Structural analysis

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. Research Article

    AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking

    Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the...

    Tanchanok Wisitponchai, Watshara Shoombuatong, Vannajan Sanghiran Lee, Kuntida Kitidee and Chatchai Tayapiwatana

    BMC Bioinformatics 2017 18:220

    Published on: 19 April 2017

  2. Research article

    Classifying kinase conformations using a machine learning approach

    Signaling proteins such as protein kinases adopt a diverse array of conformations to respond to regulatory signals in signaling pathways. Perhaps the most fundamental conformational change of a kinase is the t...

    Daniel Ian McSkimming, Khaled Rasheed and Natarajan Kannan

    BMC Bioinformatics 2017 18:86

    Published on: 2 February 2017

  3. Software

    RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation

    RNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of...

    Ying Li, Xiaohu Shi, Yanchun Liang, Juan Xie, Yu Zhang and Qin Ma

    BMC Bioinformatics 2017 18:51

    Published on: 21 January 2017

  4. Research article

    Structure alignment-based classification of RNA-binding pockets reveals regional RNA recognition motifs on protein surfaces

    Many critical biological processes are strongly related to protein-RNA interactions. Revealing the protein structure motifs for RNA-binding will provide valuable information for deciphering protein-RNA recogni...

    Zhi-Ping Liu, Shutang Liu, Ruitang Chen, Xiaopeng Huang and Ling-Yun Wu

    BMC Bioinformatics 2017 18:27

    Published on: 11 January 2017

  5. Research article

    Structural prediction of the interaction of the tumor suppressor p27KIP1 with cyclin A/CDK2 identifies a novel catalytically relevant determinant

    The cyclin-dependent kinase 2 (CDK2) together with its cyclin E and A partners is a central regulator of cell growth and division. Deregulation of CDK2 activity is associated with diseases such as cancer. The ...

    Jinyu Li, Jörg Vervoorts, Paolo Carloni, Giulia Rossetti and Bernhard Lüscher

    BMC Bioinformatics 2017 18:15

    Published on: 5 January 2017

  6. Research article

    Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23

    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...

    David T. Barkan, Xiao-li Cheng, Herodion Celino, Tran T. Tran, Ashok Bhandari, Charles S. Craik, Andrej Sali and Mark L. Smythe

    BMC Bioinformatics 2016 17:481

    Published on: 23 November 2016

  7. Software

    DASP3: identification of protein sequences belonging to functionally relevant groups

    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...

    Janelle B. Leuthaeuser, John H. Morris, Angela F. Harper, Thomas E. Ferrin, Patricia C. Babbitt and Jacquelyn S. Fetrow

    BMC Bioinformatics 2016 17:458

    Published on: 11 November 2016

  8. Methodology Article

    Structural alignment of protein descriptors – a combinatorial model

    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...

    Maciej Antczak, Marta Kasprzak, Piotr Lukasiak and Jacek Blazewicz

    BMC Bioinformatics 2016 17:383

    Published on: 17 September 2016

  9. Research article

    Fold-specific sequence scoring improves protein sequence matching

    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...

    Sumudu P. Leelananda, Andrzej Kloczkowski and Robert L. Jernigan

    BMC Bioinformatics 2016 17:328

    Published on: 30 August 2016

  10. Research article

    Replica exchange molecular dynamics simulations reveal the structural and molecular properties of levan-type fructo-oligosaccharides of various chain lengths

    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...

    Pongsakorn Kanjanatanin, Rath Pichyangkura and Surasak Chunsrivirot

    BMC Bioinformatics 2016 17:306

    Published on: 17 August 2016

  11. Research article

    Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server

    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 ...

    Luciano A. Abriata, Christophe Bovigny and Matteo Dal Peraro

    BMC Bioinformatics 2016 17:242

    Published on: 17 June 2016

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

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