PDBx/mmCIF ecosystem: foundational semantic tools for structural biology
Abstract PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular
Crystallographic Information Framework (mmCIF), has become the data standard for …
Crystallographic Information Framework (mmCIF), has become the data standard for …
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 …
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 …
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB
PDB), funded by the US National Science Foundation, National Institutes of Health, and …
PDB), funded by the US National Science Foundation, National Institutes of Health, and …
RCSB protein data bank: efficient searching and simultaneous access to one million computed structure models alongside the PDB structures enabled by architectural …
S Bittrich, C Bhikadiya, C Bi, H Chao, JM Duarte… - Journal of molecular …, 2023 - Elsevier
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB
PDB) provides open access to experimentally-determined three-dimensional (3D) structures …
PDB) provides open access to experimentally-determined three-dimensional (3D) structures …
Python in chemistry: physicochemical tools
FV Ryzhkov, YE Ryzhkova, MN Elinson - Processes, 2023 - mdpi.com
The popularity of the Python programming language in chemistry is growing every year.
Python provides versatility, simplicity, and a rich ecosystem of libraries, making it the …
Python provides versatility, simplicity, and a rich ecosystem of libraries, making it the …
PLMSearch: Protein language model powers accurate and fast sequence search for remote homology
Homologous protein search is one of the most commonly used methods for protein
annotation and analysis. Compared to structure search, detecting distant evolutionary …
annotation and analysis. Compared to structure search, detecting distant evolutionary …
Assessment of the assessment—All about complexes
Predicting model quality is a fundamental component of any modeling procedure, and blind
assessment of these methods constitutes a crucial aspect of the Critical Assessment of …
assessment of these methods constitutes a crucial aspect of the Critical Assessment of …
AggreProt: a web server for predicting and engineering aggregation prone regions in proteins
J Planas-Iglesias, S Borko, J Swiatkowski… - Nucleic Acids …, 2024 - academic.oup.com
Recombinant proteins play pivotal roles in numerous applications including industrial
biocatalysts or therapeutics. Despite the recent progress in computational protein structure …
biocatalysts or therapeutics. Despite the recent progress in computational protein structure …
OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data
With the advancements in high-throughput sequencing technologies such as Illumina,
PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry …
PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry …