pSSdb - Protein Secondary Structure Database

ACKNOWLEDGMENTS:

Hardware Funding: The website and the backend are using the server funded by National Science Centre, Poland [2018/29/B/NZ2/01403]. Additionally, I gratefully acknowledge Paweł Strzelecki & Łukasz Kowalik (MIMUW, ~$2.8k from the university statutory funds for 60TB RAID disks).

I gratefully acknowledge Poland’s high-performance computing infrastructure PLGrid (HPC Centers: ACK Cyfronet AGH) for providing computer facilities and support within computational grants no. PLG/2023/016126 & PLG/2023/016128 (Allocation@Ares: 2.6M CPUh, 50k GPUh; @Athena 425k GPUh).

I acknowledge Polish high-performance computing infrastructure PLGrid for awarding this project access to the LUMI supercomputer, owned by the EuroHPC Joint Undertaking, hosted by CSC (Finland) and the LUMI consortium through grant no. PLL/2023/05/016753 (Allocation@LUMI [3rd fastest supercomputer in the world]: 9M CPUh, 500k GPUh).

Some experiments were performed using the Entropy cluster funded by NVIDIA, Intel, the Polish National Science Center grant UMO-2017/26/E/ST6/00622, and ERC Starting Grant TOTAL (Allocation: 400k CPUh, 100k GPUh).

This research was also partly carried out with the support of the Interdisciplinary Centre for Mathematical and Computational Modelling University of Warsaw (ICM UW) under computational allocation no g91-1438 (Allocation@Topola: 300k CPUh).

The author would like to thank Marek Cygan & Kamil Wilczek (Entropy team), Michał Hermanowicz (ICM), Łukasz Kitowski, Maciej Czuchry, Maciej Szpindler & Maciej Pawlik (PLGrid & LUMI).

This project employs a wide range of both general-purpose and domain-specific tools. Some notable examples include PHP, Python, MySQL, Apache2, Bootstrap, EBI Icon Fonts, as well as various databases and programs like UniProt, AlphaFold, ESMatlas, PDB, NCBI nr, BFD, DSSP, STRIDE, SSE-PSSM, Bio Embeddings, ProtTrans. Kudos for all contributors, maintainers, and developers.

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