DockAnalyse: an application for the analysis of protein-protein interactions

Amela, Isaac; Delicado, Pedro; Gómez, Antonio; Bonàs, Sílvia; Querol, Enrique; Cedano, Juan
January 2010
BMC Structural Biology;2010, Vol. 10, p37
Academic Journal
Background: Is it possible to identify what the best solution of a docking program is? The usual answer to this question is the highest score solution, but interactions between proteins are dynamic processes, and many times the interaction regions are wide enough to permit protein-protein interactions with different orientations and/or interaction energies. In some cases, as in a multimeric protein complex, several interaction regions are possible among the monomers. These dynamic processes involve interactions with surface displacements between the proteins to finally achieve the functional configuration of the protein complex. Consequently, there is not a static and single solution for the interaction between proteins, but there are several important configurations that also have to be analyzed. Results: To extract those representative solutions from the docking output datafile, we have developed an unsupervised and automatic clustering application, named DockAnalyse. This application is based on the already existing DBscan clustering method, which searches for continuities among the clusters generated by the docking output data representation. The DBscan clustering method is very robust and, moreover, solves some of the inconsistency problems of the classical clustering methods like, for example, the treatment of outliers and the dependence of the previously defined number of clusters. Conclusions: DockAnalyse makes the interpretation of the docking solutions through graphical and visual representations easier by guiding the user to find the representative solutions. We have applied our new approach to analyze several protein interactions and model the dynamic protein interaction behavior of a protein complex. DockAnalyse might also be used to describe interaction regions between proteins and, therefore, guide future flexible dockings. The application (implemented in the R package) is accessible.


Related Articles

  • Exploring Function Prediction in Protein Interaction Networks via Clustering Methods. Trivodaliev, Kire; Bogojeska, Aleksandra; Kocarev, Ljupco // PLoS ONE;Jun2014, Vol. 9 Issue 6, p1 

    Complex networks have recently become the focus of research in many fields. Their structure reveals crucial information for the nodes, how they connect and share information. In our work we analyze protein interaction networks as complex networks for their functional modular structure and later...

  • A novel method for comparing topological models of protein structures enhanced with ligand information. Mallika Veeramalai; David Gilbert // Bioinformatics;Dec2008, Vol. 24 Issue 23, p2698 

    We introduce TOPS+ strings, a highly abstract string-based model of protein topology that permits efficient computation of structure comparison, and can optionally represent ligand information. In this model, we consider loops as secondary structure elements (SSEs) as well as helices and...

  • Implications for domain fusion protein-protein interactions based on structural information. Jer-Ming Chia; Kolatkar, Prasanna R. // BMC Bioinformatics;2004, Vol. 5, p161 

    Background: Several in silico methods exist that were developed to predict protein interactions from the copious amount of genomic and proteomic data. One of these methods is Domain Fusion, which has proven to be effective in predicting functional links between proteins. Results: Analyzing the...

  • IS-Dom: a dataset of independent structural domains automatically delineated from protein structures. Ebina, Teppei; Umezawa, Yuki; Kuroda, Yutaka // Journal of Computer-Aided Molecular Design;May2013, Vol. 27 Issue 5, p419 

    Protein domains that can fold in isolation are significant targets in diverse area of proteomics research as they are often readily analyzed by high-throughput methods. Here, we report IS-Dom, a dataset of Independent Structural Domains (ISDs) that are most likely to fold in isolation. IS-Dom...

  • Exploring Angular Distance in Protein-Protein Docking Algorithms. Vreven, Thom; Hwang, Howook; Weng, Zhiping // PLoS ONE;Feb2013, Vol. 8 Issue 2, p1 

    We present a two-stage hybrid-resolution approach for rigid-body protein-protein docking. The first stage is carried out at low-resolution (15°) angular sampling. In the second stage, we sample promising regions from the first stage at a higher resolution of 6°. The hybrid-resolution...

  • Local Network Patterns in Protein-Protein Interfaces. Luo, Qiang; Hamer, Rebecca; Reinert, Gesine; Deane, Charlotte M. // PLoS ONE;Mar2013, Vol. 8 Issue 3, p1 

    Protein-protein interfaces hold the key to understanding protein-protein interactions. In this paper we investigated local interaction network patterns beyond pair-wise contact sites by considering interfaces as contact networks among residues. A contact site was defined as any residue on the...

  • The N-terminal Helix Controls the Transition between the Soluble and Amyloid States of an FF Domain. Castillo, Virginia; Chiti, Fabrizio; Ventura, Salvador // PLoS ONE;Mar2013, Vol. 8 Issue 3, p1 

    Background: Protein aggregation is linked to the onset of an increasing number of human nonneuropathic (either localized or systemic) and neurodegenerative disorders. In particular, misfolding of native α-helical structures and their self-assembly into nonnative intermolecular β-sheets...

  • Truncated and Helix-Constrained Peptides with High Affinity and Specificity for the cFos Coiled-Coil of AP-1. Rao, Tara; Ruiz-Gómez, Gloria; Hill, Timothy A.; Hoang, Huy N.; Fairlie, David P.; Mason, Jody M. // PLoS ONE;Mar2013, Vol. 8 Issue 3, p1 

    Protein-based therapeutics feature large interacting surfaces. Protein folding endows structural stability to localised surface epitopes, imparting high affinity and target specificity upon interactions with binding partners. However, short synthetic peptides with sequences corresponding to such...

  • The Evolutionary Dynamics of Protein-Protein Interaction Networks Inferred from the Reconstruction of Ancient Networks. Jin, Yuliang; Turaev, Dmitrij; Weinmaier, Thomas; Rattei, Thomas; Makse, Hernán A. // PLoS ONE;Mar2013, Vol. 8 Issue 3, p1 

    Cellular functions are based on the complex interplay of proteins, therefore the structure and dynamics of these protein-protein interaction (PPI) networks are the key to the functional understanding of cells. In the last years, large-scale PPI networks of several model organisms were...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics