ArticleBMC bioinformatics2014
MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed.
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- Unveiling CD59-Antibody Interactions to Design Paratope-Mimicking Peptides for Complement Modulation.International journal of molecular sciences · 2023Article
- Unveiling New Druggable Pockets in Influenza Non-Structural Protein 1: NS1-Host Interactions as Antiviral Targets for Flu.International journal of molecular sciences · 2023Article
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- Exploring interfacial dynamics in homodimericRSC advances · 2021Article
- The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses.BMC bioinformatics · 2020Article
- Human LC3 and GABARAP subfamily members achieve functional specificity via specific structural modulations.Autophagy · 2020Article
- Barrier-to-autointegration factor 1 (Banf1) regulates poly [ADP-ribose] polymerase 1 (PARP1) activity following oxidative DNA damage.Nature communications · 2019Article
- Hydrodynamic and Electrophoretic Properties of Trastuzumab/HER2 Extracellular Domain Complexes as Revealed by Experimental Techniques and Computational Simulations.International journal of molecular sciences · 2019Article
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- Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification.BMC bioinformatics · 2018Article
- Investigating cyclic peptides inhibiting CD2-CD58 interactions through molecular dynamics and molecular docking methods.Journal of computer-aided molecular design · 2018Article
- Further Insight into the Interactions of the Cytotoxic Macrolides Laulimalide and Peloruside A with Their Common Binding Site.ACS omega · 2018Article
- Analyzing the role of CagV, a VirB8 homolog of the type IV secretion system ofFEBS open bio · 2017Article
- Introducing a Clustering Step in a Consensus Approach for the Scoring of Protein-Protein Docking Models.PloS one · 2016Article
- Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps.Molecules (Basel, Switzerland) · 2015Review
- Structural basis for the recognition in an idiotype-anti-idiotype antibody complex related to celiac disease.PloS one · 2014Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundMolecular Dynamics (MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface.
resultsOn these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface.
conclusionsMDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.
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