Deep learning for genomics: A concise overview
Advancements in genomic research such as high-throughput sequencing techniques have
driven modern genomic studies into" big data" disciplines. This data explosion is constantly …
driven modern genomic studies into" big data" disciplines. This data explosion is constantly …
Protein disorder—a breakthrough invention of evolution?
A Schlessinger, C Schaefer, E Vicedo… - Current opinion in …, 2011 - Elsevier
As an operational definition, we refer to regions in proteins that do not adopt regular three-
dimensional structures in isolation, as disordered regions. An antipode to disorder would be …
dimensional structures in isolation, as disordered regions. An antipode to disorder would be …
SCOP2 prototype: a new approach to protein structure mining
A Andreeva, D Howorth, C Chothia… - Nucleic acids …, 2014 - academic.oup.com
We present a prototype of a new structural classification of proteins, SCOP2 (http://scop2.
mrc-lmb. cam. ac. uk/), that we have developed recently. SCOP2 is a successor to the …
mrc-lmb. cam. ac. uk/), that we have developed recently. SCOP2 is a successor to the …
Conservation of complex knotting and slipknotting patterns in proteins
The last decade has shown that there are an increasing numbers of known proteins that
contain linear open knots or slipknots in their native folded structure. In general, knots in …
contain linear open knots or slipknots in their native folded structure. In general, knots in …
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures
Abstract CATH version 3.5 (Class, Architecture, Topology, Homology, available at
http://www. cathdb. info/) contains 173 536 domains, 2626 homologous superfamilies and …
http://www. cathdb. info/) contains 173 536 domains, 2626 homologous superfamilies and …
Structural validation and assessment of AlphaFold2 predictions for centrosomal and centriolar proteins and their complexes
M van Breugel, I Rosa e Silva, A Andreeva - Communications biology, 2022 - nature.com
Obtaining the high-resolution structures of proteins and their complexes is a crucial aspect of
understanding the mechanisms of life. Experimental structure determination methods are …
understanding the mechanisms of life. Experimental structure determination methods are …
Describing sequence–ensemble relationships for intrinsically disordered proteins
Intrinsically disordered proteins participate in important protein–protein and protein–nucleic
acid interactions and control cellular phenotypes through their prominence as dynamic …
acid interactions and control cellular phenotypes through their prominence as dynamic …
Deep learning for genomics: From early neural nets to modern large language models
The data explosion driven by advancements in genomic research, such as high-throughput
sequencing techniques, is constantly challenging conventional methods used in genomics …
sequencing techniques, is constantly challenging conventional methods used in genomics …
Structures and folding pathways of topologically knotted proteins
In the last decade, a new class of proteins has emerged that contain a topological knot in
their backbone. Although these structures are rare, they nevertheless challenge our …
their backbone. Although these structures are rare, they nevertheless challenge our …
On the universe of protein folds
R Kolodny, L Pereyaslavets… - Annual review of …, 2013 - annualreviews.org
In the fifty years since the first atomic structure of a protein was revealed, tens of thousands
of additional structures have been solved. Like all objects in biology, proteins structures …
of additional structures have been solved. Like all objects in biology, proteins structures …