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Structural analysis

Section edited by Lukasz Kurgan

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. It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein mode...

    Authors: Renzhi Cao, Zheng Wang, Yiheng Wang and Jianlin Cheng

    Citation: BMC Bioinformatics 2014 15:120

    Content type: Software

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  2. Bacteroides spp. form a significant part of our gut microbiome and are well known for optimized metabolism of diverse polysaccharides. Initial analysis of the archetypal Bacteroides thetaiotaomicron genome identi...

    Authors: Anna Sheydina, Ruth Y Eberhardt, Daniel J Rigden, Yuanyuan Chang, Zhanwen Li, Christian C Zmasek, Herbert L Axelrod and Adam Godzik

    Citation: BMC Bioinformatics 2014 15:112

    Content type: Research article

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  3. The identification of functionally or structurally important non-conserved residue sites in protein MSAs is an important challenge for understanding the structural basis and molecular mechanism of protein func...

    Authors: Mehmet Gültas, Güncel Düzgün, Sebastian Herzog, Sven Joachim Jäger, Cornelia Meckbach, Edgar Wingender and Stephan Waack

    Citation: BMC Bioinformatics 2014 15:96

    Content type: Methodology article

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  4. The accumulation of protein structural data occurs more rapidly than it can be characterized by traditional laboratory means. This has motivated widespread efforts to predict enzyme function computationally. T...

    Authors: Brett Hanson, Charles Westin, Mario Rosa, Alexander Grier, Mikhail Osipovitch, Madolyn L MacDonald, Greg Dodge, Paule M Boli, Cyprian W Corwin, Haeja Kessler, Talia McKay, Herbert J Bernstein and Paul A Craig

    Citation: BMC Bioinformatics 2014 15:87

    Content type: Software

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  5. It is well known that the development of cancer is caused by the accumulation of somatic mutations within the genome. For oncogenes specifically, current research suggests that there is a small set of "driver"...

    Authors: Gregory A Ryslik, Yuwei Cheng, Kei-Hoi Cheung, Yorgo Modis and Hongyu Zhao

    Citation: BMC Bioinformatics 2014 15:86

    Content type: Methodology article

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  6. Transient protein-protein interactions (PPIs), which underly most biological processes, are a prime target for therapeutic development. Immense progress has been made towards computational prediction of PPIs u...

    Authors: Calem J Bendell, Shalon Liu, Tristan Aumentado-Armstrong, Bogdan Istrate, Paul T Cernek, Samuel Khan, Sergiu Picioreanu, Michael Zhao and Robert A Murgita

    Citation: BMC Bioinformatics 2014 15:82

    Content type: Research article

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  7. Recent efforts in HIV-1 vaccine design have focused on immunogens that evoke potent neutralizing antibody responses to a broad spectrum of viruses circulating worldwide. However, the development of effective v...

    Authors: Mark C Evans, Pham Phung, Agnes C Paquet, Anvi Parikh, Christos J Petropoulos, Terri Wrin and Mojgan Haddad

    Citation: BMC Bioinformatics 2014 15:77

    Content type: Research article

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  8. CA_C2195 from Clostridium acetobutylicum is a protein of unknown function. Sequence analysis predicted that part of the protein contained a metallopeptidase-related domain. There are over 200 homologs of similar ...

    Authors: Debanu Das, Alexey G Murzin, Neil D Rawlings, Robert D Finn, Penelope Coggill, Alex Bateman, Adam Godzik and L Aravind

    Citation: BMC Bioinformatics 2014 15:75

    Content type: Research article

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  9. RNA molecules, especially non-coding RNAs, play vital roles in the cell and their biological functions are mostly determined by structural properties. Often, these properties are related to dynamic changes in ...

    Authors: Jiabin Huang and Björn Voß

    Citation: BMC Bioinformatics 2014 15:60

    Content type: Research article

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  10. Binding free energy and binding hot spots at protein-protein interfaces are two important research areas for understanding protein interactions. Computational methods have been developed previously for accurat...

    Authors: Qian Liu, Steven CH Hoi, Chee Keong Kwoh, Limsoon Wong and Jinyan Li

    Citation: BMC Bioinformatics 2014 15:57

    Content type: Research article

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  11. Simple peak-picking algorithms, such as those based on lineshape fitting, perform well when peaks are completely resolved in multidimensional NMR spectra, but often produce wrong intensities and frequencies fo...

    Authors: Suhas Tikole, Victor Jaravine, Vladimir Rogov, Volker Dötsch and Peter Güntert

    Citation: BMC Bioinformatics 2014 15:46

    Content type: Methodology article

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  12. Protein inter-residue contact maps provide a translation and rotation invariant topological representation of a protein. They can be used as an intermediary step in protein structure predictions. However, the ...

    Authors: Predrag Kukic, Claudio Mirabello, Giuseppe Tradigo, Ian Walsh, Pierangelo Veltri and Gianluca Pollastri

    Citation: BMC Bioinformatics 2014 15:6

    Content type: Research article

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  13. The Acel_2062 protein from Acidothermus cellulolyticus is a protein of unknown function. Initial sequence analysis predicted that it was a metallopeptidase from the presence of a motif conserved amongst the Asp-z...

    Authors: Christine B Trame, Yuanyuan Chang, Herbert L Axelrod, Ruth Y Eberhardt, Penelope Coggill, Marco Punta and Neil D Rawlings

    Citation: BMC Bioinformatics 2014 15:1

    Content type: Research article

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  14. The ever on-going technical developments in Next Generation Sequencing have led to an increase in detected disease related mutations. Many bioinformatics approaches exist to analyse these variants, and of thos...

    Authors: Hanka Venselaar, Franscesca Camilli, Shima Gholizadeh, Marlou Snelleman, Han G Brunner and Gert Vriend

    Citation: BMC Bioinformatics 2013 14:352

    Content type: Research article

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  15. A novel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and LutC. Both proteins are encoded by a highly conserved LutABC operon, which has been implicated in lactat...

    Authors: William C Hwang, Constantina Bakolitsa, Marco Punta, Penelope C Coggill, Alex Bateman, Herbert L Axelrod, Neil D Rawlings, Mayya Sedova, Scott N Peterson, Ruth Y Eberhardt, L Aravind, Jaime Pascual and Adam Godzik

    Citation: BMC Bioinformatics 2013 14:341

    Content type: Research article

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  16. The NTF2-like superfamily is a versatile group of protein domains sharing a common fold. The sequences of these domains are very diverse and they share no common sequence motif. These domains serve a range of ...

    Authors: Ruth Y Eberhardt, Yuanyuan Chang, Alex Bateman, Alexey G Murzin, Herbert L Axelrod, William C Hwang and L Aravind

    Citation: BMC Bioinformatics 2013 14:327

    Content type: Research article

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  17. Since membrane protein structures are challenging to crystallize, computational approaches are essential for elucidating the sequence-to-structure relationships. Structural modeling of membrane proteins requir...

    Authors: Jhih-Siang Lai, Cheng-Wei Cheng, Allan Lo, Ting-Yi Sung and Wen-Lian Hsu

    Citation: BMC Bioinformatics 2013 14:304

    Content type: Research article

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  18. Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. Th...

    Authors: Chris Schmidt, Stephanie J Irausquin and Homayoun Valafar

    Citation: BMC Bioinformatics 2013 14:302

    Content type: Software

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  19. Molecular recognition features (MoRFs) are short binding regions located in longer intrinsically disordered protein regions. Although these short regions lack a stable structure in the natural state, they read...

    Authors: Chun Fang, Tamotsu Noguchi, Daisuke Tominaga and Hayato Yamana

    Citation: BMC Bioinformatics 2013 14:300

    Content type: Methodology article

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  20. Protein-protein docking, which aims to predict the structure of a protein-protein complex from its unbound components, remains an unresolved challenge in structural bioinformatics. An important step is the ran...

    Authors: Iain H Moal, Mieczyslaw Torchala, Paul A Bates and Juan Fernández-Recio

    Citation: BMC Bioinformatics 2013 14:286

    Content type: Research article

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  21. Pattern recognition receptors of the immune system have key roles in the regulation of pathways after the recognition of microbial- and danger-associated molecular patterns in vertebrates. Members of NOD-like ...

    Authors: János András Mótyán, Péter Bagossi, Szilvia Benkő and József Tőzsér

    Citation: BMC Bioinformatics 2013 14:275

    Content type: Research article

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  22. Assigning a protein into one of its folds is a transitional step for discovering three dimensional protein structure, which is a challenging task in bimolecular (biological) science. The present research focus...

    Authors: Alok Sharma, Kuldip K Paliwal, Abdollah Dehzangi, James Lyons, Seiya Imoto and Satoru Miyano

    Citation: BMC Bioinformatics 2013 14:233

    Content type: Research article

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  23. The knowledge of metabolic pathways and fluxes is important to understand the adaptation of organisms to their biotic and abiotic environment. The specific distribution of stable isotope labelled precursors in...

