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. Protein regions predicted with confidence less than 90 are optimized by the physics-based generic force field GFN-FF which are approaching the accuracy of semiempirical QM methods. Optimisation is accelerated by PPROpt approach which is an alternative to optimizing the structure with constrained α-carbons. The main purpose of FFFold is to optimize bond lengths and angles and inter-residual interactions as can be seen in the examples. Before optimisation, 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

Examples of structure improvements are from the structure with Uniprot AC A4QBG9. The original structure from AlphaFold DB is shown in grey, and the structure optimised by FFFold is in colour.

Bond length
TA
The bond length between CA and H atoms in MET1 is modified about 0.1 angstrom. On average, the bond lengths in MET1 are optimized by 0.05 angstrom.
Dihedral angles
HB
Dihedral angles in THR126 between atoms OG1, CB, CG2 and hydrogens HG21, HG22, HG23 are optimised from energetically unfavourable eclipsed conformation.
Hydrogen bond
PS
The hydrogen bond was formed between atoms HD1 from HIS20 and O from GLY86.
π–π stacking
PS
T-shaped π-π stacking is formed between residues PHE90 and HIS461.


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.