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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

    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

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  2. Content type: Methodology article

    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

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  3. Content type: Methodology article

    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

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  4. Content type: Software

    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

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  5. Content type: Software

    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

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  6. Content type: Research article

    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

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  7. Content type: Research article

    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

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  8. Content type: Methodology article

    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

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  9. Content type: Methodology article

    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

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  10. Content type: Methodology article

    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

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  11. Content type: Software

    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

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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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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)


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