Computational analysis

Section edited by David Burke

This section incorporates all aspects of the methods, applications and analysis of the structure of biological macromolecules incorporating substantial analysis using computational methods.

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  1. Research article

    The C-terminal domain of TPX2 is made of alpha-helical tandem repeats

    TPX2 (Targeting Protein for Xklp2) is essential for spindle assembly, activation of the mitotic kinase Aurora A and for triggering microtubule nucleation. Homologs of TPX2 in Chordata and plants were previousl...

    Luis Sanchez-Pulido, Laurent Perez, Steffen Kuhn, Isabelle Vernos and Miguel A. Andrade-Navarro

    BMC Structural Biology 2016 16:17

    Published on: 26 October 2016

  2. Research article

    3D QSAR, pharmacophore and molecular docking studies of known inhibitors and designing of novel inhibitors for M18 aspartyl aminopeptidase of Plasmodium falciparum

    The Plasmodium falciparum M18 Aspartyl Aminopeptidase (PfM18AAP) is only aspartyl aminopeptidase which is found in the genome of P. falciparum and is essential for its survival. The PfM18AAP enzyme performs vario...

    Madhulata Kumari, Subhash Chandra, Neeraj Tiwari and Naidu Subbarao

    BMC Structural Biology 2016 16:12

    Published on: 17 August 2016

  3. Research article

    Comprehensive analysis of the Co-structures of dipeptidyl peptidase IV and its inhibitor

    We comprehensively analyzed X-ray cocrystal structures of dipeptidyl peptidase IV (DPP-4) and its inhibitor to clarify whether DPP-4 alters its general or partial structure according to the inhibitor used and ...

    Hiroyuki Nojima, Kazuhiko Kanou, Genki Terashi, Mayuko Takeda-Shitaka, Gaku Inoue, Koichiro Atsuda, Chihiro Itoh, Chie Iguchi and Hajime Matsubara

    BMC Structural Biology 2016 16:11

    Published on: 5 August 2016

  4. Research article

    Comparison of human and mouse E-selectin binding to Sialyl-Lewisx

    During inflammation, leukocytes are captured by the selectin family of adhesion receptors lining blood vessels to facilitate exit from the bloodstream. E-selectin is upregulated on stimulated endothelial cells...

    Anne D. Rocheleau, Thong M. Cao, Tait Takitani and Michael R. King

    BMC Structural Biology 2016 16:10

    Published on: 2 July 2016

  5. Software

    Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces

    The term ‘molecular cartography’ encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorith...

    Dimitrios Georgios Kontopoulos, Dimitrios Vlachakis, Georgia Tsiliki and Sofia Kossida

    BMC Structural Biology 2016 16:4

    Published on: 24 February 2016

    The Publisher's Erratum to this article has been published in BMC Structural Biology 2016 16:6

  6. Research Article

    Clustering and percolation in protein loop structures

    High precision protein loop modelling remains a challenge, both in template based and template independent approaches to protein structure prediction.

    Xubiao Peng, Jianfeng He and Antti J. Niemi

    BMC Structural Biology 2015 15:22

    Published on: 29 October 2015

  7. Research article

    The origin of β-strand bending in globular proteins

    Many β-strands are not flat but bend and/or twist. However, although almost all β-strands have a twist, not all have a bend, suggesting that the underlying force(s) driving β-strand bending is distinct from th...

    Kazuo Fujiwara, Shinichi Ebisawa, Yuka Watanabe, Hiromi Fujiwara and Masamichi Ikeguchi

    BMC Structural Biology 2015 15:21

    Published on: 22 October 2015

  8. Research article

    Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study

    Helicobacter pylori is an important factor in the development of diseases such as ulcer and gastric cancer. This bacterium uses a periplasmic transporter, UreI, to deliver urea to the ...

    Javier Cáceres-Delpiano, Jaime Teneb, Rodrigo Mansilla, Apolinaria García and Alexis Salas-Burgos

    BMC Structural Biology 2015 15:11

    Published on: 26 June 2015

  9. Research Article

    A PDB-wide, evolution-based assessment of protein-protein interfaces

    Thanks to the growth in sequence and structure databases, more than 50 million sequences are now available in UniProt and 100,000 structures in the PDB. Rich information about protein-protein interfaces can be...

    Kumaran Baskaran, Jose M Duarte, Nikhil Biyani, Spencer Bliven and Guido Capitani

    BMC Structural Biology 2014 14:22

    Published on: 18 October 2014

  10. Research article

    Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species

    The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the...

    Kirill E. Medvedev, Nikolay A. Alemasov, Yuri N. Vorobjev, Elena V. Boldyreva, Nikolay A. Kolchanov and Dmitry A. Afonnikov

    BMC Structural Biology 2014 14:23

    Published on: 15 October 2014

  11. Research article

    Buried chloride stereochemistry in the Protein Data Bank

    Despite the chloride anion is involved in fundamental biological processes, its interactions with proteins are little known. In particular, we lack a systematic survey of its coordination spheres.

    Oliviero Carugo

    BMC Structural Biology 2014 14:19

    Published on: 23 September 2014

  12. Research article

    A simple method for finding a protein’s ligand-binding pockets

    This paper provides a simple and rapid method for a protein-clustering strategy. The basic idea implemented here is to use computational geometry methods to predict and characterize ligand-binding pockets of a...

    Seyed Majid Saberi Fathi and Jack A Tuszynski

    BMC Structural Biology 2014 14:18

    Published on: 19 July 2014

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