Dima Kozakov
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Explore the profile of Dima Kozakov including associated specialties, affiliations and a list of published articles.
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131
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6220
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Recent Articles
1.
Xiao Z, Gavriil E, Cao F, Zhang X, Li S, Kotelnikov S, et al.
bioRxiv
. 2025 Feb;
PMID: 39975383
Targeted protein degradation (TPD) is a rapidly emerging and potentially transformative therapeutic modality. However, the large majority of >600 known ubiquitin ligases have yet to be exploited as TPD effectors...
2.
Peng H, Kotelnikov S, Egbert M, Ofaim S, Stevens G, Phanse S, et al.
Cell
. 2025 Jan;
188(5):1441-1455.e15.
PMID: 39862855
Knowledge of protein-metabolite interactions can enhance mechanistic understanding and chemical probing of biochemical processes, but the discovery of endogenous ligands remains challenging. Here, we combined rapid affinity purification with precision...
3.
Lawton M, Inge M, Blum B, Smith-Mahoney E, Bolzan D, Lin W, et al.
PLoS Biol
. 2024 Dec;
22(12):e3002943.
PMID: 39689157
Repeated antigen exposure leads to T-cell exhaustion, a transcriptionally and epigenetically distinct cellular state marked by loss of effector functions (e.g., cytotoxicity, cytokine production/release), up-regulation of inhibitory receptors (e.g., PD-1),...
4.
Lazou M, Khan O, Nguyen T, Padhorny D, Kozakov D, Joseph-McCarthy D, et al.
Proc Natl Acad Sci U S A
. 2024 Nov;
121(48):e2412719121.
PMID: 39565312
The goal of this paper is predicting the conformational distributions of ligand binding sites using the AlphaFold2 (AF2) protein structure prediction program with stochastic subsampling of the multiple sequence alignment...
5.
Lazou M, Kozakov D, Joseph-McCarthy D, Vajda S
Drug Discov Today
. 2024 Oct;
29(11):104197.
PMID: 39368697
Cryptic sites can expand the space of druggable proteins, but the potential usefulness of such sites needs to be investigated before any major effort. Given that the binding pockets are...
6.
Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, et al.
Biophys J
. 2024 May;
123(17):2902-2909.
PMID: 38751115
The precise prediction of major histocompatibility complex (MHC)-peptide complex structures is pivotal for understanding cellular immune responses and advancing vaccine design. In this study, we enhanced AlphaFold's capabilities by fine-tuning...
7.
Khan O, Jones G, Lazou M, Joseph-McCarthy D, Kozakov D, Beglov D, et al.
J Chem Inf Model
. 2024 Mar;
64(6):2084-2100.
PMID: 38456842
The knowledge of ligand binding hot spots and of the important interactions within such hot spots is crucial for the design of lead compounds in the early stages of structure-based...
8.
Lin W, Mousavi F, Blum B, Heckendorf C, Moore J, Lampl N, et al.
Front Pharmacol
. 2024 Feb;
15:1376058.
PMID: 38405670
[This corrects the article DOI: 10.3389/fphar.2023.1243505.].
9.
Bekar-Cesaretli A, Khan O, Nguyen T, Kozakov D, Joseph-McCarthy D, Vajda S
J Chem Inf Model
. 2024 Jan;
64(3):960-973.
PMID: 38253327
The neural network-based program AlphaFold2 (AF2) provides high accuracy structure prediction for a large fraction of globular proteins. An important question is whether these models are accurate enough for reliably...
10.
Lin W, Mousavi F, Blum B, Heckendorf C, Moore J, Lampl N, et al.
Front Pharmacol
. 2023 Dec;
14:1243505.
PMID: 38089059
We hypothesize that the poor survival outcomes of end-stage kidney disease (ESKD) patients undergoing hemodialysis are associated with a low filtering efficiency and selectivity. The current gold standard criteria using...