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PepSMI: Convert Peptide to SMILES string

1. Enter sequence (Input the raw sequence, not fasta format):

Length: 0

2. Select the Constraint Type of the peptide:



PepSMI converts Peptide sequence into SMILES string

Usage: This tool accepts standard amino acids using single letter codes (ACDEFGHIKLMNPQRSTVWY). The sequence is case sensitive: uppercase letters denote L-amino acids and lowercase letters denote D-type amino acids. For special amino acids, use the "Search and add amino acids" field above to find and add them to your sequence. This tool currently supports over 440 special residues.

Special Amino Acid Search: To add special amino acids beyond the standard 20, type at least 3 characters in the "Search and add amino acids" field to search by name or code. Select the desired amino acid from the dropdown list and click "Add to Sequence" to append it to your peptide sequence. Special amino acids will be displayed in curly braces format (e.g., {Hyp} for Hydroxyproline).

About SMILES: SMILES (Simplified Molecular Input Line Entry System) is a standardized chemical notation that represents molecular structures as text strings. This machine-readable format encodes the complete structural information of a molecule, including all atoms, bonds, and stereochemistry. SMILES strings serve as universal molecular identifiers, enabling seamless data exchange between different chemical software and databases. They are essential for computational chemistry, molecular modeling, and drug discovery, as they can be automatically converted into 2D structures, 3D conformations, and used for similarity searching, property prediction, and virtual screening across chemical databases.

The SMILES string could be depicted as svg with Smi2SVG. The SMILES string could also be viewed as 2D image at: http://cdb.ics.uci.edu/cgibin/Smi2DepictWeb.py and converted/viewed at: https://pubchem.ncbi.nlm.nih.gov/edit3/index.html

Publications citing PepSMI:

