Grishin, Nick V.

Accurate prediction of protein structures and interactions using a 3-track network

Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., et al. (2021) · Science

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 5,549

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

Kato, M., Han, T. W., Xie, S., Shi, K., Du, X., Wu, L. C., Mirzaei, H., Goldsmith, E. J., Longgood, J., Pei, J., et al. (2012) · Cell

RNA Research and SplicingRNA and protein synthesis mechanisms

Cited by 2,012

Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation

Liu, S., Cai, X., Wu, J., Cong, Q., Chen, X., Li, T., Du, F., Ren, J., Wu, Y.-T., Grishin, N. V., et al. (2015) · Science

interferon and immune responsesImmune Response and Inflammation

Cited by 1,927

Substrate and Functional Diversity of Lysine Acetylation Revealed by a Proteomics Survey

Kim, S. C., Sprung, R., Chen, Y., Xu, Y., Ball, H., Pei, J., Cheng, T., Kho, Y., Xiao, H., Xiao, L., et al. (2006) · Molecular Cell

Advanced Proteomics Techniques and ApplicationsUbiquitin and proteasome pathways

Cited by 1,487

A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action

Makarova, K. S., Grishin, N. V., Shabalina, S. A., Wolf, Y. I., & Koonin, E. V. (2006) · Biology Direct

CRISPR and Genetic EngineeringBacterial Genetics and Biotechnology

Cited by 1,199

Identification of a candidate therapeutic autophagy-inducing peptide

Shoji-Kawata, S., Sumpter, R., Leveno, M., Campbell, G. R., Zou, Z., Kinch, L., Wilkins, A. D., Sun, Q., Pallauf, K., MacDuff, D., et al. (2013) · Nature

Autophagy in Disease and TherapyRNA Interference and Gene Delivery

Cited by 760

Autosomal Recessive Hypercholesterolemia Caused by Mutations in a Putative LDL Receptor Adaptor Protein

Garcia, C. K., Wilund, K., Arca, M., Zuliani, G., Fellin, R., Maioli, M., Calandra, S., Bertolini, S., Cossu, F., Grishin, N., et al. (2001) · Science

Lipoproteins and Cardiovascular HealthCholesterol and Lipid Metabolism

Cited by 624

An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis

Salahudeen, A. A., Thompson, J. W., Ruiz, J. C., Ma, H.-W., Kinch, L. N., Li, Q., Grishin, N. V., & Bruick, R. K. (2009) · Science

Iron Metabolism and DisordersUbiquitin and proteasome pathways

Cited by 432

ECOD: an evolutionary classification of protein domains

Cheng, H., Schaeffer, R. D., Liao, Y., Kinch, L. N., Pei, J., Shi, S., Kim, B.-H., & Grishin, N. V. (2014) · PLoS Computational Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 426

Evolution of Aminoacyl-tRNA Synthetases—Analysis of Unique Domain Architectures and Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer Events

Wolf, Y. I., Aravind, L., Grishin, N. V., & Koonin, E. V. (1999) · Genome Research

RNA and protein synthesis mechanismsGenomics and Phylogenetic Studies

Cited by 410

The WAVE regulatory complex links diverse receptors to the actin cytoskeleton

Chen, B., Brinkmann, K., Chen, Z., Pak, C. W., Liao, Y., Shi, S., Henry, L., Grishin, N. V., Bogdan, S., & Rosen, M. K. (2014) · Cell

Cellular Mechanics and InteractionsProtein Kinase Regulation and GTPase Signaling

Cited by 323

Structure, lipid scrambling activity and role in autophagosome formation of ATG9A

Maeda, S., Yamamoto, H., Kinch, L. N., Garza, C. M., Takahashi, S., Otomo, C., Grishin, N. V., Forli, S., Mizushima, N., & Otomo, T. (2020) · Nature Structural & Molecular Biology

Autophagy in Disease and TherapyCellular transport and secretion

Cited by 305

Large-scale determination of previously unsolved protein structures using evolutionary information

Ovchinnikov, S., Kinch, L., Park, H., Liao, Y., Pei, J., Kim, D. E., Kamisetty, H., Grishin, N. V., & Baker, D. (2015) · eLife

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 222

A minimal domain responsible for Munc13 activity

Basu, J., Shen, N., Dulubova, I., Lu, J., Guan, R., Guryev, O., Grishin, N. V., Rosenmund, C., & Rizo, J. (2005) · Nature Structural & Molecular Biology

Cellular transport and secretionNeuroscience and Neuropharmacology Research

Cited by 213

Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis

Zhang, X., Kurnasov, O. V., Karthikeyan, S., Grishin, N. V., Osterman, A. L., & Zhang, H. (2003) · Journal of Biological Chemistry

Biochemical and Molecular ResearchSirtuins and Resveratrol in Medicine

Cited by 136

DPAM: A Domain Parser for AlphaFold Models

Zhang, J., Schaeffer, R. D., Durham, J., Cong, Q., & Grishin, N. V. (2022) · Protein Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 49

CASP13 target classification into tertiary structure prediction categories

Kinch, L. N., Kryshtafovych, A., Monastyrskyy, B., & Grishin, N. V. (2019) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 36

ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2

Schaeffer, R. D., Zhang, J., Medvedev, K. E., Kinch, L. N., Cong, Q., & Grishin, N. V. (2024) · PLOS Computational Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 22

Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands

Medvedev, K. E., Zhang, J., Schaeffer, R. D., Kinch, L. N., Cong, Q., & Grishin, N. V. (2024) · Scientific Reports

Salmonella and Campylobacter epidemiologyBacterial Genetics and Biotechnology

Cited by 11

DrugDomain: the evolutionary context of drugs and small molecules bound to domains

Medvedev, K. E., Schaeffer, R. D., & Grishin, N. V. (2024) · Protein Science

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 6

DrugDomain : The evolutionary context of drugs and small molecules bound to domains

Medvedev, K. E., Schaeffer, R. D., & Grishin, N. V. (2024) · Protein Science

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 6

ECOD: Classification of domains in AFDB Swiss-Prot structure predictions

Schaeffer, R. D., Zhang, J., Cong, Q., & Grishin, N. V. (2026) · PLOS Computational Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 2

DrugDomain 2.0: Comprehensive database of protein domains-ligands/drugs interactions across the whole Protein Data Bank

Medvedev, K. E., Schaeffer, R. D., & Grishin, N. V. (2025) · Computational and Structural Biotechnology Journal

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 1

DrugDomain 2.0: comprehensive database of protein domains-ligands/drugs interactions across the whole Protein Data Bank

Medvedev, K. E., Schaeffer, R. D., & Grishin, N. V. (2025) · Computational and Structural Biotechnology Journal

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 1