Lukasz P. Kozlowski

Projects

pSSdb - the database of predicted secondary structure of (almost) all proteins. Covers databases such as UniProt, NCBI nr, PDB, BFD, Mgnify, JGI_IMG, GMGC AlphaFold database and ESMatlas sequences. Contains secondary structure predictions from up to eight methods for over 7 billion protein sequences and >90k proteomes. HPC resources used: 20M CPUh, 1M GPUh at TOP500 machines (Ares, Athena, LUMI)

Proteome-pI 2.0 - Proteome Isoelectric Point Database 2.0 (the data for over 61 million sequences from 20,115 proteomes calculated by 22 methods)

Unicorn Papers - Top ‱ cited papers from PUBMED (currently >3,600 publications in the list; updated monthly)

IPC 2.0 - prediction of isoelectric point and pKa dissociation constants using deep learning and SVR

fCite - a tool to quantify an individual's scientific research output based on citations, RCR, and the H-index divided by the number of authors in publications (the system integrates the data from over 35 million publications with half-billion citations and references for over 2 million ORCID users)

Proteome-pI - Proteome Isoelectric Point Database (the database contains the data for >21 million sequences from 5,029 proteomes calculated by 18 methods, cited >150 times)

IPC - Isoelectric Point Calculator (~200 visitors per day, cited >200 times)

MetaDisorder – prediction of intrinsic disorder in proteins (during 2008-2010 I developed the best program according to CASP beating over 20 other programs for protein disorder prediction in a blind test, see here, group 153, the publication cited >300 times)

GeneSilico fold recognition server – the development and the maintenance, in over 5 years I integrated there >100 bioinformatics tools related to protein structure prediction, the platform used 1.7TB for the programs and another 2TB for biological databases, ran in parallel on three blade servers connected through >40 GB MySQL database (>3500 users) - retired in 2020

CompaRNA – continuous benchmarking of RNA structure prediction methods

GDFuzz3D – protein contact map to 3D structure retrieval service

Shannon Entropy Calculator (~100 visitors per day)

In free time active Wikipedian > 1,200 edits