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Molmil: a molecular viewer for the PDB and beyond

Gert-Jan Bekker, Haruki Nakamura, Akira R. Kinjo
2016 Journal of Cheminformatics  
We have developed a new platform-independent web-based molecular viewer using JavaScript and WebGL.  ...  The molecular viewer, Molmil, has been integrated into several services offered by Protein Data Bank Japan and can be easily extended with new functionality by third party developers.  ...  Implementation and capabilities Molmil has been designed as a light-weight and fullfeatured viewer for the PDB.  ... 
doi:10.1186/s13321-016-0155-1 pmid:27570544 pmcid:PMC5002144 fatcat:3gxi2nv6lbeyhosnwgydm52k7u

MOESM1 of Molmil: a molecular viewer for the PDB and beyond

Gert-Jan Bekker, Haruki Nakamura, Akira Kinjo
2017 Figshare  
Appendices; Example renderings using Molmil & Overview of alternative WebGL based molecular viewers.  ...  of the biological unit of 1bbt with group and chain colouring for the assymetric chains and the remaining chains respectively: Stick rendering and iso-surface of the electron density of 1ubq, part of  ...  : Coarse surface rendering with chain colouring of 3j3q (simplified): Cartoon and coarse surface rendering of the biological unit of 1bbt with group and chain colouring for the assymetric chains and the  ... 
doi:10.6084/m9.figshare.c.3696373_d1 fatcat:p4azn7jux5elfpdmu6h3miojvq

Web Apps Come of Age for Molecular Sciences

Luciano Abriata
2017 Informatics  
molecular sciences.  ...  Through examples based on JavaScript libraries, web applets, and even full web apps, either alone or coupled to each other, the article puts on the spotlight the potential of these technologies for carrying  ...  Conflicts of Interest: The author declares no conflict of interest.  ... 
doi:10.3390/informatics4030028 fatcat:xrz2ijpkdzfjfna43x6nexocam

3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories

Genís Bayarri, Adam Hospital, Modesto Orozco
2021 Frontiers in Molecular Biosciences  
The server offers a team working in different locations a single URL to share and discuss structural data in an interactive fashion, with the possibility to use it as a live figure for scientific papers  ...  Trajectories are efficiently stored and transferred to the NGL viewer thanks to an MDsrv-based data streaming.  ...  Molmil: a Molecular Viewer for the PDB and beyond. J. Cheminform 8 (1), 42. doi:10.1186/s13321-016-0155-1 PubMed Abstract | CrossRef Full Text | Google Scholar Berger, D. R., Seung, H.  ... 
doi:10.3389/fmolb.2021.726232 pmid:34485386 pmcid:PMC8414788 fatcat:rhdmwtutyzfcdetfkcvbuqb35m

Thermal stability of single-domain antibodies estimated by molecular dynamics simulations

Gert-Jan Bekker, Benson Ma, Narutoshi Kamiya
2018 Protein Science  
Because of their low molecular weight, sdAbs have advantages with respect to production and delivery to their targets and for applications such as antibody drugs and biosensors.  ...  The fraction of native atomic contacts, Q, measured for the 400 K simulations showed a fairly good correlation with the Tm values.  ...  Computational resources of a PC cluster were partly provided by the HPCI Research Project (hp170024) and the OCTOPUS system at the Cyber Media Center, Osaka University. We thank Ms.  ... 
doi:10.1002/pro.3546 pmid:30394618 pmcid:PMC6319760 fatcat:f3algbljljgqhdqiaunsvohobe

Modern Scientific Visualizations on the Web

Loraine Franke, Daniel Haehn
2020 Informatics  
These technologies, paired with the accessibility of websites, potentially offer a user experience beyond traditional standalone visualization systems.  ...  As part of this analysis, we introduce the Scientific Visualization Future Readiness Score (SciVis FRS) to rank visualizations for a technology-driven disruptive tomorrow.  ...  Popular JavaScript libraries for the visualization of particle data originated from the field of molecular sciences, primarily WebGL-based viewers, such as LiteMol [63] , MolMil [60] , NGL [66, 67]  ... 
doi:10.3390/informatics7040037 fatcat:2xfkzuv4ybdw3hxzn5ym7slgsa