Bit-vector algorithms for binary constraint satisfaction and subgraph isomorphism
JR Ullmann - Journal of Experimental Algorithmics (JEA), 2011 - dl.acm.org
A solution to a binary constraint satisfaction problem is a set of discrete values, one in each
of a given set of domains, subject to constraints that allow only prescribed pairs of values in …
of a given set of domains, subject to constraints that allow only prescribed pairs of values in …
Modulating glycoside hydrolase activity between hydrolysis and transfer reactions using an evolutionary approach
The proteins within the CAZy glycoside hydrolase family GH13 catalyze the hydrolysis of
polysaccharides such as glycogen and starch. Many of these enzymes also perform …
polysaccharides such as glycogen and starch. Many of these enzymes also perform …
Using graph indices for the analysis and comparison of chemical datasets
D Fourches, A Tropsha - Molecular Informatics, 2013 - Wiley Online Library
In cheminformatics, compounds are represented as points in multidimensional space of
chemical descriptors. When all pairs of points found within certain distance threshold in the …
chemical descriptors. When all pairs of points found within certain distance threshold in the …
PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies
A Gandhimathi, AG Nair… - Nucleic acids research, 2012 - academic.oup.com
Accurate structure-based sequence alignments of distantly related proteins are crucial in
gaining insight about protein domains that belong to a superfamily. The PASS2 database …
gaining insight about protein domains that belong to a superfamily. The PASS2 database …
An amino acid code for irregular and mixed protein packing
H Joo, AG Chavan, KJ Fraga… - … : Structure, Function, and …, 2015 - Wiley Online Library
To advance our understanding of protein tertiary structure, the development of the knob‐
socket model is completed in an analysis of the packing in irregular coil and turn secondary …
socket model is completed in an analysis of the packing in irregular coil and turn secondary …
Smolign: a spatial motifs-based protein multiple structural alignment method
Availability of an effective tool for protein multiple structural alignment (MSTA) is essential for
discovery and analysis of biologically significant structural motifs that can help solve …
discovery and analysis of biologically significant structural motifs that can help solve …
Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure
Motivation: While protein secondary structure is well understood, representing the repetitive
nature of tertiary packing in proteins remains difficult. We have developed a construct called …
nature of tertiary packing in proteins remains difficult. We have developed a construct called …
Functional neighbors: Inferring relationships between nonhomologous protein families using family-specific packing motifs
We describe a new approach for inferring the functional relationships between
nonhomologous protein families by looking at statistical enrichment of alternative function …
nonhomologous protein families by looking at statistical enrichment of alternative function …
Ballast: A Ball-based Algorithm for Structural Motifs
Structural motifs encapsulate local sequence-structure-function relationships characteristic
of related proteins, enabling the prediction of functional characteristics of new proteins …
of related proteins, enabling the prediction of functional characteristics of new proteins …
Mining Discriminative Subgraph Patterns from Structural Data
N **, W Wang - Data Mining and Knowledge Discovery for Big Data …, 2014 - Springer
Many scientific applications search for patterns in complex structural information; when this
structural information is represented as graphs, a powerful tool is efficiently mining …
structural information is represented as graphs, a powerful tool is efficiently mining …