FFFold

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FFFold is a web application for the local optimisation of protein structures predicted by the AlphaFold2 algorithm and deposited in the AlphaFold DB database. The structures are optimised by the physics-based generic force field GFN-FF accelerated by a divide-and-conquer approach which results are comparable to the optimisation of whole protein structure with constrained α-carbons. Thus, FFFold optimises in particular the bond lengths and angles and describes the interactions between nearby residues as can be seen in examples. Before computation of the charges, input protein structures are protonated by PROPKA3. The details about the methodology and usage are described in the manual. This website is free and open to all users and there is no login requirement. Source codes are freely available at GitHub.



Examples

Dihedral angles
TA
The AlphaFold 2 and the subsequent PROPKA prediction of hydrogens often created a bond with a unnatural angle (e.g., peptide bond with almost right angle). FFFold optimises bond lengths and bond angles.
Hydrogen bonds
HB
Hydrogen bonds are important contributors to the secondary and partly also to the tertiary structure of the protein. During FFFold optimisation, a large number of hydrogen bonds are formed/refined in the structure.
π–π stacking
PS
The π-π interaction stabilizes the secondary and tertiary structure of the protein. Also these interactions can be described because force field GFN-FF retains an iterative Hückel quantum-mechanical scheme for aromatic atoms.


FFFold tool is a part of services provided by ELIXIR – European research infrastructure for biological information.
For other services provided by ELIXIR's Czech Republic Node visit www.elixir-czech.cz/services.
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Licence conditions in accordance with § 11 of Act No. 130/2002 Coll. The owner of the software is Masaryk University, a public university, ID: 00216224. Masaryk University allows other companies and individuals to use this software free of charge and without territorial restrictions in usual way, that does not depreciate its value. This permission is granted for the duration of property rights. This software is not subject to special information treatment according to Act No. 412/2005 Coll., as amended. In case that a person who will use the software under this licence offer violates the licence terms, the permission to use the software terminates.