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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. 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

    Content type: Research Article

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  2. 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

    Content type: Research article

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  3. 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

    Content type: Research article

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  4. 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

    Content type: Research article

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  5. 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

    Content type: Research article

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  6. 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

    Content type: Research Article

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  7. 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

    Content type: Methodology article

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  8. 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

    Content type: Research article

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  9. 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

    Content type: Research article

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  10. 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

    Content type: Research article

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  11. 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

    Content type: Methodology article

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  12. 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

    Content type: Research article

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  13. 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

    Content type: Methodology article

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  14. 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

    Content type: Database

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  15. 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

    Content type: Software

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  16. 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

    Content type: Methodology article

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  17. 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

    Content type: Research article

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  18. 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

    Content type: Methodology Article

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  19. 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

    Content type: Research article

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  20. 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

    Content type: Software

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  21. 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

    Content type: Research article

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  22. Enzyme active sites can be connected to the exterior environment by one or more channels passing through the protein. Despite our current knowledge of enzyme structure and function, surprisingly little is know...

    Authors: Lukáš Pravda, Karel Berka, Radka Svobodová Vařeková, David Sehnal, Pavel Banáš, Roman A Laskowski, Jaroslav Koča and Michal Otyepka

    Citation: BMC Bioinformatics 2014 15:379

    Content type: Research article

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  23. Bioactive cyclic peptides derived from natural sources are well studied, particularly those derived from non-ribosomal synthetases in fungi or bacteria. Ribosomally synthesised bioactive disulphide-bonded loop...

    Authors: Fergal J Duffy, Marc Devocelle, David R Croucher and Denis C Shields

    Citation: BMC Bioinformatics 2014 15:305

    Content type: Research article

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  24. Various methods have been developed to computationally predict hotspot residues at novel protein-protein interfaces. However, there are various challenges in obtaining accurate prediction. We have developed a ...

    Authors: Prashant Shingate, Malini Manoharan, Anshul Sukhwal and Ramanathan Sowdhamini

    Citation: BMC Bioinformatics 2014 15:303

    Content type: Research article

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  25. Plasmid DNA molecules are closed circular molecules that are widely used in life sciences, particularly in gene therapy research. Monte Carlo methods have been used for several years to simulate the conformati...

    Authors: Adriano N Raposo and Abel JP Gomes

    Citation: BMC Bioinformatics 2014 15:301

    Content type: Methodology article

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  26. Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face s...

    Authors: Benjamin Lutz, Claude Sinner, Stefan Bozic, Ivan Kondov and Alexander Schug

    Citation: BMC Bioinformatics 2014 15:292

    Content type: Software

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  27. State-of-the-art protein-ligand docking methods are generally limited by the traditionally low accuracy of their scoring functions, which are used to predict binding affinity and thus vital for discriminating ...

    Authors: Hongjian Li, Kwong-Sak Leung, Man-Hon Wong and Pedro J Ballester

    Citation: BMC Bioinformatics 2014 15:291

    Content type: Research article

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  28. The identification of protein-protein interaction sites is a computationally challenging task and important for understanding the biology of protein complexes. There is a rich literature in this field. A broad...

    Authors: Zhijie Dong, Keyu Wang, Truong Khanh Linh Dang, Mehmet Gültas, Marlon Welter, Torsten Wierschin, Mario Stanke and Stephan Waack

    Citation: BMC Bioinformatics 2014 15:277

    Content type: Methodology article

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  29. The PCR technique and its variations have been increasingly used in the clinical laboratory and recent advances in this field generated new higher resolution techniques based on nucleic acid denaturation dynam...

    Authors: Raffael AC Oliveira, Ricardo VM Almeida, Márcia DA Dantas, Felipe N Castro, João Paulo MS Lima and Daniel CF Lanza

    Citation: BMC Bioinformatics 2014 15:243

    Content type: Research article

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  30. The characterization of protein binding sites is a major challenge in computational biology. Proteins interact with a wide variety of molecules and understanding of such complex interactions is essential to ga...

    Authors: Saulo HP Oliveira, Felipe AN Ferraz, Rodrigo V Honorato, José Xavier-Neto, Tiago JP Sobreira and Paulo SL de Oliveira

    Citation: BMC Bioinformatics 2014 15:197

    Content type: Software

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  31. Gut microbiome metagenomics has revealed many protein families and domains found largely or exclusively in that environment. Proteins containing the GxGYxYP domain are over-represented in the gut microbiota, a...

    Authors: Daniel J Rigden, Ruth Y Eberhardt, Harry J Gilbert, Qingping Xu, Yuanyuan Chang and Adam Godzik

    Citation: BMC Bioinformatics 2014 15:196

    Content type: Research article

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  32. The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation...

    Authors: Mikel Diez, Víctor Petuya, Luis Alfonso Martínez-Cruz and Alfonso Hernández

    Citation: BMC Bioinformatics 2014 15:184

    Content type: Research article

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  33. Since proteins function by interacting with other molecules, analysis of protein-protein interactions is essential for comprehending biological processes. Whereas understanding of atomic interactions within a ...

    Authors: Reyhaneh Esmaielbeiki and Jean-Christophe Nebel

    Citation: BMC Bioinformatics 2014 15:171

    Content type: Research article

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  34. The locations of the TM segments inside the membrane proteins are the consequence of a cascade of several events: the localizing of the nascent chain to the membrane, its insertion through the translocon, and ...

    Authors: Dominique Tessier, Sami Laroum, Béatrice Duval, Emma M Rath, W Bret Church and Jin-Kao Hao

    Citation: BMC Bioinformatics 2014 15:156

    Content type: Research article

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  35. It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein mode...

    Authors: Renzhi Cao, Zheng Wang, Yiheng Wang and Jianlin Cheng

    Citation: BMC Bioinformatics 2014 15:120

    Content type: Software

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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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