NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems

Bioinformatics
Sergio DecherchiWalter Rocchia

Abstract

NanoShaper is a program specifically aiming the construction and analysis of the molecular surface of nanoscopic systems. It uses ray-casting for parallelism and it performs analytical computations whenever possible to maximize robustness and accuracy of the approach. Among the other features, NanoShaper provides volume, surface area, including that of internal cavities, for any considered molecular system. It identifies pockets via a very intuitive definition based on the concept of probe radius, intrinsic to the definition of the solvent excluded surface. We show here that, with a suitable choice of the parameters, the same approach can also permit the visualisation of molecular channels. NanoShaper has now been interfaced with the widely used molecular visualization software VMD, further enriching its already well furnished toolset. VMD is available at http://www.ks.uiuc.edu/Research/vmd/. NanoShaper, its documentation, tutorials and supporting programs are available at http://concept.iit.it/downloads. Supplementary data are available at Bioinformatics online.

References

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Oct 6, 2017·ACS Central Science·Giuseppina La SalaWalter Rocchia

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Citations

Mar 12, 2020·Frontiers in Molecular Biosciences·Artemi BendandiWalter Rocchia
Nov 3, 2020·Computational and Structural Biotechnology Journal·Artemi BendandiWalter Rocchia
Jun 8, 2021·Journal of Chemical Information and Modeling·Daniel J EvansAlbert Y Lau
Jun 11, 2021·The Journal of Physical Chemistry Letters·Laura RiccardiMarco De Vivo
Dec 11, 2020·The Journal of Physical Chemistry Letters·Andrea SpitaleriWalter Rocchia
Nov 9, 2021·Journal of Chemical Information and Modeling·Mohammed BenabderrahmaneJana Sopkova-de Oliveira Santos

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