• Corpus ID: 236034325

New algorithm to determine a minimal representation of the molecular surface

@inproceedings{Grassmann2021NewAT,
  title={New algorithm to determine a minimal representation of the molecular surface},
  author={Greta Grassmann and Mattia Miotto and Lorenzo Di Rienzo and Giorgio Gosti and Giancarlo Ruocco and Edoardo Milanetti},
  year={2021}
}
Most proteins perform their biological function by interacting with one or more molecular partners. In this respect, characterizing the features of the molecular surface, especially in the portions where the interaction takes place, turned out to be a crucial step in the investigation of the mechanisms of recognition and binding between molecules. Predictive methods often rely on extensive samplings of molecular patches with the aim to identify hot spots on the surface. In this framework… 

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References

SHOWING 1-10 OF 31 REFERENCES
Efficient molecular surface generation using level-set methods.
Protein-protein docking using region-based 3D Zernike descriptors
TLDR
A novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape that is adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction is presented.
Protein Molecular Surface Mapped at Different Geometrical Resolutions
TLDR
The contribution presents a methodology for describing and quantifying the molecular properties of proteins, by geometrical and physico-chemical mapping of the molecular surfaces, with several analytical relationships being proposed for molecular surface properties.
Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking.
TLDR
The 3D Zernike descriptor (3DZD), an emerging technique to describe molecular surfaces, is introduced, a series expansion of mathematical three-dimensional function which allows rapid comparison of surface shapes, which is sufficient for real-time structure database screening.
The Role of Water Occlusion for the Definition of a Protein Binding Hot-Spot.
  • I. Moreira
  • Biology, Chemistry
    Current topics in medicinal chemistry
  • 2015
TLDR
This review has focused on the structural data available that support the occlusion of HS from solvent, and therefore the "O-ring theory" not only on protein-protein but also onprotein-DNA complexes and the use of Solvent Accessible Surface Area (SASA) features in a variety of machine-learning approaches that aim to detect binding HS.
How proteins get in touch: interface prediction in the study of biomolecular complexes.
TLDR
An overview of the state of the art in the field of protein-protein interface prediction is provided, and the performance of existing interface predictors is discussed.
Contacts-based prediction of binding affinity in protein–protein complexes
TLDR
A new and simple approach to predict binding affinity based on functional and structural features of the biological system, namely the network of interfacial contacts, which reaches a high prediction accuracy for such a diverse dataset outperforming all other tested methods.
Protein-protein docking: from interaction to interactome.
  • I. Vakser
  • Biology, Chemistry
    Biophysical journal
  • 2014
Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles
TLDR
It is shown that a scoring function based on interface structure profiles collected from analogous protein-protein interactions in the PDB is a powerful predictor of protein binding affinity changes upon mutation and should find useful application in human-disease mutation recognition and protein interface design studies.
Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0
TLDR
Patch-Surfer2.0, which predicts binding ligands for a protein pocket by representing and comparing pockets at the level of small local surface patches that characterize physicochemical properties of the local regions, can identify binding pockets of the same ligand even if they do not share globally similar shapes.
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