🤖 TXGemma-2B-Predict Property Prediction

Enter a prompt below, or select a task from the table to load its template, and the model (google/txgemma-2b-predict) will generate text. Adjust the parameters for different results. Prompt templates loaded from tdc_prompts.json. Selected templates will use the SMILES string C1=CC=CC=C1 (Benzene) as a placeholder.

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Prompt Templates

m1_muscarinic_receptor_antagonists_butkiewicz	Instructions: Answer the following question about CRISPR repair outcomes. Context: CRISPR-Cas9 is a gene editing technology that allows targeted deletion or modification of specific regions of the DNA within an organism. This is achieved through designing a guide RNA sequence that binds upstream of the target site which is then cleaved through a Cas9-mediated double stranded DNA break. The cell responds by employing DNA repair mechanisms (such as non-homologous end joining) that result in heterogeneous outcomes including gene insertion or deletion mutations (indels) of varying lengths and frequencies. Primary T cells are a promising cell type for therapeutic genome editing, as they can be engineered efficiently ex vivo and transferred to patients. An experiment is carried out to quantify the DNA repair outcomes of CRISPR-CAS9 knockout experiments on primary CD4+ T cells drawn from donors. For a genomic location, a GuideSeq sequence is provided, which is a 20-nucleotide guide sequence along with the 3-nucletoide PAM sequence. The PAM (protospacer adjacent motif) is a short DNA sequence that follows the DNA region targeted for cleavage by the CRISPR-Cas9 system. One particular measure of interest for repair outcome quantification is the fraction of repair outcomes with a frameshift. Question: Given a GuideSeq sequence, predict its normalized fraction of repair outcomes with a frameshift from 000 to 1000, where 000 is minimum fraction of repair outcomes with a frameshift and 1000 is maximum fraction of repair outcomes with a frameshift. GuideSeq: {GuideSeq} Answer:


Pgp_Broccatelli	Instructions: Answer the following question about drug properties. Context: P-glycoprotein (Pgp) is an ABC transporter protein involved in intestinal absorption, drug metabolism, and brain penetration, and its inhibition can seriously alter a drug's bioavailability and safety. In addition, inhibitors of Pgp can be used to overcome multidrug resistance. Question: Given a drug SMILES string, predict whether it (A) is not a PgP inhibitor (B) is a PgP inhibitor Drug SMILES: {Drug SMILES} Answer:
Bioavailability_Ma	Instructions: Answer the following question about drug properties. Context: Oral bioavailability is defined as “the rate and extent to which the active ingredient or active moiety is absorbed from a drug product and becomes available at the site of action”. Question: Given a drug SMILES string, predict whether it (A) has oral bioavailability < 20% (B) has oral bioavailability ≥ 20% Drug SMILES: {Drug SMILES} Answer:
BBB_Martins	Instructions: Answer the following question about drug properties. Context: As a membrane separating circulating blood and brain extracellular fluid, the blood-brain barrier (BBB) is the protection layer that blocks most foreign drugs. Thus the ability of a drug to penetrate the barrier to deliver to the site of action forms a crucial challenge in development of drugs for central nervous system. Question: Given a drug SMILES string, predict whether it (A) does not cross the BBB (B) crosses the BBB Drug SMILES: {Drug SMILES} Answer:
CYP2D6_Veith	Instructions: Answer the following question about drug properties. Context: The CYP P450 genes are involved in the formation and breakdown (metabolism) of various molecules and chemicals within cells. Specifically, CYP2D6 is primarily expressed in the liver. It is also highly expressed in areas of the central nervous system, including the substantia nigra. Question: Given a drug SMILES string, predict whether it (A) does not inhibit CYP2D6 (B) inhibits CYP2D6 Drug SMILES: {Drug SMILES} Answer:
