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Online database of metabolic pathways
Small Molecule Pathway Database (SMPDB) is a comprehensive, high-quality, freely accessible, online database containing more than 600 small molecule (i
Small Molecule Pathway Database
Small_Molecule_Pathway_Database
Nonsteroidal anti-inflammatory drug
DD, et al. (January 2010). "SMPDB: The Small Molecule Pathway Database". Nucleic Acids Research. 38 (Database issue): D480–D487. doi:10.1093/nar/gkp1002
Ibuprofen
Online database containing information on drugs and drug targets
The latest release of the database (version 6.0) contains 11,891 drug entries including 4030 FDA-approved small molecule drugs, 1601 FDA-approved biotech
DrugBank
Database of human metabolites
The Human Metabolome Database (HMDB) is a comprehensive online database of small molecule metabolites found in the human body. It has been created by the
Human_Metabolome_Database
Reactions describing metabolism
synthesize molecules with the utilization of energy (anabolic pathway), or break down complex molecules and release energy in the process (catabolic pathway).
Metabolic_pathway
Online tools for metabolomic data analysis
metabolomics databases that also includes Human Metabolome Database (HMDB), DrugBank, Toxin and Toxin-Target Database, and The Small Molecule Pathway Database. The
MetaboAnalyst
Embryonic signaling pathway for proper cell differentiation
present in all bilaterians. The pathway takes its name from its polypeptide ligand, an intracellular signaling molecule called Hedgehog (Hh) found in fruit
Hedgehog_signaling_pathway
containing information on small molecule structures and interactions. The databank integrates a number of existing databases to provide a comprehensive
Biomolecular Object Network Databank
Biomolecular_Object_Network_Databank
Immunosuppressive medication
Verlag. p. 340. ISBN 978-3-7692-3483-1. "Azathioprine Pathway". Small Molecule Pathway Database. Archived from the original on 2 July 2012. Retrieved
Azathioprine
System of communication
PMID 15908344. Camilli A, Bassler BL (February 2006). "Bacterial small-molecule signaling pathways". Science. 311 (5764): 1113–6. Bibcode:2006Sci...311.1113C
Cell_signaling
Type of analysis in molecular biology
molecular interactions. A pathway is most often represented as a relatively small graph with gene, protein, and/or small molecule nodes connected by edges
Pathway_analysis
Collection of bioinformatics databases
Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is
KEGG
Genus of amphibians
obtained, all modalities of Xenopus research are now being used for small-molecule based screens. Chemical genetics of vascular growth in Xenopus tadpoles:
Xenopus
Process of releasing energy from nutrients using inorganic electron acceptors
using inorganic molecules other than oxygen as final electron acceptors in the electron transport chain. They share the initial pathway of glycolysis but
Cellular_respiration
Database of biological pathways
complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways. The pathways represented
Reactome
Cascade of intracellular and molecular events for transmission/amplification of signals
development. The majority of signal transduction pathways involve the binding of signaling molecules, known as ligands, to receptors that trigger events
Signal_transduction
Class of enzymes which transfer functional groups between molecules
group) from one molecule (called the donor) to another (called the acceptor). They are involved in hundreds of different biochemical pathways throughout biology
Transferase
Set of chemical reactions in organisms
reused in different pathways and perform similar functions on different molecules. As well as the evolution of new metabolic pathways, evolution can also
Metabolism
Type of therapy
Waldenström's macroglobulinemia. Vintafolide is a small molecule drug conjugate consisting of a small molecule targeting the folate receptor. It is currently
Targeted_therapy
Class of enzymes
release by growth hormone-releasing hormone. Cannabinoid receptors Small molecule U73122: aminosteroid, putative PLC inhibitor. However, the specificity
Phospholipase_C
Medical condition
Wishart, David (6 March 2010). "Glycerol Kinase Deficiency". Small Molecule Pathway Database. Archived from the original on 2 July 2012. Retrieved 21 December
Glycerol_kinase_deficiency
Class of enzymes
of the glucuronic acid component of UDP-glucuronic acid to a small hydrophobic molecule. This is a glucuronidation reaction. Alternative names: glucuronyltransferase
Glucuronosyltransferase
Complete set of small molecules in a biological sample
The metabolome is the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle
Metabolome
American biopharmaceutical company
signaling pathway. The company focuses on potential treatments for several diseases; its osteoarthritis program is its most advanced. "Small-molecule therapeutics
Biosplice_Therapeutics
Chemical compound
El-Sayed. "Pheromone database". Pherobase.com. Retrieved 2018-07-26. KenjiMatsui (2006). "Green leaf volatiles: hydroperoxide lyase pathway of oxylipin metabolism"
Cis-3-Hexenal
Database of protein targets in drug design
