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, USA

4 October 2012

  1. Research

    Modeling protein conformational transitions by a combination of coarse-grained normal mode analysis and robotics-inspired methods

    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...

    Ibrahim Al-Bluwi, Marc Vaisset, Thierry Siméon and Juan Cortés

    BMC Structural Biology 2013 13(Suppl 1):S2

    Published on: 8 November 2013

  2. Research

    Enhancement of accuracy and efficiency for RNA secondary structure prediction by sequence segmentation and MapReduce

    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...

    Boyu Zhang, Daniel T Yehdego, Kyle L Johnson, Ming-Ying Leung and Michela Taufer

    BMC Structural Biology 2013 13(Suppl 1):S3

    Published on: 8 November 2013

  3. Research

    Estimating loop length from CryoEM images at medium resolutions

    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...

    Andrew McKnight, Dong Si, Kamal Al Nasr, Andrey Chernikov, Nikos Chrisochoides and Jing He

    BMC Structural Biology 2013 13(Suppl 1):S5

    Published on: 8 November 2013

  4. Research

    An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility

    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...

    Brian G Godshall, Yisheng Tang, Wenjie Yang and Brian Y Chen

    BMC Structural Biology 2013 13(Suppl 1):S10

    Published on: 8 November 2013

  5. Research

    DINC: A new AutoDock-based protocol for docking large ligands

    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...

    Ankur Dhanik, John S McMurray and Lydia E Kavraki

    BMC Structural Biology 2013 13(Suppl 1):S11

    Published on: 8 November 2013