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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. There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. However...

    Authors: Mark Moll, Drew H Bryant and Lydia E Kavraki

    Citation: BMC Bioinformatics 2010 11:555

    Content type: Methodology article

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  2. Many newly detected point mutations are located in protein-coding regions of the human genome. Knowledge of their effects on the protein's 3D structure provides insight into the protein's mechanism, can aid th...

    Authors: Hanka Venselaar, Tim AH te Beek, Remko KP Kuipers, Maarten L Hekkelman and Gert Vriend

    Citation: BMC Bioinformatics 2010 11:548

    Content type: Methodology article

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  3. Conformational sampling for small molecules plays an essential role in drug discovery research pipeline. Based on multi-objective evolution algorithm (MOEA), we have developed a conformational generation metho...

    Authors: Fang Bai, Xiaofeng Liu, Jiabo Li, Haoyun Zhang, Hualiang Jiang, Xicheng Wang and Honglin Li

    Citation: BMC Bioinformatics 2010 11:545

    Content type: Methodology article

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  4. The Medium-chain Dehydrogenases/Reductases (MDR) form a protein superfamily whose size and complexity defeats traditional means of subclassification; it currently has over 15000 members in the databases, the p...

    Authors: Joel Hedlund, Hans Jörnvall and Bengt Persson

    Citation: BMC Bioinformatics 2010 11:534

    Content type: Research article

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  5. Many structural properties such as solvent accessibility, dihedral angles and helix-helix contacts can be assigned to each residue in a membrane protein. Independent studies exist on the analysis and sequence-...

    Authors: Shandar Ahmad, Yumlembam Hemajit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita and Kenji Mizuguchi

    Citation: BMC Bioinformatics 2010 11:533

    Content type: Research article

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  6. The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms ...

    Authors: Andreas Hildebrandt, Anna Katharina Dehof, Alexander Rurainski, Andreas Bertsch, Marcel Schumann, Nora C Toussaint, Andreas Moll, Daniel Stöckel, Stefan Nickels, Sabine C Mueller, Hans-Peter Lenhof and Oliver Kohlbacher

    Citation: BMC Bioinformatics 2010 11:531

    Content type: Software

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  7. The binding of peptide fragments of antigens to class II MHC is a crucial step in initiating a helper T cell immune response. The identification of such peptide epitopes has potential applications in vaccine d...

    Authors: Andrew J Bordner and Hans D Mittelmann

    Citation: BMC Bioinformatics 2010 11:482

    Content type: Research article

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  8. New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and i...

    Authors: Thomas M Asbury, Matt Mitman, Jijun Tang and W Jim Zheng

    Citation: BMC Bioinformatics 2010 11:444

    Content type: Software

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  9. Genome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution structure determination methods make it unlikely that t...

    Authors: Kasper Stovgaard, Christian Andreetta, Jesper Ferkinghoff-Borg and Thomas Hamelryck

    Citation: BMC Bioinformatics 2010 11:429

    Content type: Research article

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  10. Accurate prediction of antigenic epitopes is important for immunologic research and medical applications, but it is still an open problem in bioinformatics. The case for discontinuous epitopes is even worse - ...

    Authors: Shide Liang, Dandan Zheng, Daron M Standley, Bo Yao, Martin Zacharias and Chi Zhang

    Citation: BMC Bioinformatics 2010 11:381

    Content type: Methodology article

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  11. The study of protein-small molecule interactions is vital for understanding protein function and for practical applications in drug discovery. To benefit from the rapidly increasing structural data, it is esse...

    Authors: Ratna R Thangudu, Manoj Tyagi, Benjamin A Shoemaker, Stephen H Bryant, Anna R Panchenko and Thomas Madej

    Citation: BMC Bioinformatics 2010 11:365

    Content type: Research article

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  12. PDZ domain is a well-conserved, structural protein domain found in hundreds of signaling proteins that are otherwise unrelated. PDZ domains can bind to the C-terminal peptides of different proteins and act as ...

    Authors: Sibel Kalyoncu, Ozlem Keskin and Attila Gursoy

    Citation: BMC Bioinformatics 2010 11:357

    Content type: Research article

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  13. The impressive increase of novel RNA structures, during the past few years, demands automated methods for structure comparison. While many algorithms handle only small motifs, few techniques, developed in rece...

    Authors: Svetlana Kirillova, Silvio CE Tosatto and Oliviero Carugo

    Citation: BMC Bioinformatics 2010 11:327

    Content type: Software

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  14. Accurately covering the conformational space of amino acid side chains is essential for important applications such as protein design, docking and high resolution structure prediction. Today, the most common w...

    Authors: Tim Harder, Wouter Boomsma, Martin Paluszewski, Jes Frellsen, Kristoffer E Johansson and Thomas Hamelryck

    Citation: BMC Bioinformatics 2010 11:306

    Content type: Research article

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  15. Many functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of p...

    Authors: Changhoon Kim, Jodi Basner and Byungkook Lee

    Citation: BMC Bioinformatics 2010 11:303

    Content type: Research article

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  16. The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The databa...

    Authors: Tomás Norambuena and Francisco Melo

    Citation: BMC Bioinformatics 2010 11:262

    Content type: Database

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