Dima Kozakov

Stony Brook University — United States

Biochemistry, Genetics and Molecular Biology · Life Sciences

56h-index15.5kcitations181works5.02yr avg
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Research Topics

Protein Structure and Dynamics(98), Computational Drug Discovery Methods(63), Enzyme Structure and Function(51), RNA and protein synthesis mechanisms(28), Monoclonal and Polyclonal Antibodies Research(18)

Publications181 total

Photo-proximity labeling in live primary neurons identifies an AMPA-receptor signal transducer in homeostatic synaptic plasticity
Cell chemical biology·2025Open Access
CDR-aware masked language models for paired antibodies enable state-of-the-art binding prediction
2025· 1 citedOpen Access
Modeling Protein–Protein and Protein–Ligand Interactions by the ClusPro Team in CASP16
UNC Libraries·2025Open Access
Modeling Protein–Protein and Protein–Ligand Interactions by the <scp>ClusPro</scp> Team in <scp>CASP16</scp>
Proteins Structure Function and Bioinformatics·2025· 3 citedOpen Access
CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2
2025Open Access
ANALYSIS OF THE PHOSPHORYLATION NETWORKS CHARACTERIZING DISTINCT PHENOTYPIC STATES IN GLIOBLASTOMA CELL POPULATIONS
2025Open Access
Impact of Protein Conformational Diversity on Structure-Based Prediction of Druggability
Journal of Chemical Information and Modeling·2025
Conventional and non-conventional antigen-binding sites promote the development and function of chronic lymphocytic leukemia stereotyped subset #4 clones
Frontiers in Immunology·2025Open Access
Modulating the Binding Kinetics of Bruton’s Tyrosine Kinase Inhibitors through Transition-State Effects
Journal of the American Chemical Society·2025· 2 citedOpen Access
Identification of Actionable Targeted Protein Degradation Effector Sites through Site-Specific Ligand Incorporation-Induced Proximity (SLIP)
Journal of the American Chemical Society·2025· 3 citedOpen Access
Identification of actionable targeted protein degradation effector sites through Site-specific Ligand Incorporation-induced Proximity (SLIP)
2025· 1 citedOpen Access
Ligand interaction landscape of transcription factors and essential enzymes in E. coli
Cell·2025· 10 cited
E-FTMap: A Protein Structure Based Pharmacophore Identification Server for Guiding Fragment Expansion
Journal of Molecular Biology·2025· 3 citedOpen Access
Multiomic profiling of chronically activated CD4+ T cells identifies drivers of exhaustion and metabolic reprogramming
PLoS Biology·2024· 13 citedOpen Access
Predicting multiple conformations of ligand binding sites in proteins suggests that AlphaFold2 may remember too much
Proceedings of the National Academy of Sciences·2024· 21 citedOpen Access
Which cryptic sites are feasible drug targets?
Drug Discovery Today·2024· 14 citedOpen Access
A critical overview of computational approaches employed for COVID-19 drug discovery
UNC Libraries·2024· 5 citedOpen Access
MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction
Biophysical Journal·2024· 14 citedOpen Access
Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites
Journal of Chemical Information and Modeling·2024· 11 citedOpen Access
Phospho-Tune: Enhanced Structural Modeling of Phosphorylated Protein Interactions
2024· 7 citedOpen Access
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Frequent Co-authors

Sándor Vajda(39), Dmitri Beglov(21), David R. Hall(13), Dzmitry Padhorny(10), Ryan Brenke(8), Tanggis Bohnuud(8), Kathryn A. Porter(7), David Hall(7), Adrian Whitty(7), Scott E. Mottarella(6), Yang Shen(6), Daisuke Kihara(6), Christine Yueh(5), Stephen R. Comeau(5), Israel Desta(5), Bing Xia(5), Paul A. Bates(5), Brian G. Pierce(5), Juan Fernández‐Recio(5), Sergei Kotelnikov(5)