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J Comput Aided Mol Des (2009) 23:773–784 DOI 10.1007/s10822-009-9273-4
"... Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development ..."
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Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development
Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs
- Journal of Computational Biology
, 2005
"... We find recurring amino-acid residue packing patterns, or spatial motifs, that are characteristic of protein structural families, by applying a novel frequent subgraph mining algorithm to graph representations of protein three-dimensional structure. Graph nodes represent amino acids, and edges are c ..."
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Cited by 36 (5 self)
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We find recurring amino-acid residue packing patterns, or spatial motifs, that are characteristic of protein structural families, by applying a novel frequent subgraph mining algorithm to graph representations of protein three-dimensional structure. Graph nodes represent amino acids, and edges
Functional Neighbors: Inferring Relationships between Non-Homologous Protein Families Using Family-Specific Packing Motifs
"... We describe a new approach for inferring the functional relationships between non-homologous protein families by looking at statistical enrichment of alternative function predictions in classification hierarchies such as Gene Ontology (GO) and Structural Classification of Proteins (SCOP). Protein st ..."
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Cited by 1 (0 self)
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structures are represented by robust graphs, and the Fast Frequent Subgraph Mining algorithm is applied to protein families to generate sets of family-specific packing motifs, i.e. amino acid residue packing patterns shared by most family members but infrequent in other proteins. The function of a protein
J Comput Aided Mol Des (2009) 23:785–797 DOI 10.1007/s10822-009-9277-0 Identification
, 2009
"... of family-specific residue packing motifs and their use for structure-based protein function prediction: ..."
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of family-specific residue packing motifs and their use for structure-based protein function prediction:
Development of physics-based energy functions that predict mediumresolution structures for proteins of the a, beta, and a/h structural classes
- J. Phys. Chem., B
"... The development of three physics-based energy functions (force fields), designed to simulate the restricted free energy of proteins of the R, β, and R/β structural classes, is described. Each force field corresponds to a particular weighting of the united-residue (UNRES) interactions defined in earl ..."
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Cited by 4 (0 self)
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The development of three physics-based energy functions (force fields), designed to simulate the restricted free energy of proteins of the R, β, and R/β structural classes, is described. Each force field corresponds to a particular weighting of the united-residue (UNRES) interactions defined
Predicting metal-binding sites from protein sequence
- IEEE/ACM Trans. Comput. Biology Bioinform
"... Abstract—Prediction of binding sites from sequence can significantly help toward determining the function of uncharacterized proteins on a genomic scale. The task is highly challenging due to the enormous amount of alternative candidate configurations. Previous research has only considered this pred ..."
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Cited by 3 (1 self)
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this prediction problem starting from 3D information. When starting from sequence alone, only methods that predict the bonding state of selected residues are available. The sole exception consists of pattern-based approaches, which rely on very specific motifs and cannot be applied to discover truly novel sites
Computational Tools for Protein-DNA Interactions How Many Binding Proteins Exist?
"... Abstract Interactions between DNA and proteins are central to living systems, and characterizing how and when they occur would greatly enhance our understanding of working genomes. We review the different computational problems associated with protein-DNA interactions and the various methods used t ..."
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for various structural classes of TFs Finally, a true head-to-head comparison of the various methods for DNA-binding protein identification and DNA-binding residue prediction would guide further development in this area. Dividing a benchmark into sequence-based and structure-based predictions would elucidate
Detection of protein SUMOylation in vivo
- Nat Protoc
, 2009
"... The small ubiquitin-like modifiers (SUMOs) are posttranslationally conjugated to eukaryotic cellular proteins with generally unpredictable consequences. SUMO substrates are found in many cellular systems, and functional analysis has revealed that substrate SUMOylation often has an important role in ..."
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Cited by 1 (0 self)
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substrate, three important questions need to be answered: (i) is the protein linked covalently to SUMO? (ii) at which lysine acceptor residue(s) does the conjugation occur? and (iii) what is the functional consequence of SUMO conjugation? When a protein is a suspected SUMO substrate before attempting
Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell.
, 2000
"... A major quantitative trait locus (QTL) controlling response to photoperiod, Hd1 , was identified by means of a mapbased cloning strategy. High-resolution mapping using 1505 segregants enabled us to define a genomic region of ف 12 kb as a candidate for Hd1 . Further analysis revealed that the Hd1 ..."
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Cited by 49 (5 self)
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. The sequence obtained indicates that rice Hd1 is composed of two exons that encode a 395-amino acid protein and is a member of the Arabidopsis CO family with a zinc finger domain ( 2476 The Plant Cell Functional Complementation with Candidate Gene in Transgenic Rice A 7.1-kb ApaI fragment of Nipponbare
RESEARCH ARTICLE Open Access
"... MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts Xin Deng 1 and Jianlin Cheng 1,2,3* Background: Multiple Sequence Alignment (MSA) is a basic tool for bioinformatics research and analysis. It has been used essenti ..."
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designed and developed a new method, MSACompro, to synergistically incorporate predicted secondary structure, relative solvent accessibility, and residue-residue contact information into the currently most accurate posterior probability-based MSA methods to improve the accuracy of multiple sequence
Results 1 - 10
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