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 …
[HTML][HTML] 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 …
High-resolution de novo structure prediction from primary sequence
Recent breakthroughs have used deep learning to exploit evolutionary information in
multiple sequence alignments (MSAs) to accurately predict protein structures. However …
multiple sequence alignments (MSAs) to accurately predict protein structures. However …
[HTML][HTML] Clustering predicted structures at the scale of the known protein universe
Proteins are key to all cellular processes and their structure is important in understanding
their function and evolution. Sequence-based predictions of protein structures have …
their function and evolution. Sequence-based predictions of protein structures have …
FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately
I Budowski-Tal, Y Nov… - Proceedings of the …, 2010 - National Acad Sciences
Fast identification of protein structures that are similar to a specified query structure in the
entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We …
entire Protein Data Bank (PDB) is fundamental in structure and function prediction. We …
[HTML][HTML] A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction
Protein sequence alignment is essential for template-based protein structure prediction and
function annotation. We collect 20 sequence alignment algorithms, 10 published and 10 …
function annotation. We collect 20 sequence alignment algorithms, 10 published and 10 …
STRAP: editor for STRuctural Alignments of Proteins
C Gille, C Frömmel - Bioinformatics, 2001 - academic.oup.com
STRAP is a comfortable and extensible tool for the generation and refinement of multiple
alignments of protein sequences. Various sequence ordered input file formats are …
alignments of protein sequences. Various sequence ordered input file formats are …
The protein structure prediction problem could be solved using the current PDB library
Y Zhang, J Skolnick - … of the National Academy of Sciences, 2005 - National Acad Sciences
For single-domain proteins, we examine the completeness of the structures in the current
Protein Data Bank (PDB) library for use in full-length model construction of unknown …
Protein Data Bank (PDB) library for use in full-length model construction of unknown …
mTM-align: a server for fast protein structure database search and multiple protein structure alignment
With the rapid increase of the number of protein structures in the Protein Data Bank, it
becomes urgent to develop algorithms for efficient protein structure comparisons. In this …
becomes urgent to develop algorithms for efficient protein structure comparisons. In this …
The I-TASSER Suite: protein structure and function prediction
To the Editor: Assignment of structure and function to all genes and gene products (such as
proteins) of all organisms represents a major challenge in this postgenomic era. Here we …
proteins) of all organisms represents a major challenge in this postgenomic era. Here we …