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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. The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is im...

    Authors: Bharat Panwar, Sudheer Gupta and Gajendra P S Raghava

    Citation: BMC Bioinformatics 2013 14:44

    Content type: Research article

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  2. Protein pairs that have the same secondary structure packing arrangement but have different topologies have attracted much attention in terms of both evolution and physical chemistry of protein structures. Fur...

    Authors: Shintaro Minami, Kengo Sawada and George Chikenji

    Citation: BMC Bioinformatics 2013 14:24

    Content type: Methodology article

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  3. Amyloids are proteins capable of forming fibrils. Many of them underlie serious diseases, like Alzheimer disease. The number of amyloid-associated diseases is constantly increasing. Recent studies indicate tha...

    Authors: Jerzy Stanislawski, Malgorzata Kotulska and Olgierd Unold

    Citation: BMC Bioinformatics 2013 14:21

    Content type: Research article

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  4. Distinguishing biologically relevant interfaces from lattice contacts in protein crystals is a fundamental problem in structural biology. Despite efforts towards the computational prediction of interface chara...

    Authors: Jose M Duarte, Adam Srebniak, Martin A Schärer and Guido Capitani

    Citation: BMC Bioinformatics 2012 13:334

    Content type: Research article

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  5. The structures of biological macromolecules provide a framework for studying their biological functions. Three-dimensional structures of proteins, nucleic acids, or their complexes, are difficult to visualize ...

    Authors: Michal J Pietal, Natalia Szostak, Kristian M Rother and Janusz M Bujnicki

    Citation: BMC Bioinformatics 2012 13:333

    Content type: Software

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  6. This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interact...

    Authors: Rodrigo C Barros, Ana T Winck, Karina S Machado, Márcio P Basgalupp, André CPLF de Carvalho, Duncan D Ruiz and Osmar Norberto de Souza

    Citation: BMC Bioinformatics 2012 13:310

    Content type: Research article

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  7. Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the ...

    Authors: Jim Jing-Yan Wang, Halima Bensmail and Xin Gao

    Citation: BMC Bioinformatics 2012 13:307

    Content type: Methodology article

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  8. Computational models of protein structures were proved to be useful as search models in Molecular Replacement (MR), a common method to solve the phase problem faced by macromolecular crystallography. The succe...

    Authors: Marcin Pawlowski and Janusz M Bujnicki

    Citation: BMC Bioinformatics 2012 13:289

    Content type: Research article

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  9. X-converting enzyme (XCE) involved in nervous control of respiration, is a member of the M13 family of zinc peptidases, for which no natural substrate has been identified yet. In contrast, it’s well characteri...

    Authors: Zaheer Ul-Haq, Sadaf Iqbal and Syed Tarique Moin

    Citation: BMC Bioinformatics 2012 13:285

    Content type: Research article

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  10. The generation of focused mutant libraries at hotspot residues is an important strategy in directed protein evolution. Existing methods, such as combinatorial active site testing and residual coupling analysis...

    Authors: Chenghua Wang, Ribo Huang, Bingfang He and Qishi Du

    Citation: BMC Bioinformatics 2012 13:263

    Content type: Research article

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  11. RNA secondary structure prediction, or folding, is a classic problem in bioinformatics: given a sequence of nucleotides, the aim is to predict the base pairs formed in its three dimensional conformation. The i...

    Authors: Rune B Lyngsø, James WJ Anderson, Elena Sizikova, Amarendra Badugu, Tomas Hyland and Jotun Hein

    Citation: BMC Bioinformatics 2012 13:260

    Content type: Research article

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  12. Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the numbe...

    Authors: Bogumil M Konopka, Jean-Christophe Nebel and Malgorzata Kotulska

    Citation: BMC Bioinformatics 2012 13:242

    Content type: Methodology article

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  13. Protein interactions play a key role in life processes. Characterization of conformational properties of protein-protein interactions is important for understanding the mechanisms of protein association. The r...

    Authors: Tatsiana Kirys, Anatoly M Ruvinsky, Alexander V Tuzikov and Ilya A Vakser

    Citation: BMC Bioinformatics 2012 13:236

    Content type: Research article

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  14. Protein-DNA interactions are important for many cellular processes, however structural knowledge for a large fraction of known and putative complexes is still lacking. Computational docking methods aim at the ...

    Authors: Piotr Setny, Ranjit Prasad Bahadur and Martin Zacharias

    Citation: BMC Bioinformatics 2012 13:228

    Content type: Methodology article

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  15. Employing methods to assess the quality of modeled protein structures is now standard practice in bioinformatics. In a broad sense, the techniques can be divided into methods relying on consensus prediction on...

