MCQ4Structures to compute similarity of molecule structures

Zok, Tomasz; Popenda, Mariusz; Szachniuk, Marta
September 2014
Central European Journal of Operations Research;Sep2014, Vol. 22 Issue 3, p457
Academic Journal
Comparison of molecular structures in order to identify their similarity is an important step in solving various problems derived from computational biology, like structure alignment and modelling, motif search or clustering. Thus, there is a constant need for the development of good measures to determine distances between the structures and tools to display these distances in an easily interpretable form. In the paper we present MCQ4Structures, a new method and tool for structural similarity computation based on molecule tertiary structure representation in torsional angle space. We discuss its unique features as compared with the other measures, including RMSD and LGA, and we show its experimental use in comparison of a number of 3D structures as well as evaluation of models predicted within RNA-Puzzles contest. MCQ4Structures software is available as a free Java WebStart application at: . The source code licensed under BSD can be downloaded from the same website.


Related Articles

  • Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences. Xiaohui Cai; Haiyan Hu; Xiaoman Shawn Li // Bioinformatics;Aug2007, Vol. 23 Issue 15, p2013 

    Summary: Tree Gibbs Sampler is a software for identifying motifs by simultaneously using the motif overrepresentation property and the motif evolutionary conservation property. It identifies motifs without depending on pre-aligned orthologous sequences, which makes it useful for the extraction...

  • Genetic Algorithm Based Probabilistic Motif Discovery in Unaligned Biological Sequences. Hemalatha, M.; Vivekanandan, K. // Journal of Computer Science;2008, Vol. 4 Issue 8, p625 

    Finding motif in biosequences is the most important primitive operation in computational biology. There are many computational requirements for a motif discovery algorithm such as computer memory space requirement and computational complexity. To overcome the complexity of motif discovery, we...

  • Efficient sequential and parallel algorithms for planted motif search. Nicolae, Marius; Rajasekaran, Sanguthevar // BMC Bioinformatics;2014, Vol. 15 Issue 1, p2 

    Background Motif searching is an important step in the detection of rare events occurring in a set of DNA or protein sequences. One formulation of the problem is known as (l, d)-motif search or Planted Motif Search (PMS). In PMS we are given two integers l and d and n biological sequences. We...

  • Discriminative motif analysis of high-throughput dataset. Yao, Zizhen; MacQuarrie, Kyle L.; Fong, Abraham P.; Tapscott, Stephen J.; Ruzzo, Walter L.; Gentleman, Robert C. // Bioinformatics;Mar2014, Vol. 30 Issue 6, p775 

    Motivation: High-throughput ChIP-seq studies typically identify thousands of peaks for a single transcription factor (TF). It is common for traditional motif discovery tools to predict motifs that are statistically significant against a naïve background distribution but are of questionable...

  • Identifying Y-shape motifs in the San rock art of the Limpopo-Shashi confluence area, southern Africa: new painted and ethnographic evidence. Blundell, Geoffrey; Eastwood, Edward B. // South African Journal of Science;Jul/Aug2001, Vol. 97 Issue 7/8, p305 

    Presents painted and ethnographic evidence identifying Y-shape motifs in the San rock art of the Limpopo-Shashi confluence area in southern Africa. Account of a related interpretation of the Y-shape motifs; Description of the site; Identification of the Y-shape motifs. INSET: New initiatives...

  • Motif statistics and spike correlations in neuronal networks. Yu Hu; Trousdale, James; Josić, Krěsimir; Shea-Brown, Eric // BMC Neuroscience;2012 Supplement 1, Vol. 13 Issue Suppl 1, p1 

    An abstract of the article "Motif statistics and spike correlations in neuronal networks," by Yu Hu, James Trousdale, Kresimir Josic, Eric Shea-Brown is presented.

  • Focus on Dance Careers: Labanotation. Bartlett, Katie // Dancing Times;May2005, Vol. 95 Issue 1137, p94 

    Focuses on the opportunities for an individual with labanotation knowledge to work with dancers and choreographers when recording or reconstructing a score and lecturing in the field of dance education. Strategy to gain qualifications in learning labanotation; Analysis of all kinds of human...

  • L1Tc non-LTR retrotransposons from Trypanosoma cruzi contain a functional viral-like self-cleaving 2A sequence in frame with the active proteins they encode. Heras, S. R.; Thomas, M. C.; García-Canadas, M.; De Felipe, P.; García-Pérez, J. L.; Ryan, M. D.; López, M. C. // Cellular & Molecular Life Sciences;Jun2006, Vol. 63 Issue 12, p1449 

    A comparative analysis of 40 Trypanosoma cruzi L1Tc elements showed that the 2A self-cleaving sequence described in viruses is present in them. Of these elements, 72% maintain the canonical 2A motif (DxExNPGP). A high percentage has a conserved point mutation within the motif that has not been...

  • Screening of Feral and Wood Pigeons for Viruses Harbouring a Conserved Mobile Viral Element: Characterization of Novel Astroviruses and Picornaviruses. Kofstad, Tone; Jonassen, Christine M. // PLoS ONE;2011, Vol. 6 Issue 10, p1 

    A highly conserved RNA-motif of yet unknown function, called stem-loop-2-like motif (s2m), has been identified in the 39 end of the genomes of viruses belonging to different RNA virus families which infect a broad range of mammal and bird species, including Astroviridae, Picornaviridae,...


Read the Article


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

Try another library?
Sign out of this library

Other Topics