    Authors: Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Wolfgang Eisenreich and Thomas Dandekar

    Citation: BMC Bioinformatics 2013 14:218

    Content type: Software

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  24. We present the algorithm PFClust (Parameter Free Clustering), which is able automatically to cluster data and identify a suitable number of clusters to group them into without requiring any parameters to be sp...

    Authors: Lazaros Mavridis, Neetika Nath and John BO Mitchell

    Citation: BMC Bioinformatics 2013 14:213

    Content type: Research article

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  25. A growing number of crystal and NMR structures reveals a considerable structural polymorphism of DNA architecture going well beyond the usual image of a double helical molecule. DNA is highly variable with din...

    Authors: Petr Čech, Jaromír Kukal, Jiří Černý, Bohdan Schneider and Daniel Svozil

    Citation: BMC Bioinformatics 2013 14:205

    Content type: Research article

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  26. Influenza A viruses possess RNA genomes that mutate frequently in response to immune pressures. The mutations in the hemagglutinin genes are particularly significant, as the hemagglutinin proteins mediate atta...

    Authors: Xavier I Ambroggio, Jennifer Dommer, Vivek Gopalan, Eleca J Dunham, Jeffery K Taubenberger and Darrell E Hurt

    Citation: BMC Bioinformatics 2013 14:197

    Content type: Database

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  27. Human cancer is caused by the accumulation of somatic mutations in tumor suppressors and oncogenes within the genome. In the case of oncogenes, recent theory suggests that there are only a few key “driver” mut...

    Authors: Gregory A Ryslik, Yuwei Cheng, Kei-Hoi Cheung, Yorgo Modis and Hongyu Zhao

    Citation: BMC Bioinformatics 2013 14:190

    Content type: Methodology article

    Published on:

  28. Normal Mode Analysis is one of the most successful techniques for studying motions in proteins and macromolecules. It can provide information on the mechanism of protein functions, used to aid crystallography ...

    Authors: Thomas L Rodgers, David Burnell, Phil D Townsend, Ehmke Pohl, Martin J Cann, Mark R Wilson and Tom CB McLeish

    Citation: BMC Bioinformatics 2013 14:183

    Content type: Software

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  29. Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile app...

    Authors: Nima Aghaeepour and Holger H Hoos

    Citation: BMC Bioinformatics 2013 14:139

    Content type: Methodology article

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  30. Clustering sequences into groups of putative homologs (families) is a critical first step in many areas of comparative biology and bioinformatics. The performance of clustering approaches in delineating biolog...

    Authors: Cheong Xin Chan, Maisarah Mahbob and Mark A Ragan

    Citation: BMC Bioinformatics 2013 14:120

    Content type: Methodology article

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  31. NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking results can pro...

    Authors: Anna Katharina Dehof, Simon Loew, Hans-Peter Lenhof and Andreas Hildebrandt

    Citation: BMC Bioinformatics 2013 14:98

    Content type: Research article

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  32. In protein sequence classification, identification of the sequence motifs or n-grams that can precisely discriminate between classes is a more interesting scientific question than the classification itself. A num...

    Authors: Satish M Srinivasan, Suleyman Vural, Brian R King and Chittibabu Guda

    Citation: BMC Bioinformatics 2013 14:96

    Content type: Methodology article

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  33. The cellular function of a vast majority of proteins is performed through physical interactions with other biomolecules, which, most of the time, are other proteins. Peptides represent templates of choice for ...

    Authors: Sébastien Giguère, Mario Marchand, François Laviolette, Alexandre Drouin and Jacques Corbeil

    Citation: BMC Bioinformatics 2013 14:82

    Content type: Research article

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  34. Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation.

    Authors: J Eduardo Fajardo and Andras Fiser

    Citation: BMC Bioinformatics 2013 14:63

    Content type: Methodology article

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  35. The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native struc...

    Authors: Michal Jamroz and Andrzej Kolinski

    Citation: BMC Bioinformatics 2013 14:62

    Content type: Software

    Published on:

  36. CD4+ T-cell epitopes play a crucial role in eliciting vigorous protective immune responses during peptide (epitope)-based vaccination. The prediction of these epitopes focuses on the peptide binding process by...

    Authors: Patricio Oyarzún, Jonathan J Ellis, Mikael Bodén and Boštjan Kobe

    Citation: BMC Bioinformatics 2013 14:52

    Content type: Research article

    Published on:

2019 Journal Metrics

  • Citation Impact
    3.242 - 2-year Impact Factor
    3.213 - 5-year Impact Factor
    1.156 - Source Normalized Impact per Paper (SNIP)
    1.626 - SCImago Journal Rank (SJR)

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