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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. Content type: Research article

    Three dimensional (3D) genome spatial organization is critical for numerous cellular functions, including transcription, while certain conformation-driven structural alterations are frequently oncogenic. Genom...

    Authors: Mark R. Segal and Henrik L. Bengtsson

    Citation: BMC Bioinformatics 2018 19:196

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  2. Content type: Database

    PDZ-containing proteins comprise one of the most widely distributed protein families playing major role in localization and membrane receptor clustering. They are hence important regulators of signal transduct...

    Authors: Jitesh Doshi, Raja Reddy Kuppili, Siddharth Gurdasani, Navneet Venkatakrishnan, Amit Saxena and Kakoli Bose

    Citation: BMC Bioinformatics 2018 19:160

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  3. Content type: Methodology article

    Despite the rapid progress of protein residue contact prediction, predicted residue contact maps frequently contain many errors. However, information of residue pairing in β strands could be extracted from a n...

    Authors: Wenzhi Mao, Tong Wang, Wenxuan Zhang and Haipeng Gong

    Citation: BMC Bioinformatics 2018 19:146

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  4. Content type: Research article

    Conventional de novo drug design is costly and time consuming, making it accessible to only the best resourced research organizations. An emergent approach to new drug development is drug repurposing, in which...

    Authors: Matthew D. King, Thomas Long, Daniel L. Pfalmer, Timothy L. Andersen and Owen M. McDougal

    Citation: BMC Bioinformatics 2018 19:138

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  5. Content type: Research Article

    Protein structure can be described by backbone torsion angles: rotational angles about the N-Cα bond (φ) and the Cα-C bond (ψ) or the angle between Cαi-1-Cαi-Cαi + 1 (θ) and the rotational angle about the Cαi-Cαi...

    Authors: Jianzhao Gao, Yuedong Yang and Yaoqi Zhou

    Citation: BMC Bioinformatics 2018 19:29

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  6. Content type: Research Article

    Biocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve the...

    Authors: Ana Julia Velez Rueda, Alexander Miguel Monzon, Sebastián M. Ardanaz, Luis E. Iglesias and Gustavo Parisi

    Citation: BMC Bioinformatics 2018 19:27

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  7. Content type: Research Article

    Next-generation sequencing of individuals with genetic diseases often detects candidate rare variants in numerous genes, but determining which are causal remains challenging. We hypothesized that the spatial d...

    Authors: R. Michael Sivley, Jonathan H. Sheehan, Jonathan A. Kropski, Joy Cogan, Timothy S. Blackwell, John A. Phillips, William S. Bush, Jens Meiler and John A. Capra

    Citation: BMC Bioinformatics 2018 19:18

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  8. Content type: Research Article

    Hot spots are interface residues that contribute most binding affinity to protein-protein interaction. A compact and relevant feature subset is important for building machine learning methods to predict hot sp...

    Authors: Yanhua Qiao, Yi Xiong, Hongyun Gao, Xiaolei Zhu and Peng Chen

    Citation: BMC Bioinformatics 2018 19:14

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  9. Content type: Methodology Article

    Knowledge of catalytic residues can play an essential role in elucidating mechanistic details of an enzyme. However, experimental identification of catalytic residues is a tedious and time-consuming task, whic...

    Authors: Preeti Choudhary, Shailesh Kumar, Anand Kumar Bachhawat and Shashi Bhushan Pandit

    Citation: BMC Bioinformatics 2017 18:583

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  10. Content type: Research Article

    As one of the most successful knowledge-based energy functions, the distance-dependent atom-pair potential is widely used in all aspects of protein structure prediction, including conformational search, model ...

    Authors: Yuangen Yao, Rong Gui, Quan Liu, Ming Yi and Haiyou Deng

    Citation: BMC Bioinformatics 2017 18:542

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  11. Content type: Software

    Protein cavities play a key role in biomolecular recognition and function, particularly in protein-ligand interactions, as usual in drug discovery and design. Grid-based cavity detection methods aim at finding...

    Authors: Sérgio E. D. Dias, Ana Mafalda Martins, Quoc T. Nguyen and Abel J. P. Gomes

    Citation: BMC Bioinformatics 2017 18:493

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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