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Structural analysis

This section incorporates all aspects of structural analysis including but not limited to: methods and applications for the analysis of biological structures, protein structural and biophysical analysis, and structure-based drug design.

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1.

Methodology article   Open Access

Protein structure based prediction of catalytic residues

J Eduardo Fajardo, Andras Fiser BMC Bioinformatics 2013, 14:63 (22 February 2013)

Abstract | Provisional PDF | PubMed

2.

Software   Open Access

ClusCo: clustering and comparison of protein models

Michal Jamroz, Andrzej Kolinski BMC Bioinformatics 2013, 14:62 (22 February 2013)

Abstract | Provisional PDF | PubMed

3.

Methodology article   Open Access Highly Accessed

Predictive modeling of anti-malarial molecules inhibiting apicoplast formation

Salma Jamal, Vinita Periwal, Open Source Drug Discovery Consortium , Vinod Scaria BMC Bioinformatics 2013, 14:55 (15 February 2013)

Abstract | Provisional PDF | PubMed

4.

Research article   Open Access

PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity

Patricio Oyarzún, Jonathan J Ellis, Mikael Bodén, Bo¿tjan Kobe BMC Bioinformatics 2013, 14:52 (14 February 2013)

Abstract | Provisional PDF | PubMed

5.

Research article   Open Access Highly Accessed

Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information

Bharat Panwar, Sudheer Gupta, Gajendra P S Raghava BMC Bioinformatics 2013, 14:44 (7 February 2013)

Abstract | Full text | PDF | PubMed

6.

Research article   Open Access Highly Accessed

Predicting PDZ domain mediated protein interactions from structure

Shirley Hui, Xiang Xing, Gary D Bader BMC Bioinformatics 2013, 14:27 (21 January 2013)

Abstract | Provisional PDF | PubMed

7.

Methodology article   Open Access Highly Accessed

MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Ca only models, Alternative alignments, and Non-sequential alignments

Shintaro Minami, Kengo Sawada, George Chikenji BMC Bioinformatics 2013, 14:24 (18 January 2013)

Abstract | Provisional PDF | PubMed

8.

Research article   Open Access

Machine learning methods can replace 3D profile method in classification of amyloidogenic hexapeptides

Jerzy Stanislawski, Malgorzata Kotulska, Olgierd Unold BMC Bioinformatics 2013, 14:21 (17 January 2013)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

9.

Methodology article   Open Access Highly Accessed

An improved method to detect correct protein folds using partial clustering

Jianjun Zhou, David S Wishart BMC Bioinformatics 2013, 14:11 (16 January 2013)

Abstract | Provisional PDF | PubMed |  Editor’s summary

HS-Forest performs rapid, but incomplete, clustering for decoy selection in protein structure prediction, generating multiple independent trees for a consensus result by means of local sensitive hashing. 

10.

Research article   Open Access Highly Accessed

Protein interface classification by evolutionary analysis

Jose M Duarte, Adam Srebniak, Martin A Schärer, Guido Capitani BMC Bioinformatics 2012, 13:334 (22 December 2012)

Abstract | Full text | PDF | PubMed

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