82,626 research outputs found
Protein multi-scale organization through graph partitioning and robustness analysis: Application to the myosin-myosin light chain interaction
Despite the recognized importance of the multi-scale spatio-temporal
organization of proteins, most computational tools can only access a limited
spectrum of time and spatial scales, thereby ignoring the effects on protein
behavior of the intricate coupling between the different scales. Starting from
a physico-chemical atomistic network of interactions that encodes the structure
of the protein, we introduce a methodology based on multi-scale graph
partitioning that can uncover partitions and levels of organization of proteins
that span the whole range of scales, revealing biological features occurring at
different levels of organization and tracking their effect across scales.
Additionally, we introduce a measure of robustness to quantify the relevance of
the partitions through the generation of biochemically-motivated surrogate
random graph models. We apply the method to four distinct conformations of
myosin tail interacting protein, a protein from the molecular motor of the
malaria parasite, and study properties that have been experimentally addressed
such as the closing mechanism, the presence of conserved clusters, and the
identification through computational mutational analysis of key residues for
binding.Comment: 13 pages, 7 Postscript figure
On the Complexity of Reconstructing Chemical Reaction Networks
The analysis of the structure of chemical reaction networks is crucial for a
better understanding of chemical processes. Such networks are well described as
hypergraphs. However, due to the available methods, analyses regarding network
properties are typically made on standard graphs derived from the full
hypergraph description, e.g.\ on the so-called species and reaction graphs.
However, a reconstruction of the underlying hypergraph from these graphs is not
necessarily unique. In this paper, we address the problem of reconstructing a
hypergraph from its species and reaction graph and show NP-completeness of the
problem in its Boolean formulation. Furthermore we study the problem
empirically on random and real world instances in order to investigate its
computational limits in practice
BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction
A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN
Statistical Mechanics of maximal independent sets
The graph theoretic concept of maximal independent set arises in several
practical problems in computer science as well as in game theory. A maximal
independent set is defined by the set of occupied nodes that satisfy some
packing and covering constraints. It is known that finding minimum and
maximum-density maximal independent sets are hard optimization problems. In
this paper, we use cavity method of statistical physics and Monte Carlo
simulations to study the corresponding constraint satisfaction problem on
random graphs. We obtain the entropy of maximal independent sets within the
replica symmetric and one-step replica symmetry breaking frameworks, shedding
light on the metric structure of the landscape of solutions and suggesting a
class of possible algorithms. This is of particular relevance for the
application to the study of strategic interactions in social and economic
networks, where maximal independent sets correspond to pure Nash equilibria of
a graphical game of public goods allocation
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