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Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

by Wolfgang Kabsch, Christian Sander , 1983
"... For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-r ..."
Abstract - Cited by 2096 (5 self) - Add to MetaCart
. ” Solvent “exposure ” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs

BioGRID: a General Repository for Interaction Datasets

by Chris Stark, Bobby-joe Breitkreutz, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Mike Tyers , 2006
"... Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/ protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at ..."
Abstract - Cited by 424 (1 self) - Add to MetaCart
Access to unified datasets of protein and genetic interactions is critical for interrogation of gene/ protein function and analysis of global network properties. BioGRID is a freely accessible database of physical and genetic interactions available at

Modeling and simulation of genetic regulatory systems: A literature review

by Hidde De Jong - JOURNAL OF COMPUTATIONAL BIOLOGY , 2002
"... In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between ..."
Abstract - Cited by 738 (14 self) - Add to MetaCart
DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools

Using Bayesian networks to analyze expression data

by Nir Friedman, Michal Linial, Iftach Nachman - Journal of Computational Biology , 2000
"... DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biologica ..."
Abstract - Cited by 1088 (17 self) - Add to MetaCart
DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key

RQL: A Declarative Query Language for RDF

by Greg Karvounarakis, Sofia Alexaki, Vassilis Christophides, Dimitris Plexousakis, Michel Scholl
"... Real-scale Semantic Web applications, such as Web Portals and E-Marketplaces, require the management of voluminous metadata repositories containing descriptive information (i.e., metadata) about the available Web resources and services. Better knowledge about the meaning, usage, accessibility or qua ..."
Abstract - Cited by 247 (27 self) - Add to MetaCart
Real-scale Semantic Web applications, such as Web Portals and E-Marketplaces, require the management of voluminous metadata repositories containing descriptive information (i.e., metadata) about the available Web resources and services. Better knowledge about the meaning, usage, accessibility

Graph Indexing: A Frequent Structure-based Approach

by Xifeng Yan , Philip S. Yu, Jiawei Han , 2004
"... Graph has become increasingly important in modelling complicated structures and schemaless data such as proteins, chemical compounds, and XML documents. Given a graph query, it is desirable to retrieve graphs quickly from a large database via graph-based indices. In this paper, we investigate the is ..."
Abstract - Cited by 201 (25 self) - Add to MetaCart
Graph has become increasingly important in modelling complicated structures and schemaless data such as proteins, chemical compounds, and XML documents. Given a graph query, it is desirable to retrieve graphs quickly from a large database via graph-based indices. In this paper, we investigate

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

by Andrea Franceschini, Damian Szklarczyk, Sune Frankild, Michael Kuhn, Milan Simonovic, Er Roth, Jianyi Lin, Pablo Minguez, Peer Bork, Christian Von Mering, Lars J. Jensen - Nucleic Acids Res , 2013
"... Complete knowledge of all direct and indirect inter-actions between proteins in a given cell would represent an important milestone towards a com-prehensive description of cellular mechanisms and functions. Although this goal is still elusive, consid-erable progress has been made—particularly for ce ..."
Abstract - Cited by 183 (9 self) - Add to MetaCart
—particularly for certain model organisms and functional systems. Currently, protein interactions and associations are annotated at various levels of detail in online resources, ranging from raw data repositories to highly formalized pathway databases. For many applications, a global view of all the available inter

YARS2: A federated repository for querying graph structured data from the Web

by Andreas Harth, Aidan Hogan, Stefan Decker - In ISWC , 2007
"... Abstract. We present the architecture of an end-to-end semantic search engine that uses a graph data model to enable interactive query answer-ing over structured and interlinked data collected from many disparate sources on the Web. In particular, we study distributed indexing meth-ods for graph-str ..."
Abstract - Cited by 112 (11 self) - Add to MetaCart
Abstract. We present the architecture of an end-to-end semantic search engine that uses a graph data model to enable interactive query answer-ing over structured and interlinked data collected from many disparate sources on the Web. In particular, we study distributed indexing meth-ods for graph

Qualitative Simulation of Genetic Regulatory Networks Using Piecewise-Linear Models

by Hidde De Jong, Jean-Luc Gouze, Celine Hernandez, Michel Page, Tewfik Sari, Johannes Geiselmann , 2001
"... In order to cope with the large amounts of data that have become available in genomics, mathematical tools for the analysis of networks of interactions between genes, proteins, and other molecules are indispensable. We present a method for the qualitative simulation of genetic regulatory networks ..."
Abstract - Cited by 190 (30 self) - Add to MetaCart
In order to cope with the large amounts of data that have become available in genomics, mathematical tools for the analysis of networks of interactions between genes, proteins, and other molecules are indispensable. We present a method for the qualitative simulation of genetic regulatory

Reverse engineering of regulatory networks in human B cells.

by Katia Basso , Adam A Margolin , Gustavo Stolovitzky , Ulf Klein , Riccardo Dalla-Favera , Andrea Califano - Nat. Genet. , 2005
"... Cellular phenotypes are determined by the differential activity of networks linking coregulated genes. Available methods for the reverse engineering of such networks from genome-wide expression profiles have been successful only in the analysis of lower eukaryotes with simple genomes. Using a new m ..."
Abstract - Cited by 178 (2 self) - Add to MetaCart
of cellular networks as graphs, where nodes represent genes and edges between them represent interactions, either between the encoded proteins or between the encoded proteins and the genes (we use 'genetic interaction' to refer to both types of mechanisms). Available methods fall into four broad
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