CYP3A4_Veith	Instructions: Answer the following question about drug properties. Context: The CYP P450 genes are involved in the formation and breakdown (metabolism) of various molecules and chemicals within cells. Specifically, CYP3A4 is an important enzyme in the body, mainly found in the liver and in the intestine. It oxidizes small foreign organic molecules (xenobiotics), such as toxins or drugs, so that they can be removed from the body. Question: Given a drug SMILES string, predict whether it (A) does not inhibit CYP3A4 (B) inhibits CYP3A4 Drug SMILES: {Drug SMILES} Answer:
CYP2C9_Veith	Instructions: Answer the following question about drug properties. Context: The CYP P450 genes are involved in the formation and breakdown (metabolism) of various molecules and chemicals within cells. Specifically, the CYP P450 2C9 plays a major role in the oxidation of both xenobiotic and endogenous compounds. Question: Given a drug SMILES string, predict whether it (A) does not inhibit CYP2C9 (B) inhibits CYP2C9 Drug SMILES: {Drug SMILES} Answer:
CYP2D6_Substrate_CarbonMangels	Instructions: Answer the following question about drug properties. Context: CYP2D6 is primarily expressed in the liver. It is also highly expressed in areas of the central nervous system, including the substantia nigra. Substrates are drugs that are metabolized by the enzyme. Question: Given a drug SMILES string, predict whether it (A) is not a substrate to the enzyme CYP2D6 (B) is a substrate to the enzyme CYP2D6 Drug SMILES: {Drug SMILES} Answer:
CYP3A4_Substrate_CarbonMangels	Instructions: Answer the following question about drug properties. Context: CYP3A4 is an important enzyme in the body, mainly found in the liver and in the intestine. It oxidizes small foreign organic molecules (xenobiotics), such as toxins or drugs, so that they can be removed from the body. Substrates are drugs that are metabolized by the enzyme. Question: Given a drug SMILES string, predict whether it (A) is not a substrate to the enzyme CYP3A4 (B) is a substrate to the enzyme CYP3A4 Drug SMILES: {Drug SMILES} Answer:
CYP2C9_Substrate_CarbonMangels	Instructions: Answer the following question about drug properties. Context: CYP P450 2C9 plays a major role in the oxidation of both xenobiotic and endogenous compounds. Substrates are drugs that are metabolized by the enzyme. Question: Given a drug SMILES string, predict whether it (A) is not a substrate to the enzyme CYP2C9 (B) is a substrate to the enzyme CYP2C9 Drug SMILES: {Drug SMILES} Answer:
hERG	Instructions: Answer the following question about drug properties. Context: Human ether-à-go-go related gene (hERG) is crucial for the coordination of the heart's beating. Thus, if a drug blocks the hERG, it could lead to severe adverse effects. Therefore, reliable prediction of hERG liability in the early stages of drug design is quite important to reduce the risk of cardiotoxicity-related attritions in the later development stages. Question: Given a drug SMILES string, predict whether it (A) does not block hERG (B) blocks hERG Drug SMILES: {Drug SMILES} Answer:
AMES	Instructions: Answer the following question about drug properties. Context: Mutagenicity means the ability of a drug to induce genetic alterations. Drugs that can cause damage to the DNA can result in cell death or other severe adverse effects. Nowadays, the most widely used assay for testing the mutagenicity of compounds is the Ames experiment which was invented by a professor named Ames. The Ames test is a short-term bacterial reverse mutation assay detecting a large number of compounds which can induce genetic damage and frameshift mutations. Question: Given a drug SMILES string, predict whether it (A) is not mutagenic (B) is mutagenic Drug SMILES: {Drug SMILES} Answer:
DILI	Instructions: Answer the following question about drug properties. Context: Drug-induced liver injury (DILI) is fatal liver disease caused by drugs and it has been the single most frequent cause of safety-related drug marketing withdrawals for the past 50 years (e.g. iproniazid, ticrynafen, benoxaprofen). Question: Given a drug SMILES string, predict whether it (A) cannot cause DILI (B) can cause DILI Drug SMILES: {Drug SMILES} Answer:
