Supersecondary structures (SSS) are blocks of protein molecules with a unique and compact fold. Such structures are stable outside the protein globule due to the developed hydrophobic core. In the field of structural biology, SSSs are considered as nuclei of protein folding and starting structures to search for possible folds of the polypeptide chain when modeling the structure of proteins.  The study of SSS in aberrant forms of proteins caused by post-translational modification, amino acid substitutions, and non-canonical splice forms of proteins is promising in the field of biomedicine.

The PSSKB (protein supersecondary structure knowledge base) service provides a researcher with the following tools:

1) Search for SSS with the characteristics of interest: primary sequence, UniProt ID and PDB ID, SSS type, origin, composition of elements of secondary structures, length of elements of secondary structures, length of connectors, etc.,

2) 3D model of the supersecondary structure visualization,

3) molecular dynamics (MD) simulations of SSS in intact proteins,

4) post-translational modification (150 types of PTMs) for supersecondary structure modeling

5) MD of supersecondary structures with PTM,

6) comparative analysis of MD results for intact SSS and after modification.

Construction of histograms of the distribution of the studied characteristics of the SSS taking into account particular filters. The indisputable advantage of the PSSKB service is the execution of a complete MD study script with the ability to analyze and visualize MD trajectories.

An integral component of the service is a unique and extensive database of known types of supersecondary structures. The SSS database is filled with all protein structures annotated in the PDB and AlphaFold banks using an artificial intelligence module as a part of the service. The ensemble of deep learning models, which are a part of the service, makes it possible to extract SSS from PDB data according to the geometric characteristics of the protein structure and to classify them.

 

Example 1  https://psskb.org/fragment-dynamics/2F69_A143_A173

                 https://psskb.org/fragment-dynamics/1B3R_B212_B243

Example 2 https://psskb.org/fragment-modifications/2F69_A143_A173?mod_id=2F69_A143_A173_16_3CF

                      https://psskb.org/fragment-modifications/1B3R_B212_B243?mod_id=1B3R_B212_B243_14_D4P

IMPORTANT: All calculation results are saved in the database and, if desired, you can return to them.

Browsers/OSs tested

Four specialists took part in testing the service (not the developers of the service).