• Issue

    Proteins: Structure, Function, and Bioinformatics: Volume 83, Issue 8

    1375-1554
    August 2015
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Articles

Allosteric sites can be identified based on the residue–residue interaction energy difference

Xiaomin Ma,  Yifei Qi,  Luhua Lai, 
  • Pages: 1375-1384
  • First Published: 03 September 2014

AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences

Gideon D. Lapidoth,  Dror Baran,  Gabriele M. Pszolla,  Christoffer Norn,  Assaf Alon,  Michael D. Tyka,  Sarel J. Fleishman, 
  • Pages: 1385-1406
  • First Published: 09 February 2015

The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein

Yu-Wen Huang,  Chih-Min Chang,  Chi-Wen Lee,  Jenn-Kang Hwang, 
  • Pages: 1407-1413
  • First Published: 03 April 2015

Molecular modeling of the binding modes of the iron-sulfur protein to the Jac1 co-chaperone from Saccharomyces cerevisiae by all-atom and coarse-grained approaches

Magdalena A. Mozolewska,  Paweł Krupa,  Harold A. Scheraga,  Adam Liwo, 
  • Pages: 1414-1426
  • First Published: 13 May 2015
Open Access

Accuracy issues involved in modeling in vivo protein structures using PM7

Benjamin P. Martin,  Christopher J. Brandon,  James J. P. Stewart,  Sonja B. Braun-Sand, 
  • Pages: 1427-1435
  • First Published: 13 May 2015

CONFOLD: Residue-residue contact-guided ab initio protein folding

Badri Adhikari,  Debswapna Bhattacharya,  Renzhi Cao,  Jianlin Cheng, 
  • Pages: 1436-1449
  • First Published: 13 May 2015

Clustering and visualizing similarity networks of membrane proteins

Geng-Ming Hu,  Te-Lun Mai,  Chi-Ming Chen, 
  • Pages: 1450-1461
  • First Published: 25 May 2015

Domain position prediction based on sequence information by using fuzzy mean operator

Runyu Jing,  Jing Sun,  Yuelong Wang,  Menglong Li, 
  • Pages: 1462-1469
  • First Published: 25 May 2015
Open Access

A less-biased analysis of metalloproteins reveals novel zinc coordination geometries

Sen Yao,  Robert M. Flight,  Eric C. Rouchka,  Hunter N. B. Moseley, 
  • Pages: 1470-1487
  • First Published: 25 May 2015

Equilibrium transitions between side-chain conformations in leucine and isoleucine

Diego Caballero,  W. Wendell Smith,  Corey S. O'Hern,  Lynne Regan, 
  • Pages: 1488-1499
  • First Published: 28 May 2015

BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles

Daniel K. Putnam,  Brian E. Weiner,  Nils Woetzel,  Edward W. Lowe Jr.,  Jens Meiler, 
  • Pages: 1500-1512
  • First Published: 27 May 2015

Co-evolutionary analysis implies auxiliary functions of HSP110 in Plasmodium falciparum

Deeksha Bhartiya,  Balasubramanian Chandramouli,  Niti Kumar, 
  • Pages: 1513-1525
  • First Published: 06 June 2015

Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase

Ryan L. Slack,  Justin Spiriti,  Jinwoo Ahn,  Michael A. Parniak,  Daniel M. Zuckerman,  Rieko Ishima, 
  • Pages: 1526-1538
  • First Published: 09 June 2015

Structure Notes

The three-dimensional structure of “Lonely Guy” from Claviceps purpurea provides insights into the phosphoribohydrolase function of Rossmann fold-containing lysine decarboxylase-like proteins

Lenka Dzurová,  Federico Forneris,  Simone Savino,  Petr Galuszka,  Josef Vrabka,  Ivo Frébort, 
  • Pages: 1539-1546
  • First Published: 25 May 2015

Structural characterization of AtmS13, a putative sugar aminotransferase involved in indolocarbazole AT2433 aminopentose biosynthesis

Shanteri Singh,  Youngchang Kim,  Fengbin Wang,  Lance Bigelow,  Michael Endres,  Madan K. Kharel,  Gyorgy Babnigg,  Craig A. Bingman,  Andrzej Joachimiak,  Jon S. Thorson,  George N. Phillips Jr., 
  • Pages: 1547-1554
  • First Published: 09 June 2015