122 research outputs found
New statistical potential for quality assessment of protein models and a survey of energy functions
No full textAbstract Background Scoring functions, such as molecular mechanic forcefields and statistical potentials are fundamentally important tools in protein structure modeling and quality assessment. Results The performances of a number of publicly available scoring functions are compared with a statistical rigor, with an emphasis on knowledge-based potentials. We explored the effect on accuracy of alternative choices for representing interaction center types and other features of scoring functions, such as using information on solvent accessibility, on torsion angles, accounting for secondary structure preferences and side chain orientation. Partially based on the observations made, we present a novel residue based statistical potential, which employs a shuffled reference state definition and takes into account the mutual orientation of residue side chains. Atom- and residue-level statistical potentials and Linux executables to calculate the energy of a given protein proposed in this work can be downloaded from http://www.fiserlab.org/potentials. Conclusions Among the most influential terms we observed a critical role of a proper reference state definition and the benefits of including information about the microenvironment of interaction centers. Molecular mechanical potentials were also tested and found to be over-sensitive to small local imperfections in a structure, requiring unfeasible long energy relaxation before energy scores started to correlate with model quality.</p
Identifying functionally informative evolutionary sequence profiles
No full textAbstract
Motivation
Multiple sequence alignments (MSAs) can provide essential input to many bioinformatics applications, including protein structure prediction and functional annotation. However, the optimal selection of sequences to obtain biologically informative MSAs for such purposes is poorly explored, and has traditionally been performed manually.
Results
We present Selection of Alignment by Maximal Mutual Information (SAMMI), an automated, sequence-based approach to objectively select an optimal MSA from a large set of alternatives sampled from a general sequence database search. The hypothesis of this approach is that the mutual information among MSA columns will be maximal for those MSAs that contain the most diverse set possible of the most structurally and functionally homogeneous protein sequences. SAMMI was tested to select MSAs for functional site residue prediction by analysis of conservation patterns on a set of 435 proteins obtained from protein–ligand (peptides, nucleic acids and small substrates) and protein–protein interaction databases.
Availability and implementation
A freely accessible program, including source code, implementing SAMMI is available at https://github.com/nelsongil92/SAMMI.git.
Supplementary information
Supplementary data are available at Bioinformatics online.
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A Modular Perspective of Protein Structures: Application to Fragment Based Loop Modeling
No full textProtLID, a Residue-Based Pharmacophore Approach to Identify Cognate Protein Ligands in the Immunoglobulin Superfamily
No full textExploiting PUF Variation to Detect Fault Injection Attacks
No full textThe massive deployment of Internet of Things (IoT) devices makes them vulnerable against physical tampering attacks, such as fault injection. These kind of hardware attacks are very popular as they typically do not require complex equipment or high expertise. Hence, it is important that IoT devices are protected against them. In this work, we present a novel fault injection attack detector with high flexibility and low overhead. Our solution is based on the reuse of a security primitive used in many IoT devices, i.e., ring oscillator (RO) physically unclonable function (PUF). Our results show that we obtain a high detection effectiveness and no false alarms against most popular fault injection attacks based on voltage and clock manipulations.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Computer EngineeringQuantum & Computer Engineerin
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