HIA_Hou	Instructions: Answer the following question about drug properties. Context: When a drug is orally administered, it needs to be absorbed from the human gastrointestinal system into the bloodstream of the human body. This ability of absorption is called human intestinal absorption (HIA) and it is crucial for a drug to be delivered to the target. Question: Given a drug SMILES string, predict whether it (A) cannot be absorbed (B) can be absorbed Drug SMILES: {Drug SMILES} Answer:
Tox21_NR_AhR	Instructions: Answer the following question about drug properties. Context: Humans are exposed to a variety of chemicals through food, household products, and medicines, some of which can be toxic, leading to over 30% of promising pharmaceuticals failing in human trials due to toxicity. The Aryl hydrocarbon Receptor (AhR), a nuclear receptor member of the family of basic helix-loop-helix transcription factors, is crucial to adaptive responses to environmental changes. AhR mediates cellular responses to environmental pollutants such as aromatic hydrocarbons through induction of phase I and II enzymes but also interacts with other nuclear receptor signaling pathways. Question: Given a drug SMILES string, predict whether it (A) is not toxic in a NR aryl hydrocarbon receptor assay (B) is toxic in a NR aryl hydrocarbon receptor assay Drug SMILES: {Drug SMILES} Answer:
Tox21_NR_Aromatase	Instructions: Answer the following question about drug properties. Context: Humans are exposed to a variety of chemicals through food, household products, and medicines, some of which can be toxic, leading to over 30% of promising pharmaceuticals failing in human trials due to toxicity. Endocrine disrupting chemicals (EDCs) interfere with the biosynthesis and normal functions of steroid hormones including estrogen and androgen in the body. Aromatase is an enzyme that catalyzes the conversion of androgen to estrogen and plays a key role in maintaining the androgen and estrogen balance in many of the EDC-sensitive organs. Question: Given a drug SMILES string, predict whether it (A) is not toxic in an Aromatase assay (B) is toxic in an Aromatase assay Drug SMILES: {Drug SMILES} Answer:
Tox21_NR_AR	Instructions: Answer the following question about drug properties. Context: Humans are exposed to a variety of chemicals through food, household products, and medicines, some of which can be toxic, leading to over 30% of promising pharmaceuticals failing in human trials due to toxicity. Androgen receptor (AR), a nuclear hormone receptor, plays a critical role in AR-dependent prostate cancer and other androgen related diseases. Endocrine disrupting chemicals (EDCs) and their interactions with steroid hormone receptors like AR may cause disruption of normal endocrine function as well as interfere with metabolic homeostasis, reproduction, developmental and behavioral functions. Question: Given a drug SMILES string, predict whether it (A) is not toxic in an AR full length assay (B) is toxic in an AR full length assay Drug SMILES: {Drug SMILES} Answer:
Tox21_NR_AR_LBD	Instructions: Answer the following question about drug properties. Context: Humans are exposed to a variety of chemicals through food, household products, and medicines, some of which can be toxic, leading to over 30% of promising pharmaceuticals failing in human trials due to toxicity. Androgen receptor (AR), a nuclear hormone receptor, plays a critical role in AR-dependent prostate cancer and other androgen related diseases. The ligand-binding domain (LBD) is a specific region of the androgen receptor where hormones attach. Endocrine disrupting chemicals (EDCs) and their interactions with steroid hormone receptors like AR may cause disruption of normal endocrine function as well as interfere with metabolic homeostasis, reproduction, developmental and behavioral functions. Question: Given a drug SMILES string, predict whether it (A) is not toxic in an AR LBD assay (B) is toxic in an AR LBD assay Drug SMILES: {Drug SMILES} Answer:
