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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. Biomacromolecular structural data outgrew the legacy Protein Data Bank (PDB) format which the scientific community relied on for decades, yet the use of its successor PDBx/Macromolecular Crystallographic Infor...

    Authors: Glen van Ginkel, Lukáš Pravda, José M. Dana, Mihaly Varadi, Peter Keller, Stephen Anyango and Sameer Velankar

    Citation: BMC Bioinformatics 2021 22:383

    Content type: Software

    Published on:

  2. Driven by deep learning, inter-residue contact/distance prediction has been significantly improved and substantially enhanced ab initio protein structure prediction. Currently, most of the distance prediction ...

    Authors: Tianqi Wu, Zhiye Guo, Jie Hou and Jianlin Cheng

    Citation: BMC Bioinformatics 2021 22:30

    Content type: Methodology article

    Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:354

  3. Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein–protein interaction (PPI) ...

    Authors: Joaquim Aguirre-Plans, Alberto Meseguer, Ruben Molina-Fernandez, Manuel Alejandro Marín-López, Gaurav Jumde, Kevin Casanova, Jaume Bonet, Oriol Fornes, Narcis Fernandez-Fuentes and Baldo Oliva

    Citation: BMC Bioinformatics 2021 22:4

    Content type: Software

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  4. Protein–peptide interactions play a fundamental role in a wide variety of biological processes, such as cell signaling, regulatory networks, immune responses, and enzyme inhibition. Peptides are characterized ...

    Authors: Pedro M. Martins, Lucianna H. Santos, Diego Mariano, Felippe C. Queiroz, Luana L. Bastos, Isabela de S. Gomes, Pedro H. C. Fischer, Rafael E. O. Rocha, Sabrina A. Silveira, Leonardo H. F. de Lima, Mariana T. Q. de Magalhães, Maria G. A. Oliveira and Raquel C. de Melo-Minardi

    Citation: BMC Bioinformatics 2021 22:1

    Content type: Database

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  5. Proteases are key drivers in many biological processes, in part due to their specificity towards their substrates. However, depending on the family and molecular function, they can also display substrate promi...

    Authors: Rodrigo Ochoa, Mikhail Magnitov, Roman A. Laskowski, Pilar Cossio and Janet M. Thornton

    Citation: BMC Bioinformatics 2020 21:586

    Content type: Methodology article

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  6. Classification of certain proteins with specific functions is momentous for biological research. Encoding approaches of protein sequences for feature extraction play an important role in protein classification...

    Authors: Jian Zhang, Lixin Lv, Donglei Lu, Denan Kong, Mohammed Abdoh Ali Al-Alashaari and Xudong Zhao

    Citation: BMC Bioinformatics 2020 21:480

    Content type: Methodology article

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  7. Despite continued efforts using chemical similarity methods in virtual screening, currently developed approaches suffer from time-consuming multistep procedures and low success rates. We recently developed a m...

    Authors: Prasannavenkatesh Durai, Young-Joon Ko, Cheol-Ho Pan and Keunwan Park

    Citation: BMC Bioinformatics 2020 21:309

    Content type: Research article

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  8. The interaction between proteins and nucleic acids plays pivotal roles in various biological processes such as transcription, translation, and gene regulation. Hot spots are a small set of residues that contri...

    Authors: Xiaolei Zhu, Ling Liu, Jingjing He, Ting Fang, Yi Xiong and Julie C. Mitchell

    Citation: BMC Bioinformatics 2020 21:289

    Content type: Research article

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  9. Protein engineering has many applications for industry, such as the development of new drugs, vaccines, treatment therapies, food, and biofuel production. A common way to engineer a protein is to perform mutat...

    Authors: José Renato M. S. Barroso, Diego Mariano, Sandro R. Dias, Rafael E. O. Rocha, Lucianna H. Santos, Ronaldo A. P. Nagem and Raquel C. de Melo-Minardi

    Citation: BMC Bioinformatics 2020 21:275

    Content type: Software

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  10. Analysis of secondary structures is essential for understanding the functions of RNAs. Because RNA molecules thermally fluctuate, it is necessary to analyze the probability distributions of their secondary str...

