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BMC Bioinformatics

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. Content type: Methodology Article

    Single-particle analysis of electron cryo-microscopy (cryo-EM) is a key technology for elucidation of macromolecular structures. Recent technical advances in hardware and software developments significantly en...

    Authors: Jochen Ismer, Alexander S. Rose, Johanna K. S. Tiemann and Peter W. Hildebrand

    Citation: BMC Bioinformatics 2017 18:475

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  2. Content type: Methodology Article

    Artificially synthesized RNA molecules provide important ways for creating a variety of novel functional molecules. State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of ...

    Authors: Xiufeng Yang, Kazuki Yoshizoe, Akito Taneda and Koji Tsuda

    Citation: BMC Bioinformatics 2017 18:468

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  3. Content type: Research Article

    In modern structural bioinformatics, comparison of molecular structures aimed to identify and assess similarities and differences between them is one of the most commonly performed procedures. It gives the bas...

    Authors: Jakub Wiedemann, Tomasz Zok, Maciej Milostan and Marta Szachniuk

    Citation: BMC Bioinformatics 2017 18:456

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  4. Content type: Methodology Article

    Deep learning is one of the most powerful machine learning methods that has achieved the state-of-the-art performance in many domains. Since deep learning was introduced to the field of bioinformatics in 2012,...

    Authors: Haiou Li, Jie Hou, Badri Adhikari, Qiang Lyu and Jianlin Cheng

    Citation: BMC Bioinformatics 2017 18:417

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  6. Content type: Research Article

    Residue-residue contacts are key features for accurate de novo protein structure prediction. For the optimal utilization of these predicted contacts in folding proteins accurately, it is important to study the...

    Authors: Badri Adhikari and Jianlin Cheng

    Citation: BMC Bioinformatics 2017 18:380

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  7. Content type: Methodology Article

    In structure-based drug design, binding affinity prediction remains as a challenging goal for current scoring functions. Development of target-biased scoring functions provides a new possibility for tackling t...

    Authors: Jie Liu, Minyi Su, Zhihai Liu, Jie Li, Yan Li and Renxiao Wang

    Citation: BMC Bioinformatics 2017 18:343

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  8. Content type: Research Article

    In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein–small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (M...

    Authors: Hongrui Wang, Hongwei Liu, Leixin Cai, Caixia Wang and Qiang Lv

    Citation: BMC Bioinformatics 2017 18:327

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  9. Content type: Research Article

    Accurately predicted contacts allow to compute the 3D structure of a protein. Since the solution space of native residue-residue contact pairs is very large, it is necessary to leverage information to identify...

    Authors: Kolja Stahl, Michael Schneider and Oliver Brock

    Citation: BMC Bioinformatics 2017 18:303

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  12. Content type: Research Article

    RNA secondary structure prediction is a compute intensive task that lies at the core of several search algorithms in bioinformatics. Fortunately, the RNA folding approaches, such as the Nussinov base pair maxi...

    Authors: Marek Palkowski and Wlodzimierz Bielecki

    Citation: BMC Bioinformatics 2017 18:290

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  13. Content type: Software

    Knowledge of HLA haplotypes is helpful in many settings as disease association studies, population genetics, or hematopoietic stem cell transplantation. Regarding the recruitment of unrelated hematopoietic ste...

    Authors: Christian Schäfer, Alexander H. Schmidt and Jürgen Sauter

    Citation: BMC Bioinformatics 2017 18:284

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  14. Content type: Software

    Essential Dynamics (ED) is a common application of principal component analysis (PCA) to extract biologically relevant motions from atomic trajectories of proteins. Covariance and correlation based PCA are two...

    Authors: Charles C. David, Ettayapuram Ramaprasad Azhagiya Singam and Donald J. Jacobs

    Citation: BMC Bioinformatics 2017 18:271

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  17. Content type: Research Article

    Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the...

    Authors: Tanchanok Wisitponchai, Watshara Shoombuatong, Vannajan Sanghiran Lee, Kuntida Kitidee and Chatchai Tayapiwatana

    Citation: BMC Bioinformatics 2017 18:220

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Page 2 of 15
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BMC Bioinformatics

ISSN: 1471-2105

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