Skip to main content

SMPDB (The Small Molecule Pathway Database)

 https://smpdb.ca/


SMPDB (The Small Molecule Pathway Database) is an interactive, visual database containing more than 30 000 small molecule pathways found in humans only. The majority of these pathways are not found in any other pathway database.

 SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein_complex cofactors, protein_complex locations, metabolite locations, chemical structures and protein_complex quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein_complex or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes/protein_complex names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein_complex concentration data can also be visualized through SMPDB's mapping interface. All of SMPDB's images, image maps, descriptions and tables are downloadable.

Comments

Post a Comment

Popular posts from this blog

Dementia Research

Disclaimer: I am not a doctor so I cannot diagnose or offer treatments, I am sharing this information that is considered educational. Much of the research on dementia/Alzheimer's is centered on what is referred to as Tight Junction Proteins. These are proteins that act like clamps that hold tissues together in terms of neurological, these "clamps" hold the blood vessels together. And when the tight junction proteins become damaged, the blood vessels begin to "leak".  Science refers the tight junction proteins as barrier as in the blood brain barrier. They will also refer to as barrier integrity. AI says this:  Tight junction proteins are vital for various physiological processes, including the formation of barriers in the brain (blood-brain barrier), intestines, and other tissues. They also play a role in disease mechanisms when their function is disrupted. The barrier function occurs in the blood vessels, and they think that when they leak, this is affecting co...
Post a Comment
Read more

Microbiome SCFAs & AutoImmunity

  Does SCFA impact immune and inflammatory pathways? Show thinking Yes, absolutely! Short-Chain Fatty Acids (SCFAs) are major players in controlling immune and inflammatory pathways, both within the gut and systemically. This is one of the most significant and exciting areas of research on SCFAs. Here's how they exert their control: Interaction with G-Protein Coupled Receptors (GPCRs): GPR41 and GPR43: These are the most well-studied SCFA receptors, found on various cell types throughout the body, including immune cells (e.g., neutrophils, macrophages, T cells), gut epithelial cells, and adipocytes. When SCFAs (particularly acetate, propionate, and butyrate) bind to these receptors, they trigger intracellular signaling pathways that can influence immune cell function, cytokine production, and inflammatory responses. Histone Deacetylase (HDAC) Inhibition: Butyrate (and to a lesser extent propionate) are potent inhibitors of HDACs. HDACs are enzymes that modify histones, proteins aro...
Post a Comment
Read more
You can buy most of this at Kroger's, I listed the pictures below. The idea is that you are targeting the gut, the microbiome to be exact. I am not going to list out all the studies but they have discovered that the right bacteria in the gut can change a lot of things including metabolic, neurological, immune responses, weight gain and many other things.  Increasing the good bacteria such as bifidobacteria etc. can also suppress the bad bacteria which have been linked to numerous problems.  There are products that you can buy on Amazon and these will also support the microbiome by giving the nutrients they need.  Kroger's has the ones in the pictures below, you will find the Cleveland Kraut in the refrigerated section and so is the Kefir. Both of these are live foods meaning they contain the good bacteria. Sauerkraut as canned does not work since there are no live organisms.  You will have to experiment with the doses; I do a couple of tablespoons of the kraut and ju...
Post a Comment
Read more