    Authors: Hiroki Takizawa, Junichi Iwakiri and Kiyoshi Asai

    Citation: BMC Bioinformatics 2020 21:210

    Content type: Methodology Article

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  11. Protein repeats can confound sequence analyses because the repetitiveness of their amino acid sequences lead to difficulties in identifying whether similar repeats are due to convergent or divergent evolution....

    Authors: Matthew Merski, Krzysztof Młynarczyk, Jan Ludwiczak, Jakub Skrzeczkowski, Stanisław Dunin-Horkawicz and Maria W. Górna

    Citation: BMC Bioinformatics 2020 21:179

    Content type: Research article

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  12. Whenever suitable template structures are not available, usage of fragment-based protein structure prediction becomes the only practical alternative as pure ab initio techniques require massive computational r...

    Authors: Jad Abbass and Jean-Christophe Nebel

    Citation: BMC Bioinformatics 2020 21:170

    Content type: Methodology article

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  13. The reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studied Escherichia coli K-12 MG1655 strain. The combination of the tw...

    Authors: Nathan Mih, Jonathan M. Monk, Xin Fang, Edward Catoiu, David Heckmann, Laurence Yang and Bernhard O. Palsson

    Citation: BMC Bioinformatics 2020 21:162

    Content type: Research article

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  14. Protein-protein interactions (PPIs) are fundamental in many biological processes and understanding these interactions is key for a myriad of applications including drug development, peptide design and identifi...

    Authors: Felippe C. Queiroz, Adriana M. P. Vargas, Maria G. A. Oliveira, Giovanni V. Comarela and Sabrina A. Silveira

    Citation: BMC Bioinformatics 2020 21:143

    Content type: Research Article

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  15. Hinge-bending movements in proteins comprising two or more domains form a large class of functional movements. Hinge-bending regions demarcate protein domains and collectively control the domain movement. Cons...

    Authors: Ruth Veevers, Gavin Cawley and Steven Hayward

    Citation: BMC Bioinformatics 2020 21:137

    Content type: Research article

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  16. The maintenance of protein structural stability requires the cooperativity among spatially neighboring residues. Previous studies have shown that conserved residues tend to occur clustered together within enzy...

    Authors: Zhen Yang, Xueqing Deng, Yang Liu, Weikang Gong and Chunhua Li

    Citation: BMC Bioinformatics 2020 21:57

    Content type: Research article

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  17. Seed and accessibility constraints are core features to enable highly accurate sRNA target screens based on RNA-RNA interaction prediction. Currently, available tools provide different (sets of) constraints an...

    Authors: Martin Raden, Teresa Müller, Stefan Mautner, Rick Gelhausen and Rolf Backofen

    Citation: BMC Bioinformatics 2020 21:15

    Content type: Research Article

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  18. Computational methods provide approaches to identify epitopes in protein Ags to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was de...

    Authors: Vincent Demolombe, Alexandre G. de Brevern, Franck Molina, Géraldine Lavigne, Claude Granier and Violaine Moreau

    Citation: BMC Bioinformatics 2019 20:738

    Content type: Methodology article

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  19. The kinase pocket structural information is important for drug discovery targeting cancer or other diseases. Although some kinase sequence, structure or drug databases have been developed, the databases cannot...

    Authors: Huiwen Wang, Jiadi Qiu, Haoquan Liu, Ying Xu, Ya Jia and Yunjie Zhao

    Citation: BMC Bioinformatics 2019 20:617

    Content type: Database

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  20. 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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    The Correction to this article has been published in BMC Bioinformatics 2019 20:616

  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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

    Published on:

  30. 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

    Published on:

  31. 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

    Published on:

Annual Journal Metrics

  • Speed
    70 days to first decision for reviewed manuscripts only
    44 days to first decision for all manuscripts
    163 days from submission to acceptance
    36 days from acceptance to publication

    Citation Impact
    3.169 - 2-year Impact Factor
    3.629 - 5-year Impact Factor
    1.276 - Source Normalized Impact per Paper (SNIP)
    1.567 - SCImago Journal Rank (SJR)

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