Fast and accurate protein structure search with Foldseek
As structure prediction methods are generating millions of publicly available protein
structures, searching these databases is becoming a bottleneck. Foldseek aligns the …
structures, searching these databases is becoming a bottleneck. Foldseek aligns the …
Evolutionary dynamics of natural product biosynthesis in bacteria
Covering: 2008 up to 2019 The forces of biochemical adaptive evolution operate at the level
of genes, manifesting in complex phenotypes and the global biodiversity of proteins and …
of genes, manifesting in complex phenotypes and the global biodiversity of proteins and …
LigPlot+: multiple ligand–protein interaction diagrams for drug discovery
RA Laskowski, MB Swindells - 2011 - ACS Publications
We describe a graphical system for automatically generating multiple 2D diagrams of ligand–
protein interactions from 3D coordinates. The diagrams portray the hydrogen-bond …
protein interactions from 3D coordinates. The diagrams portray the hydrogen-bond …
DALI and the persistence of protein shape
L Holm - Protein Science, 2020 - Wiley Online Library
DALI is a popular resource for comparing protein structures. The software is based on
distance‐matrix alignment. The associated web server provides tools to navigate, integrate …
distance‐matrix alignment. The associated web server provides tools to navigate, integrate …
Using Dali for protein structure comparison
L Holm - Structural Bioinformatics: Methods and Protocols, 2020 - Springer
The exponential growth in the number of newly solved protein structures makes correlating
and classifying the data an important task. Distance matrix alignment (Dali) is used routinely …
and classifying the data an important task. Distance matrix alignment (Dali) is used routinely …
Dali server: conservation map** in 3D
L Holm, P Rosenstrï¿ ½m - Nucleic acids research, 2010 - academic.oup.com
Abstract Our web site (http://ekhidna. biocenter. helsinki. fi/dali_server) runs the Dali
program for protein structure comparison. The web site consists of three parts:(i) the Dali …
program for protein structure comparison. The web site consists of three parts:(i) the Dali …
Foldseek: fast and accurate protein structure search
Highly accurate structure prediction methods are generating an avalanche of publicly
available protein structures. Searching through these structures is becoming the main …
available protein structures. Searching through these structures is becoming the main …
Dali server update
L Holm, LM Laakso - Nucleic acids research, 2016 - academic.oup.com
Abstract The Dali server (http://ekhidna2. biocenter. helsinki. fi/dali) is a network service for
comparing protein structures in 3D. In favourable cases, comparing 3D structures may …
comparing protein structures in 3D. In favourable cases, comparing 3D structures may …
The Bcl-2 family: structures, interactions and targets for drug discovery
Two phylogenetically and structurally distinct groups of proteins regulate stress induced
intrinsic apoptosis, the programmed disassembly of cells. Together they form the B cell …
intrinsic apoptosis, the programmed disassembly of cells. Together they form the B cell …
Synthetic genetic polymers capable of heredity and evolution
Genetic information storage and processing rely on just two polymers, DNA and RNA, yet
whether their role reflects evolutionary history or fundamental functional constraints is …
whether their role reflects evolutionary history or fundamental functional constraints is …