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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. 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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  2. 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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  3. 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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  4. 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

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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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

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  10. 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

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  11. 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

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  12. 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

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  13. 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

    Content type: Research Article

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  14. 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

    Content type: Software

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  15. 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

    Content type: Software

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  16. 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

    Content type: Research Article

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  17. 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

    Content type: Research article

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  18. 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

    Content type: Software

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  19. 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

    Content type: Research article

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  20. 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

    Content type: Research article

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  21. Protein quality assessment (QA) useful for ranking and selecting protein models has long been viewed as one of the major challenges for protein tertiary structure prediction. Especially, estimating the quality...

    Authors: Renzhi Cao, Debswapna Bhattacharya, Jie Hou and Jianlin Cheng

    Citation: BMC Bioinformatics 2016 17:495

    Content type: Research article

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  22. Disulfide-rich peptides (DRPs) are found throughout nature. They are suitable scaffolds for drug development due to their small cores, whose disulfide bonds impart extraordinary chemical and biological stabili...

    Authors: David T. Barkan, Xiao-li Cheng, Herodion Celino, Tran T. Tran, Ashok Bhandari, Charles S. Craik, Andrej Sali and Mark L. Smythe

    Citation: BMC Bioinformatics 2016 17:481

    Content type: Research article

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  23. Development of automatable processes for clustering proteins into functionally relevant groups is a critical hurdle as an increasing number of sequences are deposited into databases. Experimental function dete...

    Authors: Janelle B. Leuthaeuser, John H. Morris, Angela F. Harper, Thomas E. Ferrin, Patricia C. Babbitt and Jacquelyn S. Fetrow

    Citation: BMC Bioinformatics 2016 17:458

    Content type: Software

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  24. RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0, i.e. whose minimum free energy secondary structure is identical...

    Authors: Juan Antonio Garcia-Martin, Amir H. Bayegan, Ivan Dotu and Peter Clote

    Citation: BMC Bioinformatics 2016 17:424

    Content type: Software

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  25. Structural alignment of proteins is one of the most challenging problems in molecular biology. The tertiary structure of a protein strictly correlates with its function and computationally predicted structures...

    Authors: Maciej Antczak, Marta Kasprzak, Piotr Lukasiak and Jacek Blazewicz

    Citation: BMC Bioinformatics 2016 17:383

    Content type: Methodology Article

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  26. Sequence matching is extremely important for applications throughout biology, particularly for discovering information such as functional and evolutionary relationships, and also for discriminating between uni...

    Authors: Sumudu P. Leelananda, Andrzej Kloczkowski and Robert L. Jernigan

    Citation: BMC Bioinformatics 2016 17:328

    Content type: Research article

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  27. Levan and levan-type fructo-oligosaccharides (LFOs) have various potential applications in pharmaceutical and food industries due to their beneficial properties such as their low intrinsic viscosity and high w...

    Authors: Pongsakorn Kanjanatanin, Rath Pichyangkura and Surasak Chunsrivirot

    Citation: BMC Bioinformatics 2016 17:306

    Content type: Research article

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  28. Protein variability can now be studied by measuring high-resolution tolerance-to-substitution maps and fitness landscapes in saturated mutational libraries. But these rich and expensive datasets are typically ...

    Authors: Luciano A. Abriata, Christophe Bovigny and Matteo Dal Peraro

    Citation: BMC Bioinformatics 2016 17:242

    Content type: Research article

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    The Erratum to this article has been published in BMC Bioinformatics 2016 17:439

  29. Cryo-electron tomography (cryo-ET) enables 3D imaging of macromolecular structures. Reconstructed cryo-ET images have a “missing wedge” of data loss due to limitations in rotation of the mounting stage. Most c...

    Authors: Sukantadev Bag, Michael B Prentice, Mingzhi Liang, Martin J Warren and Kingshuk Roy Choudhury

    Citation: BMC Bioinformatics 2016 17:234

    Content type: Methodology article

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  30. RNA molecules fold into complex three-dimensional shapes, guided by the pattern of hydrogen bonding between nucleotides. This pattern of base pairing, known as RNA secondary structure, is critical to their cel...

    Authors: Nathan D. Berkowitz, Ian M. Silverman, Daniel M. Childress, Hilal Kazan, Li-San Wang and Brian D. Gregory

    Citation: BMC Bioinformatics 2016 17:215

    Content type: Database

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  31. The importance of the material properties of membranes for diverse cellular processes is well established. Notably, the elastic properties of the membrane, which depend on its composition, can directly influen...

    Authors: Niklaus Johner, Daniel Harries and George Khelashvili

    Citation: BMC Bioinformatics 2016 17:161

    Content type: Software

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    The Erratum to this article has been published in BMC Bioinformatics 2016 17:236

  32. The identification of structured units in a protein sequence is an important first step for most biochemical studies. Importantly for this study, the identification of stable structured region is a crucial fir...

    Authors: Jouhyun Jeon, Roland Arnold, Fateh Singh, Joan Teyra, Tatjana Braun and Philip M. Kim

    Citation: BMC Bioinformatics 2016 17:150

    Content type: Software

    Published on:

2019 Journal Metrics

  • Citation Impact
    3.242 - 2-year Impact Factor
    3.213 - 5-year Impact Factor
    1.156 - Source Normalized Impact per Paper (SNIP)
    1.626 - SCImago Journal Rank (SJR)

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