13,298 research outputs found
Measuring the similarity of protein structures by means of the universal similarity metric
Motivation: As an increasing number of protein structures
become available, the need for algorithms that can quantify
the similarity between protein structures increases as well.
Thus, the comparison of proteins’ structures, and their clustering
accordingly to a given similarity measure, is at the core of
today’s biomedical research. In this paper, we show how an
algorithmic information theory inspired Universal Similarity
Metric (USM) can be used to calculate similarities between
protein pairs.The method, besides being theoretically supported,
is surprisingly simple to implement and computationally
efficient.
Results: Structural similarity between proteins in four different
datasets was measured using the USM.The sample employed
represented alpha, beta, alpha–beta, tim–barrel, globins and
serpine protein types. The use of the proposed metric allows
for a correct measurement of similarity and classification of the
proteins in the four datasets.
Availability: All the scripts and programs used for the preparation
of this paper are available at http://www.cs.nott.ac.uk/
~nxk/USM/protocol.html. In that web-page the reader will find
a brief description on how to use the various scripts and
programs.TIC2002-04242-C03-0
Identification of functionally related enzymes by learning-to-rank methods
Enzyme sequences and structures are routinely used in the biological sciences
as queries to search for functionally related enzymes in online databases. To
this end, one usually departs from some notion of similarity, comparing two
enzymes by looking for correspondences in their sequences, structures or
surfaces. For a given query, the search operation results in a ranking of the
enzymes in the database, from very similar to dissimilar enzymes, while
information about the biological function of annotated database enzymes is
ignored.
In this work we show that rankings of that kind can be substantially improved
by applying kernel-based learning algorithms. This approach enables the
detection of statistical dependencies between similarities of the active cleft
and the biological function of annotated enzymes. This is in contrast to
search-based approaches, which do not take annotated training data into
account. Similarity measures based on the active cleft are known to outperform
sequence-based or structure-based measures under certain conditions. We
consider the Enzyme Commission (EC) classification hierarchy for obtaining
annotated enzymes during the training phase. The results of a set of sizeable
experiments indicate a consistent and significant improvement for a set of
similarity measures that exploit information about small cavities in the
surface of enzymes
Towards a Theory of Scale-Free Graphs: Definition, Properties, and Implications (Extended Version)
Although the ``scale-free'' literature is large and growing, it gives neither
a precise definition of scale-free graphs nor rigorous proofs of many of their
claimed properties. In fact, it is easily shown that the existing theory has
many inherent contradictions and verifiably false claims. In this paper, we
propose a new, mathematically precise, and structural definition of the extent
to which a graph is scale-free, and prove a series of results that recover many
of the claimed properties while suggesting the potential for a rich and
interesting theory. With this definition, scale-free (or its opposite,
scale-rich) is closely related to other structural graph properties such as
various notions of self-similarity (or respectively, self-dissimilarity).
Scale-free graphs are also shown to be the likely outcome of random
construction processes, consistent with the heuristic definitions implicit in
existing random graph approaches. Our approach clarifies much of the confusion
surrounding the sensational qualitative claims in the scale-free literature,
and offers rigorous and quantitative alternatives.Comment: 44 pages, 16 figures. The primary version is to appear in Internet
Mathematics (2005
An optimized TOPS+ comparison method for enhanced TOPS models
This article has been made available through the Brunel Open Access Publishing Fund.Background
Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. Previously we have discussed the basic mechanisms of our novel method for structure comparison based on our TOPS+ model (Topological descriptions of Protein Structures Enhanced with Ligand Information). In this paper we show how these results can be significantly improved using parameter optimization, and we call the resulting optimised TOPS+ method as advanced TOPS+ comparison method i.e. advTOPS+.
Results
We have developed a TOPS+ string model as an improvement to the TOPS [1-3] graph model by considering loops as secondary structure elements (SSEs) in addition to helices and strands, representing ligands as first class objects, and describing interactions between SSEs, and SSEs and ligands, by incoming and outgoing arcs, annotating SSEs with the interaction direction and type. Benchmarking results of an all-against-all pairwise comparison using a large dataset of 2,620 non-redundant structures from the PDB40 dataset [4] demonstrate the biological significance, in terms of SCOP classification at the superfamily level, of our TOPS+ comparison method.
Conclusions
Our advanced TOPS+ comparison shows better performance on the PDB40 dataset [4] compared to our basic TOPS+ method, giving 90 percent accuracy for SCOP alpha+beta; a 6 percent increase in accuracy compared to the TOPS and basic TOPS+ methods. It also outperforms the TOPS, basic TOPS+ and SSAP comparison methods on the Chew-Kedem dataset [5], achieving 98 percent accuracy. Software Availability: The TOPS+ comparison server is available at http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/.This article is available through the Brunel Open Access Publishing Fun
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