditionally, proteins have been viewed as a construct based on elements of secondary structure and their arrangement in three-dimensional space. In a departure from this perspective we show that protein structures can be modelled as network systems that exhibit small-world, single-scale, and to some degree, scale-free properties. The phenomenological network concept of degrees of separation is applied to three-dimensional protein structure networks and reveals how amino acid residues can be connected to each other within six degrees of separation. This work also illuminates the unique features of protein networks in comparison to other networks currently studied. Recognising that proteins are networks provides a means of rationalising the robustness in the overall three-dimensional fold of a protein against random mutations and suggests an alternative avenue to investigate the determinants of protein structure, function and folding. q 2003 Published by Elsevier Ltd.

Inferring Functional Relationships of Proteins from Local Sequence and Spatial Surface Patterns

by T. Andrew Binkowski, Larisa Adamian, Jie Liang - J. Mol. Biol , 2003

"... es, and for further inquiries on evolutionary origins of structural elements important for protein function. q 2003 Elsevier Ltd. All rights reserved. Keywords: protein surface; surface pattern; protein function; pocket sequence; pocket shape *Corresponding author Introduction With rapid progres ..."

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es, and for further inquiries on evolutionary origins of structural elements important for protein function. q 2003 Elsevier Ltd. All rights reserved. Keywords: protein surface; surface pattern; protein function; pocket sequence; pocket shape *Corresponding author Introduction With rapid progress in the determination of protein structures, 1,2 protein structural analysis has become an important source of information for understanding functional roles of proteins. Conservation of protein structures often reveals very distant evolutionary relationships, which are otherwise difficult to detect by sequence analysis alone. Analysis of protein structure can provide insightful ideas about the biochemical functions and mechanisms of proteins (e.g. active sites, catalytic residues, and substrate interactions). 9--11 An important approach of studying protein structures is fold analysis. Identifying the correct tertiary fold of protein is often helpful for inferring protein funct

Hidden markov models that use predicted local structure for fold recognition: alphabets of backbone geometry

by Rachel Karchin, Yael Mandel-gutfreund, Melissa Cline, Kevin Karplus - Proteins , 2003

"... An important problem in computational biology is predicting the structure of the large number of pu-tative proteins discovered by genome sequencing projects. Fold-recognition methods attempt to solve the problem by relating the target proteins to known structures, searching for template proteins hom ..."

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An important problem in computational biology is predicting the structure of the large number of pu-tative proteins discovered by genome sequencing projects. Fold-recognition methods attempt to solve the problem by relating the target proteins to known structures, searching for template proteins homologous to the target. Remote homologs which may have significant structural similarity are often not detectable by sequence similarities alone. To address this, we incorporated predicted local structure, a generalization of secondary structure, into two-track profile HMMs. We did not rely on a simple helix-strand-coil definition of secondary structure,

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De novo prediction of three-dimensional structures for major protein families

by Richard Bonneau, Charlie E. M. Strauss, Carol A. Rohl, Dylan Chivian, Phillip Bradley, Lars Malmström, Tim Robertson, David Baker - J. Mol. Biol , 2002

"... As the number of gene sequences in databases, public and private, increase dramatically, so do the number of genes of unknown function. Of the protein sequences currently available approximately ..."

Abstract - Cited by 65 (12 self) - Add to MetaCart

As the number of gene sequences in databases, public and private, increase dramatically, so do the number of genes of unknown function. Of the protein sequences currently available approximately

Recognition of spatial motifs in protein structures

by Gerard J. Kleywegt - Journal of Molecular Biology , 1999

"... As the structural database continues to expand, new methods are required to analyse and compare protein structures. Whereas the recog-nition, comparison, and classification of folds is now more or less a solved problem, tools for the study of constellations of small numbers of residues are few and f ..."

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As the structural database continues to expand, new methods are required to analyse and compare protein structures. Whereas the recog-nition, comparison, and classification of folds is now more or less a solved problem, tools for the study of constellations of small numbers of residues are few and far between. In this paper, two programs are described for the analysis of spatial motifs in protein structures. The first, SPASM, can be used to find the occurrence of a motif consisting of arbi-trary main-chain and/or side-chains in a database of protein structures. The program also has a unique capability to carry out ‘‘fuzzy pattern matching’ ’ with relaxed requirements on the types of some or all of the matching residues. The second program, RIGOR, scans a single protein structure for the occurrence of any of a set of pre-defined motifs from a database. In one application, spatial motif recognition combined with profile analysis enabled the assignment of the structural and functional class of an uncharacterised hypothetical protein in the sequence database. In another application, the occurrence of short left-handed helical segments in protein structures was investigated, and such segments were found to be fairly common. Potential applications of the techniques presented here lie in the analysis of (newly determined) structures, in comparative structural analysis, in the design and engineering of novel functional sites, and in the prediction of structure and function of unchar-acterised proteins.

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PDBsum: summaries and analyses of PDB structures

by Roman Aleksander Laskowski, See Profile, Roman A. Laskowski - Nucleic Acids Res , 2001

"... All in-text references underlined in blue are linked to publications on ResearchGate, letting you access and read them immediately. ..."

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All in-text references underlined in blue are linked to publications on ResearchGate, letting you access and read them immediately.

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CATH – a hierarchic classification of protein domain structures. (1997)

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