A5070477116- Computational Drug Discovery Methods
- Neural dynamics and brain function
- Analytical Chemistry and Chromatography
- DNA and Nucleic Acid Chemistry
- Metabolomics and Mass Spectrometry Studies
- Photoreceptor and optogenetics research
- T-cell and B-cell Immunology
- Organometallic Complex Synthesis and Catalysis
- X-ray Diffraction in Crystallography
- Immune Cell Function and Interaction
- Crystallization and Solubility Studies
- Catalysis and Hydrodesulfurization Studies
- Protein Structure and Dynamics
- EEG and Brain-Computer Interfaces
- Neuroscience and Neuropharmacology Research
- Ion-surface interactions and analysis
- Cancer-related Molecular Pathways
- Mass Spectrometry Techniques and Applications
- Asymmetric Hydrogenation and Catalysis
- Analytical chemistry methods development
- Enzyme Structure and Function
- Single-cell and spatial transcriptomics
- Pharmacogenetics and Drug Metabolism
- Advanced biosensing and bioanalysis techniques
- Visual perception and processing mechanisms
University of Tartu
2024
Qiagen (Denmark)
2024
University of Auckland
2015
Yaroslavl State Medical Academy
2002-2015
Science Applications International Corporation (United States)
2008-2013
Center for Cancer Research
2004-2013
National Institutes of Health
2008-2012
University of Arizona
1997-2012
Frederick National Laboratory for Cancer Research
2004-2012
St. Jude Children's Research Hospital
2001-2005
Until recently most scientific and patent documents dealing with chemistry have described molecular structures either systematic names or graphical images of Kekulé structures. The latter method poses inherent problems in the automated processing that is needed when number ranges hundreds thousands even millions since representations cannot be directly interpreted by a computer. To recover this structural information, which otherwise all but lost, we built an optical structure recognition...
The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Standards and Source (ODOSOS) chemistry. It aims make it easier carry out chemistry research by promoting interoperability between software, encouraging cooperation developers, developing community resources Standards. This contribution looks back on work carried past 5 years surveys progress remaining challenges areas Standards, We show that has been very successful bringing together researchers...
As humans age, their memory T cell compartment expands due to the lifelong exposure antigens. This expansion is characterized by terminally differentiated CD8 + cells (Temra), which possess NK cell-like phenotype and are associated with chronic inflammatory conditions. Temra predominantly driven sporadic reactivation of cytomegalovirus (CMV), yet epigenomic patterns cellular heterogeneity remain understudied. To address this gap, we correlated gene expression profiles chromatin openness...
We present here a greatly updated version of an earlier study on the conformational energies protein-ligand complexes in Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with goal improving all possible aspects such as number and selection ligand instances, energy calculations performed, additional analyses conducted. Starting from about 357,000 instances deposited 2008 Ligand Expo database experimental 3D coordinates small-molecule PDB, we created...
We report the preparation, structure, and reactions of a stable metallapyridine complex tantalum prepared in course model studies hydrodenitrogenation (HDN) reactions. is isolated upon thermolyzing η2(N,C)-pyridine [η2(N,C)-2,4,6-NC5tBu3H2]Ta(OAr)2Me (2) presence THF, while when this reaction carried out benzene. Complete NMR characterization 5·THF described, along with its conversion into 6. The bis(pyridine) also described. shown to react tBuNCO iPrNCNiPr afford σ (η1) π (η3) insertion...
Immune tolerance fails in autoimmune polyendocrine syndrome type 1 (APS-1) because of
A Pseudo-Rotational Online Service and Interactive Tool (PROSIT) designed to perform complete pseudorotational analysis of nucleosides nucleotides is described. This service freely available at http://cactus.nci.nih.gov/prosit/. Files containing nucleosides/nucleotides or DNA/RNA segments, isolated bound other molecules (e.g., a protein) can be uploaded processed by PROSIT. The outputs the phase angle P, puckering amplitude numax, related information for each nucleoside/nucleotide detected....
