AlphaFill: enriching AlphaFold models with ligands and cofactors

ML Hekkelman, I de Vries, RP Joosten, A Perrakis - Nature Methods, 2023 - nature.com
Artificial intelligence-based protein structure prediction approaches have had a
transformative effect on biomolecular sciences. The predicted protein models in the …

From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling

MPA Sanders, R McGuire, L Roumen, IJP de Esch… - …, 2012 - pubs.rsc.org
A pharmacophore describes the arrangement of molecular features a ligand must contain to
efficaciously bind a receptor. Pharmacophore models are developed to improve molecular …

Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces

H Venselaar, TAH Te Beek, RKP Kuipers… - BMC …, 2010 - Springer
Background Many newly detected point mutations are located in protein-coding regions of
the human genome. Knowledge of their effects on the protein's 3D structure provides insight …

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 …

A series of PDB related databases for everyday needs

RP Joosten, TAH Te Beek, E Krieger… - Nucleic acids …, 2010 - academic.oup.com
Abstract The Protein Data Bank (PDB) is the world-wide repository of macromolecular
structure information. We present a series of databases that run parallel to the PDB. Each …

A planarian nidovirus expands the limits of RNA genome size

A Saberi, AA Gulyaeva, JL Brubacher… - PLoS …, 2018 - journals.plos.org
RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous
replication (albeit within a permissive host environment). A 33.5 kilobase (kb) nidovirus has …

GPCRDB: information system for G protein-coupled receptors

B Vroling, M Sanders, C Baakman… - Nucleic acids …, 2010 - academic.oup.com
The GPCRDB is a Molecular Class-Specific Information System (MCSIS) that collects,
combines, validates and disseminates large amounts of heterogeneous data on G protein …

Bioinformatics methods for identifying candidate disease genes

MA Van Driel, HG Brunner - Human genomics, 2006 - Springer
With the explosion in genomic and functional genomics information, methods for disease
gene identification are rapidly evolving. Databases are now essential to the process of …

GMOMETHODS: The European Union database of reference methods for GMO analysis

L Bonfini, MH Van den Bulcke… - Journal of AOAC …, 2012 - academic.oup.com
In order to provide reliable and harmonized information on methods for GMO (genetically
modified organism) analysis we have published a database called “GMOMETHODS” that …

DEOP: a database on osmoprotectants and associated pathways

S Bougouffa, A Radovanovic, M Essack, VB Bajic - Database, 2014 - academic.oup.com
Microorganisms are known to counteract salt stress through salt influx or by the
accumulation of osmoprotectants (also called compatible solutes). Understanding the …