Chemistry 410: Proteins

Basic Local Alignment Search Tool (BLAST)
"The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families."
From the source

RCSB Protein Data Bank (RCSB PDB)
"RCSB Protein Data Bank (RCSB PDB) enables breakthroughs in science and education by providing access and tools for exploration, visualization, and analysis of:

• Experimentally-determined 3D structures from the Protein Data Bank (PDB) archive
• Computed Structure Models (CSM) from AlphaFold DB and ModelArchive

These data can be explored in context of external annotations providing a structural view of biology."
From the source

Binding Database
"The first public molecular recognition database, BindingDB supports research, education and practice in drug discovery, pharmacology and related fields.  BindingDB contains 2.8M data for 1.2M Compounds and 9.2K Targets. Of those, 1,268K data for 582K Compounds and 4.5K Targets were curated by BindingDB curators. BindingDB is a FAIRsharing resource."
From the source

CheShift 2- Validate your protein model

"CheShift has been developed to predict ¹³C^α and ¹³C^β chemical shifts of protein structures. It is based on the generation of ~1,200,000 conformations as a function of the torsional angles for all 20 naturally occurring amino acids. Their ¹³C^α and ¹³C^β chemical shifts were computed at the DFT level. For further details on the CheShift ¹³C^α chemical shift predictions please read reference 5. The description of the visual, per residue validation, was discused in reference 2. Other references related to the method and its applications are listed below."

From the source

The Kinase Knowledgebase (KKB)
"Eidogen-Sertanty's database of kinase structure-activity data. The KKB represents the first gene-family wide database of chemical structure and biological activity data from scientific literature and patents.

Content & Curation
Currently the Kinase Knowledgebase Q2 2023 Release includes the following data:

• Journal articles and patents: 9,834
• Number of Biological Activity Data Points: 2,343,895
• Number of unique kinase molecules with annotated assay data: 417,004
• Number of all unique kinase molecules from patents and articles (with or without bio-activity data): 761,788
• Number of unique kinase targets with assay data: 565
• Number of annotated assay protocols: 65,131"
• CheShift 2- Validate your protein model

From the source

Dock Blaster
DOCK Blaster, is a public access service for structure-based ligand discovery. DOCK Blaster aims to answer the question: What small molecules should I purchase and test for activity against my biological target for which I have a structure?

From the source