M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures
Abstract Background The field of computational drug design is undergoing rapid advancements, highlighting the need for innovative methods to enhance the efficiency and accuracy of calculating ligand-receptor interactions. In this context, we introduce the M01 tool, a comprehensive computational pack...
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| Language: | English |
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BMC
2025-04-01
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| Series: | BMC Bioinformatics |
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| Online Access: | https://doi.org/10.1186/s12859-025-06120-5 |
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| author | Mahsa Sheikholeslami Mohammad Hasan Nazari Afshin Fassihi |
| author_facet | Mahsa Sheikholeslami Mohammad Hasan Nazari Afshin Fassihi |
| author_sort | Mahsa Sheikholeslami |
| collection | DOAJ |
| description | Abstract Background The field of computational drug design is undergoing rapid advancements, highlighting the need for innovative methods to enhance the efficiency and accuracy of calculating ligand-receptor interactions. In this context, we introduce the M01 tool, a comprehensive computational package designed to facilitate the generation and docking of small molecule-peptide hybrids. M01 integrates several established tools, such as RDKit and EasyDock, into a user-friendly platform that automates the workflow from hybrid generation to docking simulations. This tool is particularly beneficial for researchers with limited chemistry expertise, helping them leverage advanced computational techniques. Results The M01 tool features an intuitive interface for visualizing molecules and selecting connection points in generating new ligands. It also offers automated receptor preparation using UniProt or PDB IDs and generates default docking configuration files. Furthermore, it includes ligand preparation and docking capabilities through EasyDock and calculates molecular descriptors relevant to drug-likeness properties. Validation studies with peptide-alkoxyamine hybrids demonstrated the tool’s effectiveness, generating over 14,000 unique hybrid molecules and showcasing its versatility in drug design applications. Conclusions The M01 tool represents a significant advancement in computational drug design, streamlining the process of creating hybrid molecules and conducting docking studies. Its ability to automate complex workflows and provide essential molecular insights can empower researchers and enhance the development of novel therapeutics, ultimately contributing to more efficient drug discovery efforts. |
| format | Article |
| id | doaj-art-35afc2955ecf4da3bb4510ec16fc43ac |
| institution | DOAJ |
| issn | 1471-2105 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-35afc2955ecf4da3bb4510ec16fc43ac2025-08-20T03:18:42ZengBMCBMC Bioinformatics1471-21052025-04-0126111610.1186/s12859-025-06120-5M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structuresMahsa Sheikholeslami0Mohammad Hasan Nazari1Afshin Fassihi2Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical ScienceDepartment of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical ScienceDepartment of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical ScienceAbstract Background The field of computational drug design is undergoing rapid advancements, highlighting the need for innovative methods to enhance the efficiency and accuracy of calculating ligand-receptor interactions. In this context, we introduce the M01 tool, a comprehensive computational package designed to facilitate the generation and docking of small molecule-peptide hybrids. M01 integrates several established tools, such as RDKit and EasyDock, into a user-friendly platform that automates the workflow from hybrid generation to docking simulations. This tool is particularly beneficial for researchers with limited chemistry expertise, helping them leverage advanced computational techniques. Results The M01 tool features an intuitive interface for visualizing molecules and selecting connection points in generating new ligands. It also offers automated receptor preparation using UniProt or PDB IDs and generates default docking configuration files. Furthermore, it includes ligand preparation and docking capabilities through EasyDock and calculates molecular descriptors relevant to drug-likeness properties. Validation studies with peptide-alkoxyamine hybrids demonstrated the tool’s effectiveness, generating over 14,000 unique hybrid molecules and showcasing its versatility in drug design applications. Conclusions The M01 tool represents a significant advancement in computational drug design, streamlining the process of creating hybrid molecules and conducting docking studies. Its ability to automate complex workflows and provide essential molecular insights can empower researchers and enhance the development of novel therapeutics, ultimately contributing to more efficient drug discovery efforts.https://doi.org/10.1186/s12859-025-06120-5Computational drug designHybrid moleculesDocking simulationsLigand-receptor interactionsADMET propertiesPeptide–drug conjugates |
| spellingShingle | Mahsa Sheikholeslami Mohammad Hasan Nazari Afshin Fassihi M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures BMC Bioinformatics Computational drug design Hybrid molecules Docking simulations Ligand-receptor interactions ADMET properties Peptide–drug conjugates |
| title | M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures |
| title_full | M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures |
| title_fullStr | M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures |
| title_full_unstemmed | M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures |
| title_short | M01 tool: an automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures |
| title_sort | m01 tool an automated comprehensive computational tool for generating small molecule peptide hybrids and docking them into curated protein structures |
| topic | Computational drug design Hybrid molecules Docking simulations Ligand-receptor interactions ADMET properties Peptide–drug conjugates |
| url | https://doi.org/10.1186/s12859-025-06120-5 |
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