R. Schaeffer

Jan 19, 2025 | biorxiv.org | Kirill Medvedev |R. Schaeffer |Nick V. Grishin

AbstractPost-translational modifications (PTMs) play a crucial role in allowing cells to expand the functionality of their proteins and adaptively regulate their signaling pathways. Defects in PTMs have been linked to numerous developmental disorders and human diseases, including cancer, diabetes, heart, neurodegenerative and metabolic diseases. PTMs are important targets in drug discovery, as they can significantly influence various aspects of drug interactions including binding affinity.

Jul 9, 2024 | onlinelibrary.wiley.com | Kirill Medvedev |R. Schaeffer |Nick V. Grishin |Pires DEV

1 INTRODUCTION Proteins are vital components of cells, playing essential roles in regulating a myriad of cellular processes. The three-dimensional (3D) structure of a protein provides valuable information about protein interactions and functions. Protein domains are functionally, evolutionarily, and structurally distinct units that ensure evolutionary viability by fulfilling specific functions (Buljan & Bateman, 2009; Grishin, 2001).

Mar 23, 2024 | biorxiv.org | Kirill Medvedev |R. Schaeffer |Nick V. Grishin

AbstractInteractions between proteins and small organic compounds play a crucial role in regulating protein functions. These interactions can modulate various aspects of protein behavior, including enzymatic activity, signalling cascades, and structural stability. By binding to specific sites on proteins, small organic compounds can induce conformational changes, alter protein-protein interactions, or directly affect catalytic activity.

Feb 28, 2024 | journals.plos.org | R. Schaeffer |Kirill Medvedev |Lisa N. Kinch

Loading metrics Open Access Peer-reviewedResearch Article ? This is an uncorrected proof. Citation: Schaeffer RD, Zhang J, Medvedev KE, Kinch LN, Cong Q, Grishin NV (2024) ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. PLoS Comput Biol 20(2): e1011586. https://doi.org/10.1371/journal.pcbi.1011586Editor: Roland L.

Jan 31, 2024 | biorxiv.org | Kirill Medvedev |R. Schaeffer |Lisa N. Kinch

AbstractSalmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome.