Network pharmacology prediction and molecular docking-based strategy to explore the potential mechanism of Huanglian Jiedu Decoction against sepsis
X Li, S Wei, S Niu, X Ma, H Li, M Jing, Y Zhao - Computers in biology and …, 2022 - Elsevier
Abstract Background Huanglian Jiedu Decoction (HLJDD) is a classical herbal formula with
potential efficacy in the treatment of sepsis. However, the main components and potential …
potential efficacy in the treatment of sepsis. However, the main components and potential …
Cross-linking mass spectrometry for investigating protein conformations and protein–protein interactions─ a method for all seasons
L Piersimoni, PL Kastritis, C Arlt, A Sinz - Chemical Reviews, 2021 - ACS Publications
Mass spectrometry (MS) has become one of the key technologies of structural biology. In this
review, the contributions of chemical cross-linking combined with mass spectrometry (XL …
review, the contributions of chemical cross-linking combined with mass spectrometry (XL …
RCSB Protein Data Bank (RCSB. org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from …
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB
PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center …
PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center …
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 …
The carbohydrate-active enzyme database: functions and literature
Thirty years have elapsed since the emergence of the classification of carbohydrate-active
enzymes in sequence-based families that became the CAZy database over 20 years ago …
enzymes in sequence-based families that became the CAZy database over 20 years ago …
Protein complex prediction with AlphaFold-Multimer
While the vast majority of well-structured single protein chains can now be predicted to high
accuracy due to the recent AlphaFold model, the prediction of multi-chain protein complexes …
accuracy due to the recent AlphaFold model, the prediction of multi-chain protein complexes …
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 …
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents
Drug discovery relies on the knowledge of not only drugs and targets, but also the
comparative agents and targets. These include poor binders and non-binders for developing …
comparative agents and targets. These include poor binders and non-binders for developing …
A structural biology community assessment of AlphaFold2 applications
Most proteins fold into 3D structures that determine how they function and orchestrate the
biological processes of the cell. Recent developments in computational methods for protein …
biological processes of the cell. Recent developments in computational methods for protein …
Single-sequence protein structure prediction using a language model and deep learning
R Chowdhury, N Bouatta, S Biswas, C Floristean… - Nature …, 2022 - nature.com
AlphaFold2 and related computational systems predict protein structure using deep learning
and co-evolutionary relationships encoded in multiple sequence alignments (MSAs) …
and co-evolutionary relationships encoded in multiple sequence alignments (MSAs) …