Sergio Decherchi, Andrea Spitaleri, John Stone, and Walter Rocchia.
NanoShaper-VMD interface: computing and visualizing surfaces,
pockets and channels in molecular systems.
Bioinformatics, 35:1241-1243, 2018.
(PMC: PMC6449750)
DECH2018-JS
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. Availability and implementation: 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 information: Supplementary data are available at Bioinformatics online.
Download Full Text
The manuscripts available on our site are provided for your personal
use only and may not be retransmitted or redistributed without written
permissions from the paper's publisher and author. You may not upload any
of this site's material to any public server, on-line service, network, or
bulletin board without prior written permission from the publisher and
author. You may not make copies for any commercial purpose. Reproduction
or storage of materials retrieved from this web site is subject to the
U.S. Copyright Act of 1976, Title 17 U.S.C.