drug types in TTD include small molecule, antibody, nucleic acid drug, cell therapy, gene therapy and vaccine. Small molecule: the most common medications
Therapeutic_Targets_Database
Group of signal transduction pathways involved in embryonic development
Xia Z, Dawson M, Cashman J, Mercola M (August 2011). "Small-molecule inhibitors of the Wnt pathway potently promote cardiomyocytes from human embryonic
Wnt_signaling_pathway
Mammalian protein found in Homo sapiens
Neural cell adhesion molecule (NCAM), also called CD56, is a homophilic binding glycoprotein expressed on the surface of neurons, glia and skeletal muscle
Neural_cell_adhesion_molecule
Biomolecule
Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded non-coding RNA molecules, typically
Small_interfering_RNA
Series of chemical reactions resulting in a cell response
can denote a metabolic pathway involving a sequence of enzyme-catalyzed reactions of small molecules, or a signaling pathway involving a set of protein
Biochemical_cascade
Set of biological processes
metabolic processes involving or closely related to fatty acids, a family of molecules classified within the lipid macronutrient category. These processes can
Fatty_acid_metabolism
Biological target that binds to a drug
druggability is most commonly applied to the ability of drug targets to bind small molecules—low molecular weight organic compounds. However, the term has also
Druggability
Class of ligand activated receptors localized in surface of plama cell membrane
extracellular space. The extracellular molecules may be hormones, neurotransmitters, cytokines, growth factors, cell adhesion molecules, or nutrients; they react with
Cell_surface_receptor
Cell surface proteins, part of the adaptive immune system
"Ancient features of the MHC class II presentation pathway, and a model for the possible origin of MHC molecules". Immunogenetics. 71 (3): 233–249. doi:10
Major histocompatibility complex
Major_histocompatibility_complex
Supported hypothesis for the origin of life
the origin of life. The theory first asserts that many of the small organic molecules used for life originated in space (for example, being incorporated
Pseudo-panspermia
Series of interconnected biochemical reactions
NADH and NAD+. In homolactic fermentation, one molecule of glucose is ultimately converted to two molecules of lactic acid. Heterolactic fermentation, by
Lactic_acid_fermentation
Line of stem cells for research
Matrigel, and transferred to a rotating bioreactor where different small molecules and growth factors are continuously supplemented to promote the differentiation
Myelinoid
Database for yeast metabolomics
The Yeast Metabolome Database (YMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced
Yeast_Metabolome_Database
protein localization, to manipulate signalling pathways and to induce protein activation. The first small molecule CID system was developed in 1993 and used
Chemically induced dimerization
Chemically_induced_dimerization
alternative pathway is common in many bacteria, which use GlgB and GlgE or the GlgE pathway exclusively for the biosynthesis of α-glucan. The GlgE pathway is especially
Alpha_glucan
detailed information about small molecule metabolites found in the human body KEGG PATHWAY Database (Univ. of Kyoto) MANET database (University of Illinois)
List_of_biological_databases
Molecule containing main group elements with more than eight valence electrons
In chemistry, a hypervalent molecule (the phenomenon is sometimes colloquially known as expanded octet) is a molecule that contains one or more main group
Hypervalent_molecule
Class of serine proteases
to refer to the form produced in the alternative pathway (C3bBb) or the classical and lectin pathways (C4bC2b, formerly C4b2a). Once formed, both C3 convertases
C3-convertase
Protein-coding gene in the species Homo sapiens
§ Small molecule inhibitors of PFKFB3). Several small-molecule inhibitors of PFKFB3 are currently in development. For a long time a small molecule
PFKFB3
Chemical compound
Lathosterol is a cholesterol-like molecule found in small amounts in humans. The enzyme Δ7-sterol 5(6)-desaturase converts it to 7-dehydrocholesterol
Lathosterol
Mammalian protein found in Homo sapiens
double helix after damage is initially recognized. NER is a multi-step pathway that removes a wide range of different DNA damages that distort normal
ERCC3
Branch of chemistry
those molecules. Some publicly available chemistry databases include the following. BindingDB: Contains experimental information about protein-small molecule
Computational_chemistry
Large biological molecule that acts as a catalyst
by other molecules. For example, the end product(s) of a metabolic pathway are often inhibitors for one of the first enzymes of the pathway (usually the
Enzyme
Polyatomic ion (H3, charge +1)
is almost unaffected by the relatively small energy transferred to the hydrogen when ionizing an H2 molecule. In interstellar clouds, cosmic rays leave
Trihydrogen_cation
Class of chemical compounds
A molecular glue is a type of small molecule that modulates protein–protein interactions in cells by enhancing the affinity between proteins. These compounds
Molecular_glue
Protein molecule receiving signals for a cell
