Search for: All records | NSF Public Access

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

BioJava 5: A community driven open-source bioinformatics library

https://doi.org/10.1371/journal.pcbi.1006791

Lafita, Aleix ; Bliven, Spencer ; Prlić, Andreas ; Guzenko, Dmytro ; Rose, Peter W. ; Bradley, Anthony ; Pavan, Paolo ; Myers-Turnbull, Douglas ; Valasatava, Yana ; Heuer, Michael ; et al ( February 2019 , PLOS Computational Biology)

Full Text Available
NGL viewer: web-based molecular graphics for large complexes

https://doi.org/10.1093/bioinformatics/bty419

Rose, Alexander S. ; Bradley, Anthony R. ; Valasatava, Yana ; Duarte, Jose M. ; Prlić, Andreas ; Rose, Peter W. ; Valencia, ed., Alfonso ( May 2018 , Bioinformatics)

Abstract Motivation
The interactive visualization of very large macromolecular complexes on the web is becoming a challenging problem as experimental techniques advance at an unprecedented rate and deliver structures of increasing size.
Results
We have tackled this problem by developing highly memory-efficient and scalable extensions for the NGL WebGL-based molecular viewer and by using Macromolecular Transmission Format (MMTF), a binary and compressed MMTF. These enable NGL to download and render molecular complexes with millions of atoms interactively on desktop computers and smartphones alike, making it a tool of choice for web-based molecular visualization in research and education.
Availability and implementation
The source code is freely available under the MIT license at github.com/arose/ngl and distributed on NPM (npmjs.com/package/ngl). MMTF-JavaScript encoders and decoders are available at github.com/rcsb/mmtf-javascript.

more » « less
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

https://doi.org/10.1093/nar/gky1004

Burley, Stephen K ; Berman, Helen M ; Bhikadiya, Charmi ; Bi, Chunxiao ; Chen, Li ; Di Costanzo, Luigi ; Christie, Cole ; Dalenberg, Ken ; Duarte, Jose M ; Dutta, Shuchismita ; et al ( October 2018 , Nucleic Acids Research)

Full Text Available
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

https://doi.org/10.1186/s13073-017-0509-y

Glusman, Gustavo ; Rose, Peter W. ; Prlić, Andreas ; Dougherty, Jennifer ; Duarte, José M. ; Hoffman, Andrew S. ; Barton, Geoffrey J. ; Bendixen, Emøke ; Bergquist, Timothy ; Bock, Christian ; et al ( December 2017 , Genome Medicine)

Full Text Available
Protein Data Bank: the single global archive for 3D macromolecular structure data

https://doi.org/10.1093/nar/gky949

Burley, Stephen K ; Berman, Helen M ; Bhikadiya, Charmi ; Bi, Chunxiao ; Chen, Li ; Costanzo, Luigi Di ; Christie, Cole ; Duarte, Jose M ; Dutta, Shuchismita ; Feng, Zukang ; et al ( October 2018 , Nucleic Acids Research)

Full Text Available