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Results 1 - 10
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112
The Negatome database: a reference set of non-interacting protein pairs
- Nucleic Acids Res
, 2010
"... protein pairs ..."
PreSPI: a domain combination based prediction system for protein– protein interaction
- Nucleic Acids Res
, 2004
"... With the accumulation of protein and its related data on the Internet, many domain-based computational techniques to predict protein interactions have been developed. However, most techniques still have many limitations when used in real fields. They usually suffer from low accuracy in prediction an ..."
Abstract
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Cited by 29 (8 self)
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can dis-cern the protein pairs that are more likely to interact with each other in multiple protein pairs. The validity of the prediction model was evaluated using an inter-acting set of protein pairs in yeast and an artificially generated non-interacting set of protein pairs. When 80 % of the set
Are proteins ideal mixtures of amino-acids? Analysis of energy parameter sets, Protein Sci
, 1995
"... Various existing derivations of the effective potentials of mean force for the two-body interactions between amino acid side chains in proteins are reviewed and compared to each other. The differences between different param-eter sets can be traced to the reference state used to define the zero of e ..."
Abstract
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Cited by 37 (5 self)
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Various existing derivations of the effective potentials of mean force for the two-body interactions between amino acid side chains in proteins are reviewed and compared to each other. The differences between different param-eter sets can be traced to the reference state used to define the zero
T (2009) Protein-protein interaction databases: keeping up with growing interactomes. Hum Genomics 3: 291-297. PubMed
, 1940
"... Over the past few years, the number of known protein–protein interactions has increased substantially. To make this information more readily available, a number of publicly available databases have set out to collect and store protein–protein interaction data. Protein–protein interactions have been ..."
Abstract
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Cited by 18 (2 self)
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Over the past few years, the number of known protein–protein interactions has increased substantially. To make this information more readily available, a number of publicly available databases have set out to collect and store protein–protein interaction data. Protein–protein interactions have been
Aliasserver: a web server to handle multiple aliases used to refer to proteins
- Bioinformatics
, 2004
"... Summary: AliasServer provides services that facilitate the assembly of data or data sets that make use of different identifiers to refer to the same proteins. This resource relies on a database which contains, for a given organism, a non redundant list of protein sequences associated with a set of a ..."
Abstract
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Cited by 7 (2 self)
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Summary: AliasServer provides services that facilitate the assembly of data or data sets that make use of different identifiers to refer to the same proteins. This resource relies on a database which contains, for a given organism, a non redundant list of protein sequences associated with a set
Genome Informatics 14: 250--259 (2003) A Domain Combination Based
- Genome Informatics
, 2003
"... In this paper, we propose a probabilistic framework to predict the interaction probability of proteins. The notion of domain combination and domain combination pair is newly introduced and the prediction model in the framework takes domain combination pair as a basic unit of protein interactions ..."
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frequencies of domain combination pairs in the interacting and non-interacting sets of protein pairs, respectively. Based on the appearance probability matrix, a probability equation is devised. The equation maps a protein pair to a real number in the range of 0 to 1. Two distributions of interacting
A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction
"... Background: An accurate potential function is essential to attack protein folding and structure prediction problems. The key to developing efficient knowledge-based potential functions is to design reference states that can appropriately counteract generic interactions. The reference states of many ..."
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Cited by 20 (3 self)
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knowledge-based distance-dependent atomic potential functions were derived from non-interacting particles such as ideal gas, however, which ignored the inherent sequence connectivity and entropic elasticity of proteins. Methodology: We developed a new pair-wise distance-dependent, atomic statistical
Probabilistic model of the human proteinprotein interaction network." Nat Biotechnol 23(8
, 2005
"... A catalog of all human protein-protein interactions would provide scientists with a framework to study protein deregulation in complex diseases such as cancer. Here we demonstrate that a probabilistic analysis integrating model organism interactome data, protein domain data, genomewide gene express ..."
Abstract
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Cited by 55 (0 self)
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, protein domain assignments 2 , gene expression measurements in human tissue samples 3 and biological function annotations 4 ( A gold standard positive set (GSP) of 11,678 distinct protein-protein interactions among 5,505 proteins was queried from the Human Protein Reference Database (HPRD) 12 , a
Databases and Distributed Systems Group, TU Darmstadt, Germany,
"... Message-oriented middleware (MOM) is at the core of a vast number of financial services and telco applications, and is gaining increasing traction in other industries, such as manufacturing, transportation, health-care and supply chain management. Novel messaging applications, however, pose some ser ..."
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Message-oriented middleware (MOM) is at the core of a vast number of financial services and telco applications, and is gaining increasing traction in other industries, such as manufacturing, transportation, health-care and supply chain management. Novel messaging applications, however, pose some
5-Methylation of Cytosine in CG:CG Base-pair Steps: A Physicochemical Mechanism for the Epigenetic Control of DNA Nanomechanics
, 2014
"... Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis of the ..."
Abstract
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Cited by 2 (1 self)
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Van der Waals density functional theory is integrated with analysis of a non-redundant set of protein-DNA crystal structures from the Nucleic Acid Database to study the stacking energetics of CG:CG base-pair steps, specifically the role of cytosine 5-methylation. Principal component analysis
Results 1 - 10
of
112
