大规模生物分子指令数据集助力大语言模型
Mol-Instructions是一个开放的大规模生物分子指令数据集,包含分子导向、蛋白质导向和生物分子文本三类指令。数据集涵盖分子设计、蛋白质功能预测等多个任务,通过AI协作、数据提取和模板转换等方法构建。该数据集旨在增强大语言模型在生物分子领域的表现,现已在Hugging Face平台发布。
Mol-Instructions comprises three cardinal components:
We release the dataset on Hugging Face at zjunlp/Mol-Instructions.
<h2 id="2">2. Tasks</h2> <h3 id="2-1"> 🔬 2.1 Molecule-oriented</h3> <details> <summary><b>Molecule description generation</b></summary>Please give me some details about this molecule: [C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][=Branch1][C][=O][O][C@H1][Branch2][Ring1][=Branch1][C][O][C][=Branch1][C][=O][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][C][O][P][=Branch1][C][=O][Branch1][C][O][O][C][C@@H1][Branch1][=Branch1][C][=Branch1][C][=O][O][N]
The molecule is a 3-sn-phosphatidyl-L-serine in which the phosphatidyl acyl groups at positions 1 and 2 are specified as stearoyl and arachidonoyl respectively.
It is functionally related to an arachidonic acid and an octadecanoic acid.
Create a molecule with the structure as the one described: The molecule is a primary arylamine in which an amino functional group is substituted for one of the benzene hydrogens. It is a primary arylamine and a member of anilines.
[N][C][=C][C][=C][C][=C][Ring1][=Branch1]
With the provided reactants and reagents, propose a potential product: [O][=N+1][Branch1][C][O-1][C][=C][N][=C][Branch1][C][Cl][C][Branch1][C][I][=C][Ring1][Branch2].[Fe]
[N][C][=C][N][=C][Branch1][C][Cl][C][Branch1][C][I][=C][Ring1][Branch2]
Please suggest potential reactants used in the synthesis of the provided product: [C][=C][C][C][N][C][=Branch1][C][=O][O][C][Branch1][C][C][Branch1][C][C][C]
[C][=C][C][C][N].[C][C][Branch1][C][C][Branch1][C][C][O][C][=Branch1][C][=O][O][C][=Branch1][C][=O][O][C][Branch1][C][C][Branch1][C][C][C]
Please provide possible reagents based on the following chemical reaction: [C][C][=C][C][=C][Branch1][C][N][C][=N][Ring1][#Branch1].[O][=C][Branch1][C][Cl][C][Cl]>>[C][C][=C][C][=C][Branch1][Branch2][N][C][=Branch1][C][=O][C][Cl][C][=N][Ring1][O]
[C][C][C][O][C][Ring1][Branch1].[C][C][N][Branch1][Ring1][C][C][C][C].[O]
Please provide the HOMO energy value for this molecule: [C][C][O][C][C][Branch1][C][C][C][Branch1][C][C][C]
-0.2482
MSNELVLSREQVRRVDQRAIEAYGVPGIVLMENAGRGAAEIIRAACPSAQRVLIACGPGNNGGDGFVIARHLANAGWMVELLLACPADRITGDAQGNHEIIRRMNLPCAVMADARDLEAANDRFATADVIVDALLGTGASGPPREPIASLIRAINEAHRRVSAQPAPSVFAVDIPSGLDCDTGEAANPTVRADHTITFVARKIGFRNPAARDLLGRVHVVDIGAPRAAIQDALTGKSG
</details>
<details>
<summary><b>Catalytic activity prediction</b></summary>
Please evaluate the following protein sequence and provide an explanation of the enzyme's catalytic activity, including the chemical reaction it facilitates: MDKVAVAGFLPEELCASLSLSPSFRGNQIFQWIGKGVDSFDAMTNLSAELRASLAEKAILRSTRVSDVLKADDGTVKLQIQTEDDLAVETVLLTDKAARKTACVSCQAGCAMGCAFCKTGTLGLARNLSAAEIVEQFLYLEKHAGALDNIVFMGMGEPLLNLDALRKAIAVLTDKRGRNLSSRRITVSTVGIVSGIYDLANNGPDVRLAVSLTTADETLRRELMPASLTNPLSDLRQAISYYIEKTGKRVTLEAVLLSGKNTSEKNADSLIAFAKGLDVHVNLIPWNPVEGLSFVTPDPEETAQFVSRLEKGGLNVTLRMHRGKSISGACGQLGKTNPYA
Based on the provided protein sequence, the enzyme appears to facilitate the chemical reaction: adenosine(37) in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S- adenosyl-L-methionine = 2-methyladenosine(37) in tRNA + 5'- deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S- adenosyl-L-homocysteine.
Analyze the following amino acid sequence, and determine the function of the resulting protein, its subcellular localization, and any biological processes it may be part of: MNGTVNASAPSKMSEVAVERLSNDKALKVIFVLGGPGSGKGTQCAKIAKHFGFTHLSVGDLLRAEINSGSKNGTMIESMINEGKIVRSEVTIKLLQRAMHESGNDKFLIDGFPRNEENRAAFENLEKIEPEFVLFFDCPMEEMERRILNRNQGRDDDKMETIRKRFKVFIESTLPVIEFYNLKGKLYKIDACKPADEVFEDVKAIFSRFRAKEDSSQQTNICTAKRFELVMCLIKRLFREIKRMWSSFFCKAL
The protein characterized by the amino acid sequence demonstrates ATP binding, cytidylate kinase activity, uridylate kinase activity and is implicated in the 'de novo' pyrimidine nucleobase biosynthetic process, phosphorylation, pyrimidine nucleotide biosynthetic process. Its subcellular localization is primarily within the cytoplasm, nucleus.
Examine the given protein sequence and share a brief overview of its attributes: MKIVLASNNQGKLAELKAMLAPLGVQLLRQAELGIPEAAEPFRTFVENALAKARHASALSGLPALADDAGLCVEAFGGLPGVDTAFYAVQFGYAKGDANNVKALLAQMAGITDRRAALVSTLVAVRSAEDPEPLIACGRVAGEVALEPMGSNGFGFDPVMFIPEFGQTFAQLPVEVKNANSHRGKATRQMMALMRERWIT
A concise description of the protein with the specified amino acid sequence includes: Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions.
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