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Computational analysis Section edited by Torsten Schwede

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   Open Access

Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a beta-solenoid structure

Metaxia Vlassi, Katharina Brauns, Miguel A Andrade-Navarro BMC Structural Biology 2013, 13:17 (2 October 2013)

Abstract | Provisional PDF

2.

Research article   Open Access

Detection of persistent organic pollutants binding modes with androgen receptor ligand binding domain by docking and molecular dynamics

Xian Xu, Ji Su, Anna Bizzarri, Salvatore Cannistraro, Ming Liu, Yi Zeng, Wei Chen, Cun Wang BMC Structural Biology 2013, 13:16 (22 September 2013)

Abstract | Full text | PDF | PubMed

3.

Research article   Open Access Highly Accessed

Molecular dynamics simulations on the Tre1 G protein-coupled receptor: exploring the role of the arginine of the NRY motif in Tre1 structure

Margaret M Pruitt, Monica H Lamm, Clark R Coffman BMC Structural Biology 2013, 13:15 (18 September 2013)

Abstract | Full text | PDF | PubMed

4.

Research article   Open Access

Helical ambivalency induced by point mutations

Nicholus Bhattacharjee, Parbati Biswas BMC Structural Biology 2013, 13:9 (15 May 2013)

Abstract | Full text | PDF | ePUB | PubMed

5.

Research article   Open Access Highly Accessed

Localization of putative binding sites for cyclic guanosine monophosphate and the anti-cancer drug 5-fluoro-2′-deoxyuridine-5′-monophosphate on ABCC11 in silico models

Mylène Honorat, Raphaël Terreux, Pierre Falson, Attilio Di Pietro, Charles Dumontet, Lea Payen BMC Structural Biology 2013, 13:7 (6 May 2013)

Abstract | Full text | PDF | ePUB | PubMed

6.

Research article   Open Access Highly Accessed

Structural and functional studies of S-adenosyl-L-methionine binding proteins: a ligand-centric approach

Rajaram Gana, Shruti Rao, Hongzhan Huang, Cathy Wu, Sona Vasudevan BMC Structural Biology 2013, 13:6 (25 April 2013)

Abstract | Full text | PDF | ePUB | PubMed |  Editor’s summary

A new systematic approach for grouping protein structures based upon the type and conformation of the ligand they bind to reveals some unexpected findings and extends the existing structural classification of S-adenosyl-L-13 methionine (SAM) binding proteins

7.

Research article   Open Access Highly Accessed

Disturbance of DNA conformation by the binding of testosterone-based platinum drugs via groove-face and intercalative interactions: a molecular dynamics simulation study

Shanshan Cui, Yan Wang, Guangju Chen BMC Structural Biology 2013, 13:4 (22 March 2013)

Abstract | Full text | PDF | ePUB | PubMed

8.

Research article   Open Access Highly Accessed

The role of Cysteine 6.47 in class A GPCRs

Mireia Olivella, Gianluigi Caltabiano, Arnau Cordomí BMC Structural Biology 2013, 13:3 (15 March 2013)

Abstract | Full text | PDF | ePUB | PubMed |  Editor’s summary

Analysis of G protein-coupled receptor (GPCR) crystal structures and molecular dynamics simulations of model peptides suggests Cys6.47 is the gate keeper of a hydrogen bond network involving residues known to be crucial to receptor activation.

9.

Research article   Open Access Highly Accessed

Designing and benchmarking the MULTICOM protein structure prediction system

Jilong Li, Xin Deng, Jesse Eickholt, Jianlin Cheng BMC Structural Biology 2013, 13:2 (27 February 2013)

Abstract | Full text | PDF | PubMed

10.

Research article   Open Access Highly Accessed

The possible mechanisms of CYP2E1 interactions with HSP90 and the influence of ethanol on them

Volodymyr O Kitam, Oksana V Maksymchuk, Mykola O Chashchyn BMC Structural Biology 2012, 12:33 (17 December 2012)

Abstract | Full text | PDF | PubMed

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