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Volume 13 Supplement 1

Selected articles from the Computational Structural Bioinformatics Workshop 2012


Edited by Jing He, Amarda Shehu, Nurit Haspel and Brian Chen

Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. Articles have undergone the journal's standard review process for supplements. The Supplement Editors declare that they have no competing interests.

Computational Structural Bioinformatics Workshop 2012.

Philadelphia, PA, USA4 October 2012

  1. Obtaining atomic-scale information about large-amplitude conformational transitions in proteins is a challenging problem for both experimental and computational methods. Such information is, however, important...

    Authors: Ibrahim Al-Bluwi, Marc Vaisset, Thierry Siméon and Juan Cortés
    Citation: BMC Structural Biology 2013 13(Suppl 1):S2
  2. Ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Their secondary structures are crucial for the RNA functionality, and the prediction...

    Authors: Boyu Zhang, Daniel T Yehdego, Kyle L Johnson, Ming-Ying Leung and Michela Taufer
    Citation: BMC Structural Biology 2013 13(Suppl 1):S3
  3. Elucidating the native structure of a protein molecule from its sequence of amino acids, a problem known as de novo structure prediction, is a long standing challenge in computational structural biology. Diffi...

    Authors: Sameh Saleh, Brian Olson and Amarda Shehu
    Citation: BMC Structural Biology 2013 13(Suppl 1):S4
  4. De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the lo...

    Authors: Andrew McKnight, Dong Si, Kamal Al Nasr, Andrey Chernikov, Nikos Chrisochoides and Jing He
    Citation: BMC Structural Biology 2013 13(Suppl 1):S5
  5. Conformational flexibility creates errors in the comparison of protein structures. Even small changes in backbone or sidechain conformation can radically alter the shape of ligand binding cavities. These chang...

    Authors: Brian G Godshall, Yisheng Tang, Wenjie Yang and Brian Y Chen
    Citation: BMC Structural Biology 2013 13(Suppl 1):S10
  6. Using the popular program AutoDock, computer-aided docking of small ligands with 6 or fewer rotatable bonds, is reasonably fast and accurate. However, docking large ligands using AutoDock's recommended standar...

    Authors: Ankur Dhanik, John S McMurray and Lydia E Kavraki
    Citation: BMC Structural Biology 2013 13(Suppl 1):S11