PROPTIMus
LIVE
Constrained α-carbons optimisation
of protein structures
About PROPTIMus LIVE
PROPTIMus LIVE is a freely available application for the local optimisation of (but not limited to) ML-predicted protein structures.
It is powered by the RAPHAN method, employing an almost QM-accurate GFN-Force-Field to reproduce protein structures
optimised with constrained α-carbons.
How PROPTIMus LIVE works
Repairs non-physically placed atoms with the PRIME tool, which may be present in ML-predicted protein structures.
Adds hydrogens for user-specified pH using the pdb2pqr tool if the input structure does not contain them.
Optimises protein structure using the RAPHAN method.
Why use PROPTIMus LIVE
Accurate results because of modern physics-based GFN-Force-Field.
Fast calculations within minutes due to the divide-and-conquer RAPHAN method.
Free and open to all users—no login required.
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 PROPTIMus LIVE is in colour.
Bond length
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
Dihedral angles in THR126 between atoms OG1, CB, CG2 and hydrogens HG21, HG22, HG23 are optimised from energetically unfavourable eclipsed conformation.
Hydrogen bond
The hydrogen bond was formed between atoms HD1 from HIS20 and O from GLY86.
π–π stacking
T-shaped π–π stacking is formed between residues PHE90 and HIS461.
About our optimisation method
Explore our method for fast and accurate protein structure optimisation.
How does it work?
Img: schema
PROPTIMus LIVE optimises protein structures using the RAPHAN method, which is a rapid alternative to optimisation with constrained α-carbons. RAPHAN is an iterative divide-and-conquer method, which divides the protein into overlapping substructures and optimises each substructure separately. Substructures are optimised by GFN-Force-Field, designed to combine high force-field speed with the accuracy of QM methods.
How accurate is it?
Img: histogram
The RAPHAN method produces structures comparable to structures optimised with constrained α-carbons. The mean absolute deviation of atomic positions is approximately 0.03 Å, and the 99th percentile is 0.33 Å. As can be seen in the histogram, structures may differ exceptionally for highly flexible residues.
How fast is it?
Img: times
A lot. While the duration of optimisation with constrained α-carbons grows approximately quadratically with the size of the structure, by dividing the protein into substructures, RAPHAN's calculation speed is linear with respect to the structure's size. Thanks to parallelisation, PROPTIMus LIVE optimises average proteins in a matter of minutes.
License
Legal Framework
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.
Usage Rights
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.
Terms & Conditions
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.