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Computational analysis

Section edited by David Burke

This section incorporates all aspects of the methods, applications and analysis of the structure of biological macromolecules incorporating substantial analysis using computational methods.

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  1. White Spot Syndrome Virus (WSSV) is an enveloped double-stranded DNA virus which causes mortality of several species of shrimp, being considered one of the main pathogens that affects global shrimp farming. Th...

    Authors: Cayro de Macêdo Mendes, Diego Gomes Teixeira, João Paulo Matos Santos Lima and Daniel Carlos Ferreira Lanza
    Citation: BMC Structural Biology 2019 19:8
    Content type: Research article Published on:

  3. Plasmodium vivax merozoite surface protein 3α (PvMSP3α) is a promising vaccine candidate which has shown strong association with immunogenicity and protectiveness. Its use is however complicated by evolutionary p...

    Authors: Alebachew Messele Kebede, Fitsum Girma Tadesse, Adey Desta Feleke, Lemu Golassa and Endalamaw Gadisa
    Citation: BMC Structural Biology 2019 19:6
    Content type: Research article Published on:

  4. Computational models of RNA 3D structure often present various inaccuracies caused by simplifications used in structure prediction methods, such as template-based modeling or coarse-grained simulations. To obt...

    Authors: Juliusz Stasiewicz, Sunandan Mukherjee, Chandran Nithin and Janusz M. Bujnicki
    Citation: BMC Structural Biology 2019 19:5
    Content type: Software Published on:

  5. The THAP (Thanatos Associated Proteins) protein family in humans is implicated in various important cellular processes like epigenetic regulation, maintenance of pluripotency, transposition and disorders like ...

    Authors: Hiral M. Sanghavi, Sairam S. Mallajosyula and Sharmistha Majumdar
    Citation: BMC Structural Biology 2019 19:4
    Content type: Research article Published on:

    The Correction to this article has been published in BMC Structural Biology 2019 19:7

  6. It had long been thought that a protein exhibits its specific function through its own specific 3D-structure under physiological conditions. However, subsequent research has shown that there are many proteins ...

    Authors: Takumi Shimomura, Kohki Nishijima and Takeshi Kikuchi
    Citation: BMC Structural Biology 2019 19:3
    Content type: Research article Published on:

  8. Antibody, the primary effector molecule of the immune system, evolves after initial encounter with the antigen from a precursor form to a mature one to effectively deal with the antigen. Antibodies of a lineag...

    Authors: Harmeet Kaur, Neetu Sain, Debasisa Mohanty and Dinakar M. Salunke
    Citation: BMC Structural Biology 2018 18:19
    Content type: Research article Published on:

  9. To perform a three-dimensional (3-D) reconstruction of electron cryomicroscopy (cryo-EM) images of viruses, it is necessary to determine the similarity of image blocks of the two-dimensional (2-D) projections ...

    Authors: Jianquan Ouyang, Zezhi Liang, Chunyu Chen, Zhuosong Fu, Yue Zhang and Hongrong Liu
    Citation: BMC Structural Biology 2018 18:18
    Content type: Research article Published on:

  10. In the backdrop of challenge to obtain a protein structure under the known limitations of both experimental and theoretical techniques, the need of a fast as well as accurate protein structure evaluation metho...

    Authors: Manoj Kumar Pal, Tapobrata Lahiri, Garima Tanwar and Rajnish Kumar
    Citation: BMC Structural Biology 2018 18:16
    Content type: Research article Published on:

  11. Aryl hydrocarbon receptor (AhR) ligands may act as potential carcinogens or anti-tumor agents. Understanding how some of the residues in AhR ligand binding domain (AhRLBD) modulate their interactions with liga...

    Authors: Kumaraswamy Naidu Chitrala, Xiaoming Yang, Prakash Nagarkatti and Mitzi Nagarkatti
    Citation: BMC Structural Biology 2018 18:15
    Content type: Research article Published on:

  12. One of the main concerns of the modern medicine is the frightening spread of antimicrobial resistance caused mainly by the misuse of antibiotics. The researchers worldwide are actively involved in the search f...

    Authors: Anna Verdino, Felicia Zollo, Margherita De Rosa, Annunziata Soriente, Miguel Ángel Hernández-Martínez and Anna Marabotti
    Citation: BMC Structural Biology 2018 18:13
    Content type: Research article Published on:

  13. Dramatic progress has recently been made in cryo-electron microscopy technologies, which now make possible the reconstruction of a growing number of biomolecular structures to near-atomic resolution. However, ...

    Authors: Julio A. Kovacs, Vitold E. Galkin and Willy Wriggers
    Citation: BMC Structural Biology 2018 18:12
    Content type: Methodology article Published on:

  14. Eukaryotic translation initiation factor 1A (eIF1A) is universally conserved in all organisms. It has multiple functions in translation initiation, including assembly of the ribosomal pre-initiation complexes,...

    Authors: Jielin Yu and Assen Marintchev
    Citation: BMC Structural Biology 2018 18:11
    Content type: Research article Published on:

  15. Due to dengue virus disease, half of the world population is at severe health risk. Viral encoded NS2B-NS3 protease complex causes cleavage in the nonstructural region of the viral polyprotein. The cleavage is...

    Authors: Muhammad Waseem Sarwar, Adeel Riaz, Syed Muhammad Raihan Dilshad, Ahmed Al-Qahtani, Muhammad Shah Nawaz-Ul-Rehman and Muhammad Mubin
    Citation: BMC Structural Biology 2018 18:6
    Content type: Research article Published on:

  16. Membrane proteins are difficult targets for structure prediction due to the limited structural data deposited in Protein Data Bank. Most computational methods for membrane protein structure prediction are base...

    Authors: Dorota Latek
    Citation: BMC Structural Biology 2017 17:8
    Content type: Research Article Published on:

  18. The Spumaretrovirinae (foamy viruses) and the Orthoretrovirinae (e.g. HIV) share many similarities both in genome structure and the sequences of the core viral encoded proteins, such as the aspartyl protease and ...

    Authors: William R. Taylor, Jonathan P. Stoye and Ian A. Taylor
    Citation: BMC Structural Biology 2017 17:3
    Content type: Research Article Published on:

  19. TPX2 (Targeting Protein for Xklp2) is essential for spindle assembly, activation of the mitotic kinase Aurora A and for triggering microtubule nucleation. Homologs of TPX2 in Chordata and plants were previousl...

    Authors: Luis Sanchez-Pulido, Laurent Perez, Steffen Kuhn, Isabelle Vernos and Miguel A. Andrade-Navarro
    Citation: BMC Structural Biology 2016 16:17
    Content type: Research article Published on:

  20. The Plasmodium falciparum M18 Aspartyl Aminopeptidase (PfM18AAP) is only aspartyl aminopeptidase which is found in the genome of P. falciparum and is essential for its survival. The PfM18AAP enzyme performs vario...

    Authors: Madhulata Kumari, Subhash Chandra, Neeraj Tiwari and Naidu Subbarao
    Citation: BMC Structural Biology 2016 16:12
    Content type: Research article Published on:

  21. We comprehensively analyzed X-ray cocrystal structures of dipeptidyl peptidase IV (DPP-4) and its inhibitor to clarify whether DPP-4 alters its general or partial structure according to the inhibitor used and ...

    Authors: Hiroyuki Nojima, Kazuhiko Kanou, Genki Terashi, Mayuko Takeda-Shitaka, Gaku Inoue, Koichiro Atsuda, Chihiro Itoh, Chie Iguchi and Hajime Matsubara
    Citation: BMC Structural Biology 2016 16:11
    Content type: Research article Published on:

  22. During inflammation, leukocytes are captured by the selectin family of adhesion receptors lining blood vessels to facilitate exit from the bloodstream. E-selectin is upregulated on stimulated endothelial cells...

    Authors: Anne D. Rocheleau, Thong M. Cao, Tait Takitani and Michael R. King
    Citation: BMC Structural Biology 2016 16:10
    Content type: Research article Published on:

  23. This study investigates the allosteric coupling that exists between the intra- and extracellular parts of human β2-adrenergic receptor (β2-AR), in the presence of the intracellular loop 3 (ICL3), which is missing...

    Authors: Canan Ozgur, Pemra Doruker and E. Demet Akten
    Citation: BMC Structural Biology 2016 16:9
    Content type: Research article Published on:

  24. The term ‘molecular cartography’ encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorith...

    Authors: Dimitrios Georgios Kontopoulos, Dimitrios Vlachakis, Georgia Tsiliki and Sofia Kossida
    Citation: BMC Structural Biology 2016 16:4
    Content type: Software Published on:

    The Publisher's Erratum to this article has been published in BMC Structural Biology 2016 16:6

  25. Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions. Predicting c...

    Authors: Surabhi Maheshwari and Michal Brylinski
    Citation: BMC Structural Biology 2015 15:23
    Content type: Research article Published on:

  27. Many β-strands are not flat but bend and/or twist. However, although almost all β-strands have a twist, not all have a bend, suggesting that the underlying force(s) driving β-strand bending is distinct from th...

    Authors: Kazuo Fujiwara, Shinichi Ebisawa, Yuka Watanabe, Hiromi Fujiwara and Masamichi Ikeguchi
    Citation: BMC Structural Biology 2015 15:21
    Content type: Research article Published on:

  28. RNA ligases 2 are scarce and scattered across the tree of life. Two members of this family are well studied: the mitochondrial RNA editing ligase from the parasitic trypanosomes (Kinetoplastea), a promising dr...

    Authors: Sandrine Moreira, Emmanuel Noutahi, Guillaume Lamoureux and Gertraud Burger
    Citation: BMC Structural Biology 2015 15:20
    Content type: Research article Published on:

  30. Helicobacter pylori is an important factor in the development of diseases such as ulcer and gastric cancer. This bacterium uses a periplasmic transporter, UreI, to deliver urea to the ...

    Authors: Javier Cáceres-Delpiano, Jaime Teneb, Rodrigo Mansilla, Apolinaria García and Alexis Salas-Burgos
    Citation: BMC Structural Biology 2015 15:11
    Content type: Research article Published on:

  33. Thanks to the growth in sequence and structure databases, more than 50 million sequences are now available in UniProt and 100,000 structures in the PDB. Rich information about protein-protein interfaces can be...

    Authors: Kumaran Baskaran, Jose M Duarte, Nikhil Biyani, Spencer Bliven and Guido Capitani
    Citation: BMC Structural Biology 2014 14:22
    Content type: Research Article Published on:

  34. The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the...

    Authors: Kirill E. Medvedev, Nikolay A. Alemasov, Yuri N. Vorobjev, Elena V. Boldyreva, Nikolay A. Kolchanov and Dmitry A. Afonnikov
    Citation: BMC Structural Biology 2014 14:23
    Content type: Research article Published on:

  35. Despite the chloride anion is involved in fundamental biological processes, its interactions with proteins are little known. In particular, we lack a systematic survey of its coordination spheres.

    Authors: Oliviero Carugo
    Citation: BMC Structural Biology 2014 14:19
    Content type: Research article Published on:

  37. This paper provides a simple and rapid method for a protein-clustering strategy. The basic idea implemented here is to use computational geometry methods to predict and characterize ligand-binding pockets of a...

    Authors: Seyed Majid Saberi Fathi and Jack A Tuszynski
    Citation: BMC Structural Biology 2014 14:18
    Content type: Research article Published on:

  39. Protein model quality assessment is an essential component of generating and using protein structural models. During the Tenth Critical Assessment of Techniques for Protein Structure Prediction (CASP10), we de...

    Authors: Renzhi Cao, Zheng Wang and Jianlin Cheng
    Citation: BMC Structural Biology 2014 14:13
    Content type: Research article Published on:

  40. At least a quarter of any complete genome encodes for hypothetical proteins (HPs) which are largely non-similar to other known, well-characterized proteins. Predicting and solving their structures and function...

    Authors: Soo Huei Tan, Yahaya M Normi, Adam Thean Chor Leow, Abu Bakar Salleh, Roghayeh Abedi Karjiban, Abdul Munir Abdul Murad, Nor Muhammad Mahadi and Mohd Basyaruddin Abdul Rahman
    Citation: BMC Structural Biology 2014 14:11
    Content type: Research article Published on:

  41. High-throughput mass spectrometric (HT-MS) study is the method of choice for monitoring global changes in proteome. Data derived from these studies are meant for further validation and experimentation to disco...

    Authors: Arun Kumar Somavarapu, Satish Balakrishnan, Amit Kumar Singh Gautam, David S Palmer and Prasanna Venkatraman
    Citation: BMC Structural Biology 2014 14:9
    Content type: Research article Published on:

  42. Although many hyperthermophilic endoglucanases have been reported from archaea and bacteria, a complete survey and classification of all sequences in these species from disparate evolutionary groups, and the r...

    Authors: Hao Shi, Yu Zhang, Liangliang Wang, Xun Li, Wenqian Li, Fei Wang and Xiangqian Li
    Citation: BMC Structural Biology 2014 14:8
    Content type: Research article Published on:

  43. Klebsiella pneumoniae plays a major role in causing nosocomial infection in immunocompromised patients. Medical inflictions by the pathogen can range from respiratory and urinary tract infections, septicemia and ...

    Authors: Boon Aun Teh, Sy Bing Choi, Nasihah Musa, Few Ling Ling, See Too Wei Cun, Abu Bakar Salleh, Nazalan Najimudin, Habibah A Wahab and Yahaya M Normi
    Citation: BMC Structural Biology 2014 14:7
    Content type: Research article Published on:

  44. Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools i...

    Authors: Manuel Rueda, Modesto Orozco, Maxim Totrov and Ruben Abagyan
    Citation: BMC Structural Biology 2013 13:32
    Content type: Software Published on:

  46. Resveratrol, a naturally occurring stilbene, has been categorized as a phytoestrogen due to its ability to compete with natural estrogens for binding to estrogen receptor alpha (ERα) and modulate the biologica...

    Authors: Sandipan Chakraborty, Anait S Levenson and Pradip K Biswas
    Citation: BMC Structural Biology 2013 13:27
    Content type: Research article Published on:

  47. Pyridoxal 5′-phosphate (PLP)-dependent enzymes of fold type I, the most studied structural class of the PLP-dependent enzyme superfamily, are known to exist as stand-alone homodimers or homotetramers. These en...

    Authors: Teresa Milano, Alessandro Paiardini, Ingeborg Grgurina and Stefano Pascarella
    Citation: BMC Structural Biology 2013 13:26
    Content type: Research article Published on:

  48. Protein Structure Initiative:Biology (PSI:Biology) is the third phase of PSI where protein structures are determined in high-throughput to characterize their biological functions. The transition to the third p...

    Authors: Paul J DePietro, Elchin S Julfayev and William A McLaughlin
    Citation: BMC Structural Biology 2013 13:24
    Content type: Research article Published on:

  49. The amount of transmembrane protein (TM) structures solved to date is now large enough to attempt large scale analyses. In particular, extensive studies of oligomeric interfaces in the transmembrane region are...

    Authors: Jose M Duarte, Nikhil Biyani, Kumaran Baskaran and Guido Capitani
    Citation: BMC Structural Biology 2013 13:21
    Content type: Research article Published on:

  50. Assessing protein modularity is important to understand protein evolution. Still the question of the existence of a sub-domain modular architecture remains. We propose a graph-theory approach with significance...

    Authors: Jose Sergio Hleap, Edward Susko and Christian Blouin
    Citation: BMC Structural Biology 2013 13:20
    Content type: Methodology article Published on:

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ISSN: 1472-6807

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