1Presented at CMTPI 2007: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Moscow, Russia, September 1–5, 2007). New data, tools services recently made available on the web server (http://cactus.nci.nih.gov) of Computer-Aided Drug Design (CADD) Group, NCI, NIH, developed context chemoinformatics drug development work, are presented. These designed for searching structures very large databases small molecules. One them is a service–the Chemical Structure...
The D1A mutant of recombinant NP2 has been prepared and shown to have the expression−initiation methionine-0 cleaved during expression in E. coli, as is case for NP4, where Ala first amino acid protein well mature native protein. heme substituent 1H NMR chemical shifts NP2-D1A those its imidazole, N-methylimidazole, cyanide complexes are rather different from NP2-M0D1. This difference likely due much smaller size N-terminal (A) NP2-D1A, which allows formation closed loop form this protein,...
Background: The most important factor affecting metabolic excretion of compounds from the body is their half-life time. This provides an indication compound stability of, for example, drug molecules. We report on our efforts to develop QSAR models compounds, based in vitro assay data measured human liver microsomes. Method: A variety generated using different statistical methods and descriptor sets implemented both open-source commercial programs (KNIME, GUSAR StarDrop) were analyzed....
Arf is a tumor suppressor that regulates p53 function and frequent target for loss in human cancers. Through two novel mechanisms, inhibits the oncoprotein Hdm2, negative regulator of p53. (1) E3 ubiquitin ligase activity Hdm2 leads to degradation, (2) sequesters within nucleoli. These activities promote p53-mediated cell cycle arrest apoptosis. Fundamental these processes are interactions between Hdm2. Here we show peptide containing 37 N-terminal amino acids mouse (mArfN37) localizes...
In this work, we present a study of the influence protein matrix on its ability to tune binding small ligands such as NO, cyanide (CN(-)), and histamine ferric heme iron center in NO-storage -transport Nitrophorin 2 (NP2) from salivary glands blood-sucking insect Rhodnius prolixus. Conventional Mössbauer spectroscopy shows diamagnetic ground state NP2-NO complex Type I II electronic states NP2-CN(-) NP2-histamine complex, respectively. The change vibrational signature upon ligand has been...
Modern databases of small organic molecules contain tens millions structures. The size theoretically available chemistry is even larger. However, despite the large amount chemical information, “big data” moment for has not yet provided corresponding payoff cheaper computer‐predicted medicine or robust machine‐learning models determination efficacy and toxicity. Here, we present a study diversity datasets using measure that commonly used in socioeconomic studies. We demonstrate use this on...
Abstract Recent advances in single-cell technologies have facilitated studies on age-related alterations the immune system. However, previous often employed different marker genes to annotate cell populations, making it challenging compare results. In this study, we combined seven transcriptomic datasets, comprising more than a million cells from one hundred and three donors, create unified atlas of human peripheral blood mononuclear (PBMC) both young old individuals. Using consistent set...
A new route to sterically tuned, chelating bis(aryloxide) ligands is described and demonstrated by the synthesis of 2,2'-ethylenebis(6-isopropylphenol) (1, H(2)BIPP) transition metal complexes its dianion. The utility these in titanium tantalum organometallic chemistry shown alkylation (BIPP)TiCl(2) (7) form (BIPP)TiMe(2) (8) (BIPP)Ti(CH(2)Ph)(2) (9) (BIPP)TaCl(3) (10) base adducts (BIPP)TaMe(3) (14) (BIPP)Ta(CH(2)Ph)(3) (13). Structural comparisons 2,2'-ethylenebis(6-isopropylphenoxide)...
This paper describes an efficient NMR strategy for assigning the backbone resonances of intrinsically unstructured protein (IUP), p21-KID, bound to its biological target, Cdk2/cyclin A. In order overcome challenges associated with high molecular weight (75 kDa) and low solubility ternary complex (0.2 mM), we used perdeuteration, TROSY, high-sensitivity cryogenic probes at magnetic-field strengths (i.e. 16.4, 18.8 21.1 Tesla). p21-KID was also prepared by using specific amino acid isotope...