FoldX

The FoldX web server: an online force field. FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at http://foldx.embl.de/. The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed.


References in zbMATH (referenced in 9 articles )

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  1. Miyazawa, Sanzo: Selection maintaining protein stability at equilibrium (2016)
  2. Ruiz-Blanco, Yasser B.; Marrero-Ponce, Yovani; Paz, Waldo; García, Yamila; Salgado, Jesús: Global stability of protein folding from an empirical free energy function (2013)
  3. Sarkar, Subhra; Witham, Shawn; Zhang, Jie; Zhenirovskyy, Maxim; Rocchia, Walter; Alexov, Emil: DelPhi web server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes (2013)
  4. Zhang, Zhe; Miteva, Maria A.; Wang, Lin; Alexov, Emil: Analyzing effects of naturally occurring missense mutations (2012)
  5. Costantini, S.; Colonna, G.; Facchiano, A. M.: Simulation of conformational changes occurring when a protein interacts with its receptor (2007)
  6. Flores, Samuel C.; Gerstein, Mark B.: Flexoracle: Predicting flexible hinges by identification of stable domains (2007) ioport
  7. Zhang, Yuan; Zheng, Nan; Nan, Peng; Cao, Ying; Hasegawa, Masami; Zhong, Yang: Computational simulation of interactions between SARS coronavirus spike mutants and host species-specific receptors (2007)
  8. Zhang, Yuan; Zheng, Nan; Zhong, Yang: Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization (2007)
  9. Schymkowitz, Joost; Borg, Jesper; Stricher, Francois; Nys, Robby; Rousseau, Frederic; Serrano, Luis: The foldx web server: An online force field. (2005) ioport