The RCSB protein data bank: integrative view of protein, gene and 3D structural information

PW Rose, A Prlić, A Altunkaya, C Bi… - Nucleic acids …, 2016 - academic.oup.com
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB
PDB, http://rcsb. org), the US data center for the global PDB archive, makes PDB data freely …

TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline

JC Glaubitz, TM Casstevens, F Lu, J Harriman… - PloS one, 2014 - journals.plos.org
Genotyping by sequencing (GBS) is a next generation sequencing based method that takes
advantage of reduced representation to enable high throughput genotyping of large …

PRISM 3: expanded prediction of natural product chemical structures from microbial genomes

MA Skinnider, NJ Merwin, CW Johnston… - Nucleic acids …, 2017 - academic.oup.com
Microbial natural products represent a rich resource of pharmaceutically and industrially
important compounds. Genome sequencing has revealed that the majority of natural …

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

PW Rose, A Prlić, C Bi, WF Bluhm… - Nucleic acids …, 2015 - academic.oup.com
Abstract The RCSB Protein Data Bank (RCSB PDB, http://www. rcsb. org) provides access to
3D structures of biological macromolecules and is one of the leading resources in biology …

A series of PDB-related databanks for everyday needs

WG Touw, C Baakman, J Black… - Nucleic acids …, 2015 - academic.oup.com
We present a series of databanks (http://swift. cmbi. ru. nl/gv/facilities/) that hold information
that is computationally derived from Protein Data Bank (PDB) entries and that might …

SNP-Seek database of SNPs derived from 3000 rice genomes

N Alexandrov, S Tai, W Wang, L Mansueto… - Nucleic acids …, 2015 - academic.oup.com
We have identified about 20 million rice SNPs by aligning reads from the 3000 rice genomes
project with the Nipponbare genome. The SNPs and allele information are organized into a …

Genomes to natural products prediction informatics for secondary metabolomes (PRISM)

MA Skinnider, CA Dejong, PN Rees… - Nucleic acids …, 2015 - academic.oup.com
Microbial natural products are an invaluable source of evolved bioactive small molecules
and pharmaceutical agents. Next-generation and metagenomic sequencing indicates …

[HTML][HTML] Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective

Y Perez-Riverol, R Wang, H Hermjakob… - … et Biophysica Acta (BBA …, 2014 - Elsevier
Data processing, management and visualization are central and critical components of a
state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and …

GenomeTools: a comprehensive software library for efficient processing of structured genome annotations

G Gremme, S Steinbiss, S Kurtz - IEEE/ACM transactions on …, 2013 - ieeexplore.ieee.org
Genome annotations are often published as plain text files describing genomic features and
their subcomponents by an implicit annotation graph. In this paper, we present the …

[PDF][PDF] Mol*: Towards a Common Library and Tools for Web Molecular Graphics.

D Sehnal, AS Rose, J Koca, SK Burley, S Velankar - MolVa@ EuroVis, 2018 - diglib.eg.org
Advances in experimental techniques are providing access to structures of ever more
complex and larger macromolecular systems. Web-browser based visualization and …