Nick V. Grishin

The paper uses AI to compare biological information from UniProt records and their cited literature for human kinases, finding literature provides better coverage for certain topics.

The paper classifies archaeal proteomes at the domain level, revealing that structural diversity is conserved across archaea and that unclassified proteins are due to classification limitations, not structural novelty.

This study identifies ancient chromosomal inversions in the zebra longwing butterfly that are associated with local adaptation to environmental stressors.

The paper uses genomic analysis to distinguish two cryptic Atrytonopsis skipper species, revealing their genetic uniqueness, phylogenetic relationship, and geographic distribution.

The paper classifies over 542,000 Swiss-Prot protein structure predictions into ECOD domains, expanding domain coverage and revealing novel evolutionary groups.

This paper evaluates progress in predicting protein complex structures in CASP16, finding moderate improvements but ongoing challenges in model ranking, stoichiometry prediction, and handling difficult targets.

This paper assesses CASP16 monomer structure prediction, showing near-solution for single-domain folds but highlighting challenges in truncated sequences and model ranking.

This paper uses AI to predict how post-translational modifications affect drug binding by modeling PTM-modified protein structures and ligand interactions.

DrugDomain 2.0 maps protein domain-ligand interactions across the Protein Data Bank, integrating experimental and AI-predicted data for over 37,000 ligands and 7,560 drugs.

DrugDomain provides a database of interactions between DrugBank molecules and ECOD domains of human proteins, using experimental structures and AlphaFold models.

The paper classifies proteins from Salmonella enterica pangenome, identifies potentially pathogenic proteins, and reveals their clustering in the genome.

The paper classifies domains in 48 proteomes from the AlphaFold Database using DPAM, finding differences in domain composition between eukaryotes and bacteria.

This study identifies a genetic variant in COL11A1 associated with adolescent idiopathic scoliosis and proposes a molecular model involving Pax1, Col11a1, and Mmp3 in spinal chondrocytes.

DPAM automatically parses AlphaFold models to recognize and classify protein domains, outperforming existing methods in accuracy and boundary assignment.

The paper investigates the evolutionary origins of myoblast fusion mechanisms in chordates, identifying the emergence of Myomaker and Myomixer and their roles in muscle development across species.

This study identifies ZNF692 as a nucleolar scaffold that enhances 40S ribosome maturation and translation efficiency in rapidly proliferating cells, particularly in cancer cells.

The paper introduces a 3-track network for accurate protein structure and interaction prediction, achieving performance close to DeepMind's CASP14 results and enabling rapid modeling of protein complexes from sequence data.

The paper identifies a SNP in the cut gene responsible for yellow coloration in bumble bees, showing it affects protein structure without major external phenotypes.

The paper develops DeepSAV, a deep-learning model to predict the pathogenicity of single-amino acid variations, and uses it to assess mutation severity across genes, identifying intolerant and tolerant genes for different disease categories.

The paper sequences all butterfly species in North America north of Mexico to study diversification patterns and adaptation mechanisms across their evolutionary history.

The paper estimates the probability that protein genes navigate fitness valleys during human evolution, finding that small protein motifs cross valleys of depth 2Ns ≳ 30 with probability ≳ 0.1.