receptors. A molecule that binds to a receptor is called a ligand and can be a protein, peptide (short protein), or another small molecule, such as a neurotransmitter
Receptor_(biochemistry)
Key enzyme of photosynthesis involved in carbon fixation
the reductive acetyl CoA pathway, the 3-hydroxypropionate cycle, or the reverse Krebs cycle, these pathways are relatively small contributors to global
RuBisCO
Radioactive isotope of phosphorus
where it can be used to trace phosphorylated molecules (for example, in elucidating metabolic pathways) and radioactively label DNA and RNA. Phosphorus-32
Phosphorus-32
Sterol biosynthesized by all animal cells
cells, cholesterol is a precursor molecule for several biochemical pathways. For example, it is the precursor molecule for the synthesis of vitamin D in
Cholesterol
Biological signaling pathway h
The JAK-STAT signaling pathway is a chain of interactions between proteins in a cell, and is involved in processes such as immunity, cell division, cell
JAK-STAT_signaling_pathway
Critical protein in embryonic development
is a major signaling molecule of embryonic development in planulozoan animals, encoded by the SHH gene. This signaling molecule is key in regulating embryonic
Sonic_hedgehog_protein
Mass spectrometry software
SIRIUS is a Java-based open-source software for the identification of small molecules from fragmentation mass spectrometry data without the use of spectral
SIRIUS_(software)
Structure in molecular biology
observation that specific DNA helicases could be identified where small molecules specific for these DNA structures accumulated in cells. The length
G-quadruplex
Class of cell surface receptors coupled to G-protein-associated intracellular signaling
pheromones, hormones, and neurotransmitters. They vary in size from small molecules to peptides, to large proteins. G protein-coupled receptors are involved
G_protein-coupled_receptor
Group of simple sugar and carbohydrate compounds
cAMP-dependent signaling pathways. In cAMP signaling pathways, either a stimulative or inhibitory hormone receptor is activated by a signal molecule. These receptors
Ribose
Protein complexes which degrade ubiquitin-tagged proteins by proteolysis
itself folds into a dome with a very small pore over it. Archaea also contain a proteasome degradation pathway with a 20S core and a regulatory particle
Proteasome
Mammalian peptide found in Homo sapiens
for therapeutic purposes. Amgen has created a camel antibody and a small molecule agonist capable of mimicking the function of ELA towards it cognate
Elabela
Protein
can initiate transcriptional response to hypoxia. Another example of small molecule control of protein degradation is phytohormone auxin in plants. Auxin
Ubiquitin_ligase
RNA component of the ribosome, essential for protein synthesis in all living organisms
contains a single small rRNA molecule (~1500 nucleotides) while the LSU contains one single small rRNA and a single large rRNA molecule (~3000 nucleotides)
Ribosomal_RNA
Novel drug development method
genomics, is the systematic screening of targeted chemical libraries of small molecules against individual drug target families (e.g., GPCRs, nuclear receptors
Chemogenomics
Class of immune system proteins
(TRIF-related adaptor molecule). TLR signaling is divided into two distinct signaling pathways, the MyD88-dependent and TRIF-dependent pathway. The MyD88-dependent
Toll-like_receptor
Transportation of solutes through membranes
of mechanisms that regulate the passage of solutes such as ions and small molecules through biological membranes, which are lipid bilayers that contain
Membrane_transport
Family of large biological molecules
Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA)
RNA
Vsevolod A.; Fazli, Siamac (2020-12-17). "cheML.io: an online database of ML-generated molecules". RSC Advances. 10 (73): 45189–45198. Bibcode:2020RSCAd..1045189Z
List_of_chemical_databases
Family of waxy lipid molecules
release ceramide. Second, the de novo pathway creates ceramide from less complex molecules. Third, in the "salvage" pathway, sphingolipids that are broken down
Ceramide
Peptide hormone
change that results in the replacement of the GDP molecule that was bound to the α subunit with a GTP molecule. This substitution results in the releasing of
Glucagon
Invention of new medications based on knowledge of a biological target
cases, small molecules will be designed to enhance or inhibit the target function in the specific disease modifying pathway. Small molecules (for example
Drug_design
Regulatory protein found in most eukaryotic tissues
tauopathies. Ubiquitin and ubiquitin-like molecules extensively regulate immune signal transduction pathways at virtually all stages, including steady-state
Ubiquitin
Organelle in eukaryotic cells
larger molecules must be actively transported by carrier proteins while allowing free movement of small molecules and ions. Movement of large molecules such
Cell_nucleus
Protein-coding gene in the species Homo sapiens
mouse studies suggest it is dispensable in somatic cells. As such, small molecule inhibitors of KIF18A have been developed to block its activity. GRCh38:
KIF18A
Collection of molecular regulators