  • Shams R, Ito Y, Miyatake H. Development of an RHEB-Targeting Peptide To Inhibit mTORC1 Kinase Activity. ACS Omega. 2022 Jun 24;7(27):23479-23486. doi: 10.1021/acsomega.2c01865. PMID: 35847293; PMCID: PMC9280966.
  • Zhang J, Liang L, Shan Y, Zhou X, Sun B, Liu Y, Zhang Y. Antihypertensive Effect, ACE Inhibitory Activity, and Stability of Umami Peptides from Yeast Extract. J Agric Food Chem. 2023 Oct 9. doi: 10.1021/acs.jafc.3c04819. Epub ahead of print. PMID: 37812565.
  • Wang F, Sangfuang N, McCoubrey LE, Yadav V, Elbadawi M, Orlu M, Gaisford S, Basit AW. Advancing oral delivery of biologics: Machine learning predicts peptide stability in the gastrointestinal tract. Int J Pharm. 2023 Mar 5;634:122643. doi: 10.1016/j.ijpharm.2023.122643. Epub 2023 Jan 25. PMID: 36709014.
  • Wong FC, Ong JH, Kumar DT, Chai TT. In Silico Identification of Multi-target Anti-SARS-CoV-2 Peptides from Quinoa Seed Proteins. Int J Pept Res Ther. 2021;27(3):1837-1847. doi: 10.1007/s10989-021-10214-y. Epub 2021 Apr 9. PMID: 33867899; PMCID: PMC8034280.
  • Suo SK, Zheng SL, Chi CF, Luo HY, Wang B. Novel angiotensin-converting enzyme inhibitory peptides from tuna byproducts-milts: Preparation, characterization, molecular docking study, and antioxidant function on H2O2-damaged human umbilical vein endothelial cells. Front Nutr. 2022 Jul 22;9:957778. doi: 10.3389/fnut.2022.957778. PMID: 35938100; PMCID: PMC9355146.
  • Suo SK, Zhao YQ, Wang YM, Pan XY, Chi CF, Wang B. Seventeen novel angiotensin converting enzyme (ACE) inhibitory peptides from the protein hydrolysate of Mytilus edulis: isolation, identification, molecular docking study, and protective function on HUVECs. Food Funct. 2022 Jul 18;13(14):7831-7846. doi: 10.1039/d2fo00275b. PMID: 35770686.
  • Roque-Borda CA, Saraiva MMS, Macedo Junior WD, Márquez Montesinos JCE, Meneguin AB, Toledo Borges AB, Crusca Junior E, Garrido SS, de Almeida AM, Marchetto R, Chorilli M, Berchieri Junior A, Teixeira SR, Pavan FR, Vicente EF. Chitosan and HPMCAS double-coating as protective systems for alginate microparticles loaded with Ctx(Ile21)-Ha antimicrobial peptide to prevent intestinal infections. Biomaterials. 2023 Feb;293:121978. doi: 10.1016/j.biomaterials.2022.121978. Epub 2022 Dec 22. PMID: 36580719.
  • Zheng SL, Luo QB, Suo SK, Zhao YQ, Chi CF, Wang B. Preparation, Identification, Molecular Docking Study and Protective Function on HUVECs of Novel ACE Inhibitory Peptides from Protein Hydrolysate of Skipjack Tuna Muscle. Mar Drugs. 2022 Feb 27;20(3):176. doi: 10.3390/md20030176. PMID: 35323475; PMCID: PMC8954214.
  • Widyawati T, Yusoff NA, Bello I, Asmawi MZ, Ahmad M. Bioactivity-Guided Fractionation and Identification of Antidiabetic Compound of Syzygium polyanthum (Wight.)'s Leaf Extract in Streptozotocin-Induced Diabetic Rat Model. Molecules. 2022 Oct 12;27(20):6814. doi: 10.3390/molecules27206814. PMID: 36296407; PMCID: PMC9609764.
  • Cao X, Guo Y, Feng Y, Liu X, Yao F, Chen T, Tian L, Kang X. Recognition Receptor for Methylated Arginine at the Single Molecular Level. Anal Chem. 2023 May 2;95(17):6989-6995. doi: 10.1021/acs.analchem.3c00406. Epub 2023 Apr 21. PMID: 37083370.
  • Zhang J, Liang L, Shan Y, Zhou X, Sun B, Liu Y, Zhang Y. Antihypertensive Effect, ACE Inhibitory Activity, and Stability of Umami Peptides from Yeast Extract. J Agric Food Chem. 2023 Oct 9. doi: 10.1021/acs.jafc.3c04819. Epub ahead of print. PMID: 37812565.
  • Roque-Borda CA, Saraiva MMS, Macedo Junior WD, Márquez Montesinos JCE, Meneguin AB, Toledo Borges AB, Crusca Junior E, Garrido SS, de Almeida AM, Marchetto R, Chorilli M, Berchieri Junior A, Teixeira SR, Pavan FR, Vicente EF. Chitosan and HPMCAS double-coating as protective systems for alginate microparticles loaded with Ctx(Ile21)-Ha antimicrobial peptide to prevent intestinal infections. Biomaterials. 2023 Feb;293:121978. doi: 10.1016/j.biomaterials.2022.121978. Epub 2022 Dec 22. PMID: 36580719.
  • Wang F, Sangfuang N, McCoubrey LE, Yadav V, Elbadawi M, Orlu M, Gaisford S, Basit AW. Advancing oral delivery of biologics: Machine learning predicts peptide stability in the gastrointestinal tract. Int J Pharm. 2023 Mar 5;634:122643. doi: 10.1016/j.ijpharm.2023.122643. Epub 2023 Jan 25. PMID: 36709014.
  • Muthusamy K, Ramasamy G, Ravikumar C, Natesan S, Muthurajan R, Uthandi S, Kalyanasundaram K, Tiwari V. Exploring bixin from Bixa orellana L. seeds: quantification and in silico insights into its anti-cancer potential. J Biomol Struct Dyn. 2023 Oct 14:1-15. doi: 10.1080/07391102.2023.2268202. Epub ahead of print. PMID: 37837422.
  • Ella Mae Gamba, Lawrence Yves Uy, and Mary Ann Torio. Angiotensin I-Converting Enzyme Inhibitory and Antioxidative Activities of the Bioactive Peptides in the Crude Salt-Soluble Protein Hydrolysates of Pili Nut (Canarium ovatum Engl.) cv. Mayon Kernel. PHILIPP AGRIC SCIENTIST. 2023 Jun; Vol. 106 No. 2, 166-174; ISSN 0031-7454.