    Authors: Arjun Ray, Erik Lindahl and Björn Wallner

    Citation: BMC Bioinformatics 2012 13:224

    Content type: Methodology article

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  16. Histone deacetylase (HDAC) is a novel target for the treatment of cancer and it can be classified into three classes, i.e., classes I, II, and IV. The inhibitors selectively targeting individual HDAC have been...

    Authors: Dingfeng Wu, Qi Huang, Yida Zhang, Qingchen Zhang, Qi Liu, Jun Gao, Zhiwei Cao and Ruixin Zhu

    Citation: BMC Bioinformatics 2012 13:212

    Content type: Research article

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  17. Human TWIST1 is a highly conserved member of the regulatory basic helix-loop-helix (bHLH) transcription factors. TWIST1 forms homo- or heterodimers with E-box proteins, such as E2A (isoforms E12 and E47), MYOD...

    Authors: Amanda M Maia, João HM da Silva, André L Mencalha, Ernesto R Caffarena and Eliana Abdelhay

    Citation: BMC Bioinformatics 2012 13:184

    Content type: Research article

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  18. There is a need for automated methods to learn general features of the interactions of a ligand class with its diverse set of protein receptors. An appropriate machine learning approach is Inductive Logic Prog...

    Authors: Jose C A Santos, Houssam Nassif, David Page, Stephen H Muggleton and Michael J E Sternberg

    Citation: BMC Bioinformatics 2012 13:162

    Content type: Research article

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  19. One aim of the in silico characterization of proteins is to identify all residue-positions, which are crucial for function or structure. Several sequence-based algorithms exist, which predict functionally importa...

    Authors: Jan-Oliver Janda, Markus Busch, Fabian Kück, Mikhail Porfenenko and Rainer Merkl

    Citation: BMC Bioinformatics 2012 13:55

    Content type: Research article

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  20. Identification of the residues in protein-protein interaction sites has a significant impact in problems such as drug discovery. Motivated by the observation that the set of interface residues of a protein ten...

    Authors: Rafael A Jordan, Yasser EL-Manzalawy, Drena Dobbs and Vasant Honavar

    Citation: BMC Bioinformatics 2012 13:41

    Content type: Research article

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  21. Protein structures provide a valuable resource for rational drug design. For a protein with no known ligand, computational tools can predict surface pockets that are of suitable size and shape to accommodate a...

    Authors: Paul Ashford, David S Moss, Alexander Alex, Siew K Yeap, Alice Povia, Irene Nobeli and Mark A Williams

    Citation: BMC Bioinformatics 2012 13:39

    Content type: Methodology article

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  22. Random-sequence peptide libraries are a commonly used tool to identify novel ligands for binding antibodies, other proteins, and small molecules. It is often of interest to compare the selected peptide sequenc...

    Authors: Rebecca F Halperin, Phillip Stafford, Jack S Emery, Krupa Arun Navalkar and Stephen Albert Johnston

    Citation: BMC Bioinformatics 2012 13:1

    Content type: Software

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  23. Accurate prediction of peptide immunogenicity and characterization of relation between peptide sequences and peptide immunogenicity will be greatly helpful for vaccine designs and understanding of the immune s...

    Authors: Chun-Wei Tung, Matthias Ziehm, Andreas Kämper, Oliver Kohlbacher and Shinn-Ying Ho

    Citation: BMC Bioinformatics 2011 12:446

    Content type: Research article

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  24. In addition to sequence conservation, protein multiple sequence alignments contain evolutionary signal in the form of correlated variation among amino acid positions. This signal indicates positions in the seq...

    Authors: Janardanan Sreekumar, Cajo JF ter Braak, Roeland CHJ van Ham and Aalt DJ van Dijk

    Citation: BMC Bioinformatics 2011 12:444

    Content type: Research article

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  25. Many bioinformatics tools for RNA secondary structure analysis are based on a thermodynamic model of RNA folding. They predict a single, "optimal" structure by free energy minimization, they enumerate near-opt...

    Authors: Stefan Janssen, Christian Schudoma, Gerhard Steger and Robert Giegerich

    Citation: BMC Bioinformatics 2011 12:429

    Content type: Research article

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  26. Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been ...

    Authors: Michael Bieri and Paul R Gooley

    Citation: BMC Bioinformatics 2011 12:421

    Content type: Software

    Published on:

  27. Machine learning methods are nowadays used for many biological prediction problems involving drugs, ligands or polypeptide segments of a protein. In order to build a prediction model a so called training data ...

    Authors: Ozgur Demir-Kavuk, Mayumi Kamada, Tatsuya Akutsu and Ernst-Walter Knapp

    Citation: BMC Bioinformatics 2011 12:412

    Content type: Methodology article

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