PrimaDORAC: An improved Web Interface for Rapid GAFF2 Parameter Assignment with ABCG2 Charge Models for Drug Design Applications.
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| Title: | PrimaDORAC: An improved Web Interface for Rapid GAFF2 Parameter Assignment with ABCG2 Charge Models for Drug Design Applications. |
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| Authors: | Procacci, Piero1 (AUTHOR) piero.procacci@unifi.it |
| Source: | Journal of Computational Chemistry. 6/30/2026, Vol. 47 Issue 17, p1-7. 7p. |
| Subjects: | Web-based user interfaces, Drug design, Molecular dynamics, Computational chemistry |
| Abstract: | The accurate parameterization of drug‐like molecules is a fundamental prerequisite for molecular dynamics simulations in structure‐based drug design. While the AM1‐BCC charge model has served as the de facto "standard" for GAFF2 parameterization for two decades, the recently introduced ABCG2 model offers substantially improved accuracy in predicting hydration free energies and other key physicochemical properties. However, accessing ABCG2 parameters traditionally requires downloading and installing the full AmberTools suite—a multi‐gigabyte software package with complex dependencies—presenting a significant barrier for many practitioners, particularly experimental collaborators and researchers new to the field. Here we present a major upgrade to the PrimaDORAC web interface that makes ABCG2 parameterization readily accessible to the entire drug design community. Through a minimalistic integration of essential AmberTools components directly into the web application framework, users can now obtain GAFF2 parameters with ABCG2 charges for any drug‐like molecule in seconds, without any software installation. The interface accepts a single SMILES string or structure file and returns a complete archive containing GROMACS‐compatible topology files and a ready‐to‐use PDB structure. By removing all technical barriers to accessing state‐of‐the‐art ABCG2 parameters, the upgraded PrimaDORAC interface is aimed at empowering medicinal chemists, pharmacologists, and computational researchers alike to conduct more accurate MD simulations with minimal effort. The service is freely available at www1.chim.unifi.it/orac. [ABSTRACT FROM AUTHOR] |
| Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Engineering Source |
| FullText | Text: Availability: 0 |
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| Header | DbId: egs DbLabel: Engineering Source An: 194973520 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: PrimaDORAC: An improved Web Interface for Rapid GAFF2 Parameter Assignment with ABCG2 Charge Models for Drug Design Applications. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Procacci%2C+Piero%22">Procacci, Piero</searchLink><relatesTo>1</relatesTo> (AUTHOR)<i> piero.procacci@unifi.it</i> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Journal+of+Computational+Chemistry%22">Journal of Computational Chemistry</searchLink>. 6/30/2026, Vol. 47 Issue 17, p1-7. 7p. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Web-based+user+interfaces%22">Web-based user interfaces</searchLink><br /><searchLink fieldCode="DE" term="%22Drug+design%22">Drug design</searchLink><br /><searchLink fieldCode="DE" term="%22Molecular+dynamics%22">Molecular dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22Computational+chemistry%22">Computational chemistry</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: The accurate parameterization of drug‐like molecules is a fundamental prerequisite for molecular dynamics simulations in structure‐based drug design. While the AM1‐BCC charge model has served as the de facto "standard" for GAFF2 parameterization for two decades, the recently introduced ABCG2 model offers substantially improved accuracy in predicting hydration free energies and other key physicochemical properties. However, accessing ABCG2 parameters traditionally requires downloading and installing the full AmberTools suite—a multi‐gigabyte software package with complex dependencies—presenting a significant barrier for many practitioners, particularly experimental collaborators and researchers new to the field. Here we present a major upgrade to the PrimaDORAC web interface that makes ABCG2 parameterization readily accessible to the entire drug design community. Through a minimalistic integration of essential AmberTools components directly into the web application framework, users can now obtain GAFF2 parameters with ABCG2 charges for any drug‐like molecule in seconds, without any software installation. The interface accepts a single SMILES string or structure file and returns a complete archive containing GROMACS‐compatible topology files and a ready‐to‐use PDB structure. By removing all technical barriers to accessing state‐of‐the‐art ABCG2 parameters, the upgraded PrimaDORAC interface is aimed at empowering medicinal chemists, pharmacologists, and computational researchers alike to conduct more accurate MD simulations with minimal effort. The service is freely available at www1.chim.unifi.it/orac. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Journal of Computational Chemistry is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1002/jcc.70444 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 7 StartPage: 1 Subjects: – SubjectFull: Web-based user interfaces Type: general – SubjectFull: Drug design Type: general – SubjectFull: Molecular dynamics Type: general – SubjectFull: Computational chemistry Type: general Titles: – TitleFull: PrimaDORAC: An improved Web Interface for Rapid GAFF2 Parameter Assignment with ABCG2 Charge Models for Drug Design Applications. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Procacci, Piero IsPartOfRelationships: – BibEntity: Dates: – D: 30 M: 06 Text: 6/30/2026 Type: published Y: 2026 Identifiers: – Type: issn-print Value: 01928651 Numbering: – Type: volume Value: 47 – Type: issue Value: 17 Titles: – TitleFull: Journal of Computational Chemistry Type: main |
| ResultId | 1 |
