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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.

Page 1 of 7

  1. Accurate prediction of inter-residue contacts of a protein is important to calculating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective in inferring inter-res...

    Authors: Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng and Dongbo Bu

    Citation: BMC Bioinformatics 2019 20:537

    Content type: Methodology Article

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  2. It is widely believed that tertiary nucleotide-nucleotide interactions are essential in determining RNA structure and function. Currently, direct coupling analysis (DCA) infers nucleotide contacts in a sequenc...

    Authors: Yiren Jian, Xiaonan Wang, Jaidi Qiu, Huiwen Wang, Zhichao Liu, Yunjie Zhao and Chen Zeng

    Citation: BMC Bioinformatics 2019 20:497

    Content type: Research article

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  3. The development of accurate epitope prediction tools is important in facilitating disease diagnostics, treatment and vaccine development. The advent of new approaches making use of antibody and TCR sequence in...

    Authors: Swapnil Mahajan, Zhen Yan, Martin Closter Jespersen, Kamilla Kjærgaard Jensen, Paolo Marcatili, Morten Nielsen, Alessandro Sette and Bjoern Peters

    Citation: BMC Bioinformatics 2019 20:490

    Content type: Methodology article

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  4. The function of oligomeric proteins is inherently linked to their quaternary structure. In the absence of high-resolution data, low-resolution information in the form of spatial restraints can significantly co...

    Authors: Aljaž Gaber, Gregor Gunčar and Miha Pavšič

    Citation: BMC Bioinformatics 2019 20:464

    Content type: Research article

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  5. Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits in replacing a ...

    Authors: Vincent Demolombe, Alexandre G. de Brevern, Liza Felicori, Christophe NGuyen, Ricardo Andrez Machado de Avila, Lionel Valera, Bénédicte Jardin-Watelet, Géraldine Lavigne, Aurélien Lebreton, Franck Molina and Violaine Moreau

    Citation: BMC Bioinformatics 2019 20:387

    Content type: Methodology article

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  6. The knowledge-based statistical potential has been widely used in protein structure modeling and model quality assessment. They are commonly evaluated based on their abilities of native recognition as well as ...

    Authors: Zhongwang Yu, Yuangen Yao, Haiyou Deng and Ming Yi

    Citation: BMC Bioinformatics 2019 20:299

    Content type: Methodology article

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  7. Large-scale datasets of protein structures and sequences are becoming ubiquitous in many domains of biological research. Experimental approaches and computational modelling methods are generating biological da...

    Authors: Jaume Bonet, Zander Harteveld, Fabian Sesterhenn, Andreas Scheck and Bruno E. Correia

    Citation: BMC Bioinformatics 2019 20:240

    Content type: Software

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  8. Molecular simulations are used to provide insight into protein structure and dynamics, and have the potential to provide important context when predicting the impact of sequence variation on protein function. ...

    Authors: Matthew D. McCoy, Vikram Shivakumar, Sridhar Nimmagadda, Mohsin Saleet Jafri and Subha Madhavan

    Citation: BMC Bioinformatics 2019 20:171

    Content type: Software

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  9. Long non-coding RNAs (lncRNAs) play an important role in regulating gene expression and are thus important for determining phenotypes. Most attempts to measure selection in lncRNAs have focused on the primary ...

    Authors: Maria Beatriz Walter Costa, Christian Höner zu Siederdissen, Marko Dunjić, Peter F. Stadler and Katja Nowick

    Citation: BMC Bioinformatics 2019 20:151

    Content type: Research article

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  10. DNA inside eukaryotic cells wraps around histones to form the 11nm chromatin fiber that can further fold into higher-order DNA loops, which may depend on the binding of architectural factors. Predicting how th...

    Authors: Pau Farré, Alexandre Heurteau, Olivier Cuvier and Eldon Emberly

    Citation: BMC Bioinformatics 2018 19:372

    Content type: Research article

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  11. With increasing interest in ab initio protein design, there is a desire to be able to fully explore the design space of insertions and deletions. Nature inserts and deletes residues to optimize energy and functio...

    Authors: William F. Hooper, Benjamin D. Walcott, Xing Wang and Christopher Bystroff

    Citation: BMC Bioinformatics 2018 19:337

    Content type: Methodology article

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  12. Advancements in biophysical experimental techniques have pushed the limits in terms of the types of phenomena that can be characterized, the amount of data that can be produced and the resolution at which we c...

    Authors: Sandhya P. Tiwari, Florence Tama and Osamu Miyashita

    Citation: BMC Bioinformatics 2018 19:320

    Content type: Methodology article

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  13. In recent decades, detecting protein complexes (PCs) from protein-protein interaction networks (PPINs) has been an active area of research. There are a large number of excellent graph clustering methods that w...

    Authors: Rongquan Wang, Guixia Liu, Caixia Wang, Lingtao Su and Liyan Sun

    Citation: BMC Bioinformatics 2018 19:305

    Content type: Methodology article

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  14. Computational RNA 3D structure prediction and modeling are rising as complementary approaches to high-resolution experimental techniques for structure determination. They often apply to substitute or complemen...

    Authors: Maciej Antczak, Tomasz Zok, Maciej Osowiecki, Mariusz Popenda, Ryszard W. Adamiak and Marta Szachniuk

    Citation: BMC Bioinformatics 2018 19:304

    Content type: Software

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  15. 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

    Content type: Research article

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  16. 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

    Content type: Database

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  17. 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

    Content type: Methodology article

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  18. 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

    Content type: Research article

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  19. 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

    Content type: Research Article

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  20. 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

    Content type: Research Article

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  21. 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

    Content type: Research Article

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  22. 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

    Content type: Research Article

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  23. 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

    Content type: Methodology Article

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  24. 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

    Content type: Research Article

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  25. 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

    Content type: Software

    Published on:

  26. 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

    Content type: Methodology Article

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  27. 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

    Content type: Methodology Article

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  28. 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

    Content type: Research Article

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  29. 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

    Content type: Methodology Article

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  30. 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

    Content type: Research Article

    Published on:

  31. 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

    Content type: Methodology Article

    Published on:

  32. 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

    Content type: Research Article

    Published on:

  33. 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

    Content type: Research Article

    Published on:

2018 Journal Metrics

  • Citation Impact
    2.511 - 2-year Impact Factor
    2.970 - 5-year Impact Factor
    0.855 - Source Normalized Impact per Paper (SNIP)
    1.374 - SCImago Journal Rank (SJR)

    Usage 
    4,129,368 downloads

    Social Media Impact
    4446 mentions

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