(through transcribed RNA or translated protein). In general, each mRNA molecule goes on to make a specific protein (or set of proteins). In some cases
Gene_regulatory_network
Biochemical identification method
observe a pathway more visibly. The method involves fluorescently labeling peptide molecules that would alter an organism's natural pathway. When this
Fluorescent_tag
Neutral form of the hydroxide ion
2006 UMIST database, and the values are relative to the H2 density. The following table shows rates for each pathway relative to pathway 1a (as the ratio
Hydroxyl_radical
Coenzyme
NAD synthesis pathway at the MetaCyc database List of oxidoreductases Archived 30 November 2010 at the Wayback Machine at the SWISS-PROT database NAD+
Nicotinamide adenine dinucleotide
Nicotinamide_adenine_dinucleotide
A chemical probe is a well-characterized small molecule that selectively modulates the function or abundance of a specific protein of interest. Chemical
Chemical_probe
tissue, or pathway and match them with 150,000 shRNAs, 725,000 siRNAs, 8,000 antibodies, proteins and kits, and 1,000 bioactive small molecules within the
Your_Favorite_Gene
Chinese-American electrochemist
department at Harvard University for doctoral research, where he researched small molecule asymmetric catalysis with Eric Jacobsen and was awarded a PhD in 2013
Song_Lin_(chemist)
Naturally produced monosaccharide
degradation. The metabolic pathway that begins with molecules containing two to four carbon atoms (C) and ends in the glucose molecule containing six carbon
Glucose
Chemical compound
3H+ 3. However, as for most ion-molecule reactions speculated to be important in interstellar environments, this pathway has not been verified by laboratory
Cyclopropenylidene
Database of E. coli metabolites
The E. coli Metabolome Database (ECMDB) is a freely accessible, online database of small molecule metabolites found in or produced by Escherichia coli
E._Coli_Metabolome_Database
RNA processing within a biological cell
following transcription from a gene to produce a mature, functional RNA molecule that can then leave the nucleus and perform any of a variety of different
Post-transcriptional modification
Post-transcriptional_modification
Chemical compound
enzymes and signalling pathways according to various bio-assay results: inhibits vitamin D receptor (VDR). acts as a small molecule disruptors of the mitochondrial
Triazofos
Class of organic compounds
glutamate-1-semialdehyde 2,1-aminomutase. This pathway is known as the C5 or Beale pathway. Two molecules of dALA are then combined by porphobilinogen synthase to give porphobilinogen
Porphyrin
Family of proteins
Plückthun A (January 2021). "Complexes of the neurotensin receptor 1 with small-molecule ligands reveal structural determinants of full, partial, and inverse
Neurotensin_receptor
Biological database
(1): 3–18. doi:10.1074/mcp.R800014-MCP200. PMID 18799807. STRING site STITCH website, related database on interactions of proteins with small molecules
STRING
Peripheral membrane protein
hydrolyzing the bond between the second fatty acid "tail" and the glycerol molecule: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate
Phospholipase_A2
Fibrin degradation product present in the blood after a thrombus
tissue space (intrinsic pathway) or by activation of factor VII by tissue activating factors (extrinsic pathway). Both pathways lead to the generation
D-dimer
Protein-coding gene in humans
instructions for making a protein called K-Ras, a part of the RAS/MAPK pathway. The protein relays signals from outside the cell to the cell's nucleus
KRAS
Form of programmed cell death
inhibiting apoptosis through its possible action as a signal molecule of subsequent pathways that activate apoptosis. During apoptosis, cytochrome c is
Apoptosis
Largest class of small non-coding RNA molecules in animals
Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules expressed in animal cells. piRNAs form RNA-protein complexes through
Piwi-interacting_RNA
Polycyclic organic compound having sterane as a core structure
components of cell membranes that alter membrane fluidity; and as signaling molecules. Examples include the lipid cholesterol, sex hormones estradiol and testosterone
Steroid
South Korean pharmaceutical company
protein therapeutics using its "Lapscovery" technology, and developing small molecule tyrosine-kinase inhibitors for cancer and autoimmune diseases. Its strategy
Hanmi_Pharm
Biological process of gene regulation
types of small ribonucleic acid (RNA) molecules, microRNA (miRNA) and small interfering RNA (siRNA), are central to components to the RNAi pathway. Once
RNA_interference
P38 mitogen-activated protein kinases
– display enhanced ischemic tolerance and stroke recovery. Although small-molecule JNK inhibitors are under development, none of them proved to be effective
Mitogen-activated protein kinase
Mitogen-activated_protein_kinase
Gene found in humans and other animals
a mystery in the field. Smo is targeted and inhibited directly by a small-molecule drug, vismodegib, for the treatment of advanced basal cell cancer, however
Smoothened
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SMALL MOLECULE-PATHWAY-DATABASE
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