Structural alphabets derived from attractors in conformational space

Background: The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis.Results: A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness.Conclusions: The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics. © 2010 Pandini et al; licensee BioMed Central Ltd

GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet

Motivation: GSATools is a free software package to analyze conformational ensembles and to detect functional motions in proteins by means of a structural alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; and (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. Availability: The C source code of the GSATools, along with a set of pre-compiled binaries, is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. Contact: alessandro.pandini@kcl. ac.uk or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online. © 2013 The Author 2013. Published by Oxford University Press

Tailored graph ensembles as proxies or null models for real networks I: tools for quantifying structure

We study the tailoring of structured random graph ensembles to real networks, with the objective of generating precise and practical mathematical tools for quantifying and comparing network topologies macroscopically, beyond the level of degree statistics. Our family of ensembles can produce graphs with any prescribed degree distribution and any degree-degree correlation function, its control parameters can be calculated fully analytically, and as a result we can calculate (asymptotically) formulae for entropies and complexities, and for information-theoretic distances between networks, expressed directly and explicitly in terms of their measured degree distribution and degree correlations.Comment: 25 pages, 3 figure

Очистка водных сред от микробиологических загрязнений с использованием адсорбентов на основе газобетона

Объект исследования: газобетон (ГОСТ 25485-89), штамм бактерий E. coli ATCC-25922. Цель работы: оценка эффективности использования газобетона для очистки водных сред от микробиологических загрязнений. В процессе исследования проводились оценка гидродинамического сопротивления, определение фильтрующей способности сорбентов в отношении бактерий E. Coli. В результате исследования получены оптимальные фракции сорбента, определены физико-химические характеристики и сорбционные свойства сорбентов. Область применения: водоочистка и водоподготовка в различных отраслях промышленности.Subject of research: aerated concrete (State Standard 25485-89), a strain of the bacteria E. coli ATCC-25922. The main goal of this study was investigation of sorbent on the basis of the aerated concrete for water purification. The study assesses the hydrodynamic resistance, determining the ability of the filter sorbents against the bacteria E. Coli. The research obtained the optimal fraction of the sorbent, determined physico-chemical characteristics and sorption properties of the sorbents. Applications: water purification and water conditioning in various industries

Differential binding studies applying functional protein microarrays and surface plasmon resonance

A variety of different in vivo and in vitro technologies provide comprehensive insights in protein-protein interaction networks. Here we demonstrate a novel approach to analyze, verify and quantify putative interactions between two members of the S100 protein family and 80 recombinant proteins derived from a proteome-wide protein expression library. Surface plasmon resonance (SPR) using Biacore technology and functional protein microarrays were used as two independent methods to study protein-protein interactions. With this combined approach we were able to detect nine calcium-dependent interactions between Arg-Gly-Ser-(RGS)-His6 tagged proteins derived from the library and GST-tagged S100B and S100A6, respectively. For the protein microarray affinity-purified proteins from the expression library were spotted onto modified glass slides and probed with the S100 proteins. SPR experiments were performed in the same setup and in a vice-versa approach reversing analytes and ligands to determine distinct association and dissociation patterns of each positive interaction. Besides already known interaction partners, several novel binders were found independently with both detection methods, albeit analogous immobilization strategies had to be applied in both assays

Efficient SIMD arithmetic modulo a Mersenne number

This paper describes carry-less arithmetic operations modulo an integer 2^M − 1 in the thousand-bit range, targeted at single instruction multiple data platforms and applications where overall throughput is the main performance criterion. Using an implementation on a cluster of PlayStation 3 game consoles a new record was set for the elliptic curve method for integer factorization

On the security of 1024-bit RSA and 160-bit elliptic curve cryptography

Meeting the requirements of NIST’s new cryptographic standard ‘Suite B Cryptography’ means phasing out usage of 1024-bit RSA and 160-bit Elliptic Curve Cryptography (ECC) by the year 2010. This write-up comments on the vulnerability of these systems to an open community attack effort and aims to assess the risk of their continued usage beyond 2010. We conclude that for 1024-bit RSA the risk is small at least until the year 2014, and that 160-bit ECC may safely be used for much longer – with the current state of the art in cryptanalysis we would be surprised if a public effort can make a dent in 160-bit ECC by the year 2020. Our assessment is based on the latest practical data of large scale integer factorization and elliptic curve discrete logarithm computation efforts

Mersenne Factorization Factory

We present work in progress to completely factor seventeen Mersenne numbers using a variant of the special number field sieve where sieving on the algebraic side is shared among the numbers. It is expected that it reduces the overall factoring effort by more than 50%. As far as we know this is the first practical application of Coppersmith’s “factorization factory” idea. Most factorizations used a new double-product approach that led to additional savings in the matrix step