[HTML][HTML] Current progress in structure-based rational drug design marks a new mindset in drug discovery

V Lounnas, T Ritschel, J Kelder, R McGuire… - Computational and …, 2013 - Elsevier
The past decade has witnessed a paradigm shift in preclinical drug discovery with structure-
based drug design (SBDD) making a comeback while high-throughput screening (HTS) …

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 …

The Angiotensin II AT1 Receptor Structure-Activity Correlations in the Light of Rhodopsin Structure

L Oliveira, CM Costa-Neto, CR Nakaie… - Physiological …, 2007 - journals.physiology.org
The most prevalent physiological effects of ANG II, the main product of the renin-angiotensin
system, are mediated by the AT1 receptor, a rhodopsin-like AGPCR. Numerous studies of …

3DM: systematic analysis of heterogeneous superfamily data to discover protein functionalities

RK Kuipers, HJ Joosten… - Proteins: Structure …, 2010 - Wiley Online Library
Ten years of experience with molecular class–specific information systems (MCSIS) such as
with the hand‐curated G protein–coupled receptor database (GPCRDB) or the …

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 …

MtArt: a new model of amino acid replacement for Arthropoda

F Abascal, D Posada, R Zardoya - Molecular biology and …, 2007 - academic.oup.com
A statistical approach was applied to select those models that best fit each individual
mitochondrial (mt) protein at different taxonomic levels of metazoans. The existing …

Entropy and information within intrinsically disordered protein regions

I Pritišanac, RM Vernon, AM Moses, JD Forman Kay - Entropy, 2019 - mdpi.com
Bioinformatics and biophysical studies of intrinsically disordered proteins and regions (IDRs)
note the high entropy at individual sequence positions and in conformations sampled in …

Incorporating background frequency improves entropy-based residue conservation measures

K Wang, R Samudrala - BMC bioinformatics, 2006 - Springer
Background Several entropy-based methods have been developed for scoring sequence
conservation in protein multiple sequence alignments. High scoring amino acid positions …

Why should we care about molecular coevolution?

FM Codoñer, MA Fares - Evolutionary Bioinformatics, 2008 - journals.sagepub.com
Non-independent evolution of amino acid sites has become a noticeable limitation of most
methods aimed at identifying selective constraints at functionally important amino acid sites …

Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information

SK Gupta, Ö Osmanoglu, R Minocha, SR Bandi… - Frontiers in …, 2022 - frontiersin.org
Candida auris is a globally emerging fungal pathogen responsible for causing nosocomial
outbreaks in healthcare associated settings. It is known to cause infection in all age groups …