ArticleBioinformatics (Oxford, England)2019
NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- SHREC 2025: Protein surface shape retrieval including electrostatic potential.Computers & graphics · 2025Article
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- Bluues_cplx: Electrostatics at Protein-Protein and Protein-Ligand Interfaces.Molecules (Basel, Switzerland) · 2025Article
- Protein allosteric site identification using machine learning and per amino acid residue reported internal protein nanoenvironment descriptors.Computational and structural biotechnology journal · 2024Article
- sesA: A Program for the Analytic Computation of Solvent-Excluded Surface Areas.ChemistryOpen · 2024Article
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- SiteFerret: Beyond Simple Pocket Identification in Proteins.Journal of chemical theory and computation · 2023Article
- GSK-3β Allosteric Inhibition: A Dead End or a New Pharmacological Frontier?International journal of molecular sciences · 2023Review
- Coarse-Graining ddCOSMO through an Interface between Tinker and the ddX Library.The journal of physical chemistry. B · 2022Article
- In-Silico Selection of Aptamer Targeting SARS-CoV-2 Spike Protein.International journal of molecular sciences · 2022Article
- Chanalyzer: A Computational Geometry Approach for the Analysis of Protein Channel Shape and Dynamics.Frontiers in molecular biosciences · 2022Article
- Probabilistic Pocket Druggability PredictionFrontiers in pharmacology · 2022Article
- Finding Druggable Sites in Proteins Using TACTICS.Journal of chemical information and modeling · 2021Article
- Molecular Recognition by Gold Nanoparticle-Based Receptors as Defined through Surface Morphology and Pockets Fingerprint.The journal of physical chemistry letters · 2021Article
- Tuning Local Hydration Enables a Deeper Understanding of Protein-Ligand Binding: The PP1-Src Kinase Case.The journal of physical chemistry letters · 2021Article
- The role of histone tails in nucleosome stability: An electrostatic perspective.Computational and structural biotechnology journal · 2020Article
- Chromatin Compaction Multiscale Modeling: A Complex Synergy Between Theory, Simulation, and Experiment.Frontiers in molecular biosciences · 2020Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
summaryNanoShaper 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.
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