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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 2 of 6

  2. Content type: Research article

    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

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  3. Content type: Research article

    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

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  4. Content type: Software

    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

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  6. Content type: Software

    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

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  7. Content type: Methodology Article

    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

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  9. Content type: Research article

    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

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  10. Content type: Research article

    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

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  11. Content type: Research article

    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

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

  12. Content type: Methodology article

    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

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  13. Content type: Database

    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

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  15. Content type: Software

    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

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

  16. Content type: Software

    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

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  18. Content type: Research Article

    Drug discovery and design are important research fields in bioinformatics. Enumeration of chemical compounds is essential not only for the purpose, but also for analysis of chemical space and structure elucida...

    Authors: Jira Jindalertudomdee, Morihiro Hayashida, Yang Zhao and Tatsuya Akutsu

    Citation: BMC Bioinformatics 2016 17:113

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  20. Content type: Research Article

    Protein complexes carry out nearly all signaling and functional processes within cells. The study of protein complexes is an effective strategy to analyze cellular functions and biological processes. With the ...

    Authors: Le Ou-Yang, Min Wu, Xiao-Fei Zhang, Dao-Qing Dai, Xiao-Li Li and Hong Yan

    Citation: BMC Bioinformatics 2016 17:100

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  21. Content type: Research article

    The recent outbreak of Ebola has been cited as the largest in history. Despite this global health crisis, few drugs are available to efficiently treat Ebola infections. Drug repurposing provides a potentially ...

    Authors: Zheng Zhao, Che Martin, Raymond Fan, Philip E. Bourne and Lei Xie

    Citation: BMC Bioinformatics 2016 17:90

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  22. Content type: Research article

    Increasing resistance to anti-tuberculosis drugs has driven the need for developing new drugs. Resources such as the tropical disease research (TDR) target database and AssessDrugTarget can help to prioritize ...

    Authors: Ruben Cloete, Ekow Oppon, Edwin Murungi, Wolf-Dieter Schubert and Alan Christoffels

    Citation: BMC Bioinformatics 2016 17:75

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  24. Content type: Research article

    Malaria infection is still widespread in some parts of the world and threatens the lives of millions of people every year. Vaccines, especially oral vaccines are considered to be effective in reducing the burd...

    Authors: Shabnam Shamriz and Hamideh Ofoghi

    Citation: BMC Bioinformatics 2016 17:71

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  25. Content type: Research article

    The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its ...

    Authors: Ludmil B. Alexandrov, Alan R. Bishop, Kim Ø. Rasmussen and Boian S. Alexandrov

    Citation: BMC Bioinformatics 2016 17:68

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  26. Content type: Research Article

    Aligning similar molecular structures is an important step in the process of bio-molecular structure and function analysis. Molecular surfaces are simple representations of molecular structure that are easily ...

    Authors: Nithin Shivashankar, Sonali Patil, Amrisha Bhosle, Nagasuma Chandra and Vijay Natarajan

    Citation: BMC Bioinformatics 2016 17:26

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  27. Content type: Methodology article

    The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is incr...

    Authors: Fernando I. Gutiérrez, Felipe Rodriguez-Valenzuela, Ignacio L. Ibarra, Damien P. Devos and Francisco Melo

    Citation: BMC Bioinformatics 2016 17:20

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  29. Content type: Research article

    Viruses are the most abundant and genetically diverse biological entities on earth, yet the repertoire of viral proteins remains poorly explored. As the number of sequenced virus genomes grows into the thousan...

    Authors: David M. Kristensen, Usman Saeed, Dmitrij Frishman and Eugene V. Koonin

    Citation: BMC Bioinformatics 2015 16:380

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  31. Content type: Research article

    The central element of each enzyme is the catalytic site, which commonly catalyzes a single biochemical reaction with high specificity. It was unclear to us how often sites that catalyze the same or highly sim...

    Authors: Clemens Žváček, Gerald Friedrichs, Leonhard Heizinger and Rainer Merkl

    Citation: BMC Bioinformatics 2015 16:359

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  33. Content type: Research article

    With more and more protein sequences produced in the genomic era, predicting protein structures from sequences becomes very important for elucidating the molecular details and functions of these proteins for b...

