DOI: 10.5061/dryad.jq2bvq89s
title: UltraScan Solution Modeler (US-SOMO) hydrodynamic parameter, structural small angle scattering and SESCA circular dichroism (CD) calculations on AlphaFold predicted structures

description: Recent spectacular advances by AI programs in 3D structure predictions
 from protein sequences have revolutionized the field in terms of accuracy
 and speed. The resulting "folding frenzy" has already produced
 predicted protein structure databases for the entire human and other
 organisms' proteomes. However, rapidly ascertaining a predicted
 structure's reliability based on measured properties in solution
 should be considered. Shape-sensitive hydrodynamic parameters such as the
 diffusion and sedimentation coefficients (D0t(20,w),s0(20,w)) and the
 intrinsic viscosity ([η]) can provide a rapid assessment of the overall
 structure likeliness, and SAXS would yield the structure-related pair-wise
 distance distribution function p(r) vs. r. Using the extensively validated
 UltraScan SOlution MOdeler (US‑SOMO) suite, a database was implemented
 calculating from AlphaFold structures the corresponding D0t(20,w),
 s0(20,w), [η], p(r) vs. r, and other parameters. Circular dichroism
 spectra were computed using the SESCA program. Some of AlphaFold's
 drawbacks were mitigated, such as generating whenever possible a
 protein's mature form. Others, like the AlphaFold direct
 applicability to single-chain structures only, the absence of prosthetic
 groups, or flexibility issues, are discussed. Overall, this implementation
 of the US‑SOMO‑AF database should already aid in rapidly evaluating the
 consistency in solution of a relevant portion of AlphaFold predicted
 protein structures.
description: Production of this dataset required three major steps: collect
 the AlphaFold entries and additional metadata; prepare the structures for
 hydrodynamic, structural and CD calculations; and compute the
 hydrodynamic, structural and CD properties<br><br>Briefly,
 each entry in the entire AlphaFold database was first compared with the
 corresponding entry in the UniProt database to find the (putative)
 initiator methionine, signal peptide and transit peptide regions, which
 were subsequently removed from the AlphaFold PDB files. Additional
 variants were created when propeptides were found. Potential disulfides
 were identified (subsequently allowing a better evaluation of the partial
 specific volume and of M) and written as SSBOND records in the cured PDBs,
 together with HELIX and SHEET information identified using the DSSP
 implementation in UCSF Chimera (Pettersen et al, 2004. Journal of
 computational chemistry, 25(13), pp.1605-1612). Batch-mode US-SOMO was
 then used to calculate the mass M, The translational diffusion coefficient
 D0t(20,w), the sedimentation coefficient s0(20,w), the derived
 Stokes' (or hydrodynamic) radius Rs, the intrinsic viscosity [η], the
 radius of gyration Rg, the maximum extensions along the principal X, Y and
 Z axes of the molecule, and the generation of an anhydrous small angle
 X-ray scattering pairwise distribution function p( r ) vs. r distributions
 (that are normalized by the M of the structure). SESCA was subsequently
 used to generate 170-270 nm circular dichroism CD spectra from each cured
 structure.
description: This is a tar archive of all datasets for each AlphaFold entry.
 This includes a csv file containing all hydrodynamic parameters, a pdb
 file containing the cured pdb structure, an mmCIF file containing the
 cured pdb structure and a data file containing the circular dichroism
 spectrum, and a p(r) vs r dat file.<br><br>Use "tar xf
 somoaf_all_data.tar" to extract the primary archive.<br>This
 will result in 1,002,038 individual .txz file, each representing one
 UniProt accession code and containing 5 files.<br>When propepties
 are identified and removed, the extracted file name will contain a -pp#,
 where # is a list of the propepties removed.<br>For example, to
 extract the data from an individual txz file, use "tar Jxf
 xxxx.txz", where xxxx is replaced by the appropriate name containing
 the accession code. Further details are in the provided
 README.md file.