YouTube Video Overview for Predicting Functions BLAST, PROST, Foldseek, Alphafold, JSONWP: A protein homology search workflow (~30 minutes)
Predicted Functions of Minimal Organism from our method PROST - an AI machine language model based method see publication: Kilinc M, Jia K, Jernigan RL. Improving the Annotations of JCVI-Syn3a Proteins. Methods Mol Biol. 2025;2867:153-168. doi: 10.1007/978-1-0716-4196-5_9. PMID: 39576580.
Website for Using PROST to Predict Protein Functions see publication: Kilinc M, Jia K, Jernigan RL. Improved global protein homolog detection with major gains in function identification. Proc Natl Acad Sci U S A. 2023 Feb 28;120(9):e2211823120. doi: 10.1073/pnas.2211823120. Epub 2023 Feb 24. PMID: 36827259; PMCID: PMC9992864.
Predicted Functions of Bacillus subtilis from our method PROST
Software for Creating Protein Structure/Sequence Websites see publication: Kilinc M, Jia K, Jernigan RL. JSONWP: a static website generator for protein bioinformatics research. Bioinform Adv. 2023 Oct 26;3(1):vbad154. doi: 10.1093/bioadv/vbad154. PMID: 37904893; PMCID: PMC10613403.
Website for Predicting Protein Stabilities see: Ramos M, Jernigan RL, Kilinc M. ESMStabP: A Regression Model for Protein Thermostability Prediction. bioRxiv 2025.02.18.638450; doi: https://doi.org/10.1101/2025.02.18.638450
Website to Identify Amino Acids in Dynamic Communities in Proteins see publication: Kumar A, Khade PM, Dorman KS, Jernigan RL. Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier. Bioinformatics. 2022 May 13;38(10):2727-2733. doi: 10.1093/bioinformatics/btac159. PMID: 35561187; PMCID: PMC9113273.
Website to Predict Allosteric Pockets in Proteins see publication: Kumar A, Kaynak BT, Dorman KS, Doruker P, Jernigan RL. Predicting allosteric pockets in protein biological assemblages. Bioinformatics. 2023 May 4;39(5):btad275. doi: 10.1093/bioinformatics/btad275. PMID: 37115636; PMCID: PMC10185404.
Website for Computing Protein Packing Entropies using PACKMAN (see below) see publication: Khade PM, Jernigan RL. Entropies Derived from the Packing Geometries within a Single Protein Structure. ACS Omega. 2022 Jun 9;7(24):20719-20730. doi: 10.1021/acsomega.2c00999. PMID: 35755337; PMCID: PMC9219053.
