TITLE

Search Strategies in Structural Bioinformatics

AUTHOR(S)
Oakley, Mark T.; Barthel, Daniel; Bykov, Yuri; Garibaldi, Jonathan M.; Burke, Edmund K.; Krasnogor, Natalio; Hirst, Jonathan D.
PUB. DATE
June 2008
SOURCE
Current Protein & Peptide Science;Jun2008, Vol. 9 Issue 3, p260
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Optimisation problems pervade structural bioinformatics. In this review, we describe recent work addressing a selection of bioinformatics challenges. We begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity. We then turn to research into de novo protein structure prediction, in which structures are generated from first principles. In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled. We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm. One strategy to reduce the size of the search space is to restrict the protein chain to sites on a regular lattice. In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.
ACCESSION #
33767961

 

Related Articles

  • Exploring Dimensionality, Systematic Mutations and Number of Contacts in Simple HP ab-initio Protein Folding Using a Blackboard-based Agent Platform. Beltr�n, Hiram I.; Rojo-Dom�nguez, Arturo; S�nchez Guti�rrez, M�ximo Eduardo; Gonz�lez P�rez, Pedro Pablo // International Journal of Information Technology;2009, Vol. 5 Issue 3, p178 

    A computational platform is presented in this contribution. It has been designed as a virtual laboratory to be used for exploring optimization algorithms in biological problems. This platform is built on a blackboard-based agent architecture. As a test case, the version of the platform presented...

  • Recent developments in the MAFFT multiple sequence alignment program. Katoh, Kazutaka; Toh, Hiroyuki // Briefings in Bioinformatics;Jul2008, Vol. 9 Issue 4, p286 

    The accuracy and scalability of multiple sequence alignment (MSA) of DNAs and proteins have long been and are still important issues in bioinformatics. To rapidly construct a reasonable MSA, we developed the initial version of the MAFFT program in 2002. MSA software is now facing greater...

  • Combining Evidence, Specificity, and Proximity towards the Normalization of Gene Ontology Terms in Text. Gaudan, S.; Yepes, A. Jimeno; Lee, V.; Rebholz-Schuhmann, D. // EURASIP Journal on Bioinformatics & Systems Biology;2008, Special section p1 

    Structured information provided by manual annotation of proteins with Gene Ontology concepts represents a high-quality reliable data source for the research community. However, a limited scope of proteins is annotated due to the amount of human resources required to fully annotate each...

  • HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins. Rezaei-Ghaleh, Nasrollah; Klama, Frederik; Munari, Francesca; Zweckstetter, Markus // Bioinformatics;4/1/2015, Vol. 31 Issue 7, p1319 

    Motivation: A large fraction of eukaryotic proteins contain unstructured tails or linkers. The presence of flexible regions allows these systems to experience a high level of mobility facilitating their biological function. The complex nature of protein rotation in such flexible modular systems...

  • Solubis: optimize your protein. De Baets, Greet; Van Durme, Joost; van der Kant, Rob; Schymkowitz, Joost; Rousseau, Frederic // Bioinformatics;8/1/2015, Vol. 31 Issue 15, p2580 

    Motivation: Protein aggregation is associated with a number of protein misfolding diseases and is a major concern for therapeutic proteins. Aggregation is caused by the presence of aggregationprone regions (APRs) in the amino acid sequence of the protein. The lower the aggregation propensity of...

  • Structural Genomics.  // Encyclopedic Reference of Molecular Pharmacology;2004, p890 

    An encyclopedia entry for structural genomics is presented. Structural genomics use high-throughput structure determination and computational analysis to provide structures of three-dimensional models of tractable proteins. It determines many protein structure and to exploit the solved...

  • CMASA: an accurate algorithm for detecting local protein structural similarity and its application to enzyme catalytic site annotation. Gong-Hua Li; Jing-Fei Huang // BMC Bioinformatics;2010, Vol. 11, p439 

    Background: The rapid development of structural genomics has resulted in many "unknown function" proteins being deposited in Protein Data Bank (PDB), thus, the functional prediction of these proteins has become a challenge for structural bioinformatics. Several sequence-based and structure-based...

  • Structural Biology, Protein Conformations and Drug Designing. Kishan, K. V. Radha // Current Protein & Peptide Science;Aug2007, Vol. 8 Issue 4, p376 

    Structure based drug designing is now a popular technique used for increasing the speed of drug designing process. This was made possible by the availability of many protein structures which helped in developing tools to understand the structure function relationships, automated docking and...

  • Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be. Schaefer, Christian; Schlessinger, Avner; Rost, Burkhard // Bioinformatics;Mar2010, Vol. 26 Issue 5, p625 

    Motivation: The mutation of amino acids often impacts protein function and structure. Mutations without negative effect sustain evolutionary pressure. We study a particular aspect of structural robustness with respect to mutations: regular protein secondary structure and natively unstructured...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics