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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: 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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  2. 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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  3. 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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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. Content type: Research article

    Signaling proteins such as protein kinases adopt a diverse array of conformations to respond to regulatory signals in signaling pathways. Perhaps the most fundamental conformational change of a kinase is the t...

    Authors: Daniel Ian McSkimming, Khaled Rasheed and Natarajan Kannan

    Citation: BMC Bioinformatics 2017 18:86

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  10. Content type: Software

    RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of...

    Authors: Ying Li, Xiaohu Shi, Yanchun Liang, Juan Xie, Yu Zhang and Qin Ma

    Citation: BMC Bioinformatics 2017 18:51

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  11. Content type: Research article

    Many critical biological processes are strongly related to protein-RNA interactions. Revealing the protein structure motifs for RNA-binding will provide valuable information for deciphering protein-RNA recogni...

    Authors: Zhi-Ping Liu, Shutang Liu, Ruitang Chen, Xiaopeng Huang and Ling-Yun Wu

    Citation: BMC Bioinformatics 2017 18:27

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  12. Content type: Research article

    The cyclin-dependent kinase 2 (CDK2) together with its cyclin E and A partners is a central regulator of cell growth and division. Deregulation of CDK2 activity is associated with diseases such as cancer. The ...

    Authors: Jinyu Li, Jörg Vervoorts, Paolo Carloni, Giulia Rossetti and Bernhard Lüscher

    Citation: BMC Bioinformatics 2017 18:15

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2016 Journal Metrics

  • Citation Impact
    2.448 - 2-year Impact Factor
    3.450 - 5-year Impact Factor
    0.946 - Source Normalized Impact per Paper (SNIP)
    1.467 - SCImago Journal Rank (SJR)

    1405 Usage Factor

    Social Media Impact
    816 mentions