The FoldX web server: an online force field

The FoldX web server: an online force field

2005 | Joost Schymkowitz, Jesper Borg, Francois Stricher, Robby Nys, Frederic Rousseau and Luis Serrano
FoldX is an empirical force field designed for rapid evaluation of the effects of mutations on protein and nucleic acid stability, folding, and dynamics. It provides a web server at http://foldx.embl.de/ for free access to structural analysis tools. The server allows calculation of protein stability, proton positions, water bridges, metal binding sites, and complex formation free energy. It also includes alanine scanning, reporting functions, and detailed structural and energetic analysis. The core functionality is extended with additional applications. FoldX uses a linear combination of empirical terms to calculate free energy changes. It considers solvent interactions, Van der Waals forces, hydrogen bonds, electrostatic interactions, and entropy contributions. The server handles various calculations, including stability analysis, network printing, PDB file generation, complex analysis, and sequence detail. It also allows for the analysis of protein complexes and the prediction of binding free energy. The FoldX web server is hosted on an IBM server with Redhat Linux and PostgreSQL. It uses the ScienceHost framework for hosting scientific algorithms. The server requires a password and login, with free registration. Users can upload up to five PDB files for analysis, and results are sent via email. The server supports various options, including water bridge prediction, ionic strength adjustment, and Van der Waals design settings. PDB files must be in the old style format, with high-resolution structures providing better results. The server can handle various analyses, including stability, network printing, PDB file generation, complex analysis, and sequence detail. It also allows for the analysis of protein complexes and the prediction of binding free energy. FoldX is compared with other online resources like TANGO and SNPEffect, which are used for predicting protein aggregation and SNP effects. FoldX has been validated with experimental data, showing good correlation with experimental results. It is used for structural analysis, protein design, and understanding the effects of mutations on protein stability. The server provides detailed reports on structural issues, including residues with problematic dihedral angles and Van der Waals clashes. It is a valuable tool for structural biocomputing and drug discovery.FoldX is an empirical force field designed for rapid evaluation of the effects of mutations on protein and nucleic acid stability, folding, and dynamics. It provides a web server at http://foldx.embl.de/ for free access to structural analysis tools. The server allows calculation of protein stability, proton positions, water bridges, metal binding sites, and complex formation free energy. It also includes alanine scanning, reporting functions, and detailed structural and energetic analysis. The core functionality is extended with additional applications. FoldX uses a linear combination of empirical terms to calculate free energy changes. It considers solvent interactions, Van der Waals forces, hydrogen bonds, electrostatic interactions, and entropy contributions. The server handles various calculations, including stability analysis, network printing, PDB file generation, complex analysis, and sequence detail. It also allows for the analysis of protein complexes and the prediction of binding free energy. The FoldX web server is hosted on an IBM server with Redhat Linux and PostgreSQL. It uses the ScienceHost framework for hosting scientific algorithms. The server requires a password and login, with free registration. Users can upload up to five PDB files for analysis, and results are sent via email. The server supports various options, including water bridge prediction, ionic strength adjustment, and Van der Waals design settings. PDB files must be in the old style format, with high-resolution structures providing better results. The server can handle various analyses, including stability, network printing, PDB file generation, complex analysis, and sequence detail. It also allows for the analysis of protein complexes and the prediction of binding free energy. FoldX is compared with other online resources like TANGO and SNPEffect, which are used for predicting protein aggregation and SNP effects. FoldX has been validated with experimental data, showing good correlation with experimental results. It is used for structural analysis, protein design, and understanding the effects of mutations on protein stability. The server provides detailed reports on structural issues, including residues with problematic dihedral angles and Van der Waals clashes. It is a valuable tool for structural biocomputing and drug discovery.
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