Now showing items 1-10 of 114
MassSorter: a tool for administrating and analyzing data from mass spectrometry experiments on proteins with known amino acid sequences
(BioMed Central, 2006-01-26)
Background: Proteomics is the study of the proteome, and is critical to the understanding of cellular processes. Two central and related tasks of proteomics are protein identification and protein characterization. Many ...
Managing spatial selections with contextual snapshots
Spatial selections are a ubiquitous concept in visualization. By localizing particular features, they can be analysed and compared in different views. However, the semantics of such selections often depend on specific ...
A geometry-based generic predictor for catalytic and allosteric sites
(Oxford University Press, 2011)
An important aspect of understanding protein allostery, and of artificial effector design, is the characterization and prediction of substrate- and effector-binding sites. To find binding sites in allosteric enzymes, many ...
Computing minimal triangulation in Time o(n^2.376)
(SIAM Journals, 2005)
On a New Method for Derivative Free Optimization
A new derivative-free optimization method for unconstrained optimization of partially separable functions is presented. Using average curvature information computed from sampled function values the method generates an ...
A type system for counting instances of software components
We identify an abstract language for component software based on process algebra. Besides the usual operators for sequential, alternative and parallel composition, it has primitives for instantiating components and for ...
FreeContact: fast and free software for protein contact prediction from residue co-evolution
(BioMed Central, 2014-03-26)
Background: 20 years of improved technology and growing sequences now renders residue-residue contact constraints in large protein families through correlated mutations accurate enough to drive de novo predictions of protein ...
A Statistics-based Dimension Reduction of the Space of Path Line Attributes for Interactive Visual Flow Analysis
Recent work has shown the great potential of interactive flow analysis by the analysis of path lines. The choice of suitable attributes, describing the path lines, is, however, still an open question. This paper addresses ...
TMM@: a web application for the analysis of transmembrane helix mobility
(BioMed Central, 2007-07-02)
Background: To understand the mechanism by which a protein transmits a signal through the cell membrane, an understanding of the flexibility of its transmembrane (TM) region is essential. Normal Mode Analysis (NMA) has ...
Predicting Gene Regulatory Elements in Silico on a Genomic Scale
(Cold Spring Harbor Laboratory Press, 1998-05-18)
We performed a systematic analysis of gene upstream regions in the yeast genome for occurrences of regular expression-type patterns with the goal of identifying potential regulatory elements. To achieve this goal, we have ...