    Authors: Jilong Li, Renzhi Cao and Jianlin Cheng

    Citation: BMC Bioinformatics 2015 16:337

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  34. Content type: Research article

    The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to expl...

    Authors: Xian Jin, Mahendra Awale, Michaël Zasso, Daniel Kostro, Luc Patiny and Jean-Louis Reymond

    Citation: BMC Bioinformatics 2015 16:339

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  35. Content type: Methodology article

    The entire collection of genetic information resides within the chromosomes, which themselves reside within almost every cell nucleus of eukaryotic organisms. Each individual chromosome is found to have its ow...

    Authors: Jackson Nowotny, Sharif Ahmed, Lingfei Xu, Oluwatosin Oluwadare, Hannah Chen, Noelan Hensley, Tuan Trieu, Renzhi Cao and Jianlin Cheng

    Citation: BMC Bioinformatics 2015 16:338

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  38. Content type: Methodology article

    The function of RNA is strongly dependent on its structure, so an appropriate recognition of this structure, on every level of organization, is of great importance. One particular concern is the assessment of ...

    Authors: Agnieszka Rybarczyk, Natalia Szostak, Maciej Antczak, Tomasz Zok, Mariusz Popenda, Ryszard Adamiak, Jacek Blazewicz and Marta Szachniuk

    Citation: BMC Bioinformatics 2015 16:276

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  39. Content type: Database

    Membrane proteins represent over 25 % of human protein genes and account for more than 60 % of drug targets due to their accessibility from the extracellular environment. The increasing number of available cry...

    Authors: Marc Perea, Ivar Lugtenburg, Eduardo Mayol, Arnau Cordomí, Xavier Deupí, Leonardo Pardo and Mireia Olivella

    Citation: BMC Bioinformatics 2015 16:266

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  41. Content type: Software

    Understanding the architecture and function of RNA molecules requires methods for comparing and analyzing their tertiary and quaternary structures. While structural superposition of short RNAs is achievable in...

    Authors: Petr Čech, David Hoksza and Daniel Svozil

    Citation: BMC Bioinformatics 2015 16:253

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  42. Content type: Methodology article

    RNA-protein complexes play an essential role in many biological processes. To explore potential functions of RNA-protein complexes, it’s important to identify RNA-binding residues in proteins.

    Authors: Huizhu Ren and Ying Shen

    Citation: BMC Bioinformatics 2015 16:249

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  43. Content type: Research article

    Proteins play an important role in biological processes in living organisms. Many protein functions are based on interaction with other proteins. The structural information is important for adequate descriptio...

    Authors: Tatsiana Kirys, Anatoly M. Ruvinsky, Deepak Singla, Alexander V. Tuzikov, Petras J. Kundrotas and Ilya A. Vakser

    Citation: BMC Bioinformatics 2015 16:243

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  44. Content type: Methodology Article

    The knowledge of the spatial organisation of the chromatin fibre in cell nuclei helps researchers to understand the nuclear machinery that regulates dna activity. Recent experimental techniques of the type Chromo...

    Authors: Claudia Caudai, Emanuele Salerno, Monica Zoppè and Anna Tonazzini

    Citation: BMC Bioinformatics 2015 16:234

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  45. Content type: Research article

    Interactions that involve one or more amino acid side chains near the ends of protein helices stabilize helix termini and shape the geometry of the adjacent loops, making a substantial contribution to overall ...

    Authors: Nicholas E Newell

    Citation: BMC Bioinformatics 2015 16:231

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  46. Content type: Software

    Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dyna...

    Authors: Sandhya P Tiwari, Edvin Fuglebakk, Siv M Hollup, Lars Skjærven, Tristan Cragnolini, Svenn H Grindhaug, Kidane M Tekle and Nathalie Reuter

    Citation: BMC Bioinformatics 2014 15:427

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  49. Content type: Research article

    Genome variation is very high in influenza A viruses. However, viral evolution and spreading is strongly influenced by immunogenic features and capacity to bind host cells, depending in turn on the two major c...

    Authors: Irene Righetto, Adelaide Milani, Giovanni Cattoli and Francesco Filippini

    Citation: BMC Bioinformatics 2014 15:363

    Published on:

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