Tox21_NR_ER	Instructions: Answer the following question about drug properties. Context: Humans are exposed to a variety of chemicals through food, household products, and medicines, some of which can be toxic, leading to over 30% of promising pharmaceuticals failing in human trials due to toxicity. Estrogen receptor (ER), a nuclear hormone receptor, plays an important role in development, metabolic homeostasis and reproduction. Endocrine disrupting chemicals (EDCs) and their interactions with steroid hormone receptors like ER causes disruption of normal endocrine function. Question: Given a drug SMILES string, predict whether it (A) is not toxic in an ER alpha full length assay (B) is toxic in an ER alpha full length assay Drug SMILES: {Drug SMILES} Answer:
Tox21_NR_ER_LBD	Instructions: Answer the following question about drug properties. Context: Humans are exposed to a variety of chemicals through food, household products, and medicines, some of which can be toxic, leading to over 30% of promising pharmaceuticals failing in human trials due to toxicity. Estrogen receptor (ER), a nuclear hormone receptor, plays an important role in development, metabolic homeostasis and reproduction. The ligand-binding domain (LBD) is a specific region of the androgen receptor where hormones attach. Endocrine disrupting chemicals (EDCs) and their interactions with steroid hormone receptors like ER causes disruption of normal endocrine function. Question: Given a drug SMILES string, predict whether it (A) is not toxic in an ER alpha LBD assay (B) is toxic in an ER alpha LBD assay Drug SMILES: {Drug SMILES} Answer:
Tox21_NR_PPAR_gamma	Instructions: Answer the following question about drug properties. Context: Humans are exposed to a variety of chemicals through food, household products, and medicines, some of which can be toxic, leading to over 30% of promising pharmaceuticals failing in human trials due to toxicity. The peroxisome proliferator-activated receptors (PPARs) are lipid-activated transcription factors of the nuclear receptor superfamily with three distinct subtypes namely PPAR alpha, PPAR delta (also called PPAR beta) and PPAR gamma (PPARg). All these subtypes heterodimerize with Retinoid X receptor (RXR) and these heterodimers regulate transcription of various genes. PPAR-gamma receptor (glitazone receptor) is involved in the regulation of glucose and lipid metabolism. Question: Given a drug SMILES string, predict whether it (A) is not toxic in a PPARg assay (B) is toxic in a PPARg assay Drug SMILES: {Drug SMILES} Answer:
Tox21_SR_ARE	Instructions: Answer the following question about drug properties. Context: Humans are exposed to a variety of chemicals through food, household products, and medicines, some of which can be toxic, leading to over 30% of promising pharmaceuticals failing in human trials due to toxicity. Oxidative stress has been implicated in the pathogenesis of a variety of diseases ranging from cancer to neurodegeneration. The antioxidant response element (ARE) signaling pathway plays an important role in the amelioration of oxidative stress. Nrf2 (NF-E2-related factor 2) and Nrf1 are transcription factors that bind to AREs and activate these genes. Question: Given a drug SMILES string, predict whether it (A) is not toxic in a Nrf2/antioxidant responsive element assay (B) is toxic in a Nrf2/antioxidant responsive element assay Drug SMILES: {Drug SMILES} Answer:
Tox21_SR_ATAD5	Instructions: Answer the following question about drug properties. Context: Humans are exposed to a variety of chemicals through food, household products, and medicines, some of which can be toxic, leading to over 30% of promising pharmaceuticals failing in human trials due to toxicity. As cancer cells divide rapidly and during every cell division they need to duplicate their genome by DNA replication. The failure to do so results in the cancer cell death. Based on this concept, many chemotherapeutic agents were developed but have limitations such as low efficacy and severe side effects etc. A new cell based assay was developed to find the compounds that effectively block DNA replication either by directly damaging DNA or by inhibiting other cellular mechanisms. Enhanced Level of Genome Instability Gene 1 (ELG1; human ATAD5) protein levels increase in response to various types of DNA damage. Question: Given a drug SMILES string, predict whether it (A) is not toxic in an ATAD5 assay (B) is toxic in an ATAD5 assay Drug SMILES: {Drug SMILES} Answer: