Ivan Čmelo
YOU?
Author Swipe
View article: Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond
Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond Open
The structure and deformability of double-stranded DNA and RNA depend on the sequence of bases, affecting biological processes and nanostructure design, but this dependence is incompletely understood. Here we present mechanical properties …
View article: SARS-CoV-2 ORF8 sequence conservation and mutational analysis — insight into the influence of dataset size on identifying top mutations
SARS-CoV-2 ORF8 sequence conservation and mutational analysis — insight into the influence of dataset size on identifying top mutations Open
Given how quickly the SARS-CoV-2 virus mutates, the COVID-19 pandemic has been a major source of concern. The ORF8 accessory protein is one such protein, which is reported to have undergone many mutations. This makes ORF8 an intriguing pro…
View article: Sequence-dependent shape and stiffness of DNA and RNA double helices: hexanucleotide scale and beyond
Sequence-dependent shape and stiffness of DNA and RNA double helices: hexanucleotide scale and beyond Open
The structure and deformability of double-stranded DNA and RNA depend on the sequence of bases, affecting biological processes and nanostructure design. Despite intense research, the dependence is incompletely understood. Here we present m…
View article: Synthesis and Biochemical Evaluation of Ethanoanthracenes and Related Compounds: Antiproliferative and Pro-Apoptotic Effects in Chronic Lymphocytic Leukemia (CLL)
Synthesis and Biochemical Evaluation of Ethanoanthracenes and Related Compounds: Antiproliferative and Pro-Apoptotic Effects in Chronic Lymphocytic Leukemia (CLL) Open
Chronic lymphocytic leukemia (CLL) is a malignancy of mature B cells, and it is the most frequent form of leukemia diagnosed in Western countries. It is characterized by the proliferation and accumulation of neoplastic B lymphocytes in the…
View article: Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library
Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library Open
Computational exploration of chemical space is crucial in modern cheminformatics research for accelerating the discovery of new biologically active compounds. In this study, we present a detailed analysis of the chemical library of potenti…
View article: Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library
Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library Open
Computational exploration of chemical space is crucial in modern cheminformatics research for accelerating the discovery of new biologically active compounds. In this study, we present a detailed analysis of the chemical library of potenti…
View article: Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library
Chemical space exploration with Molpher: Generating and assessing a glucocorticoid receptor ligand library Open
Computational exploration of chemical space is important in modern cheminformatics research as it can accelerate the discovery of new biologically active compounds. In this study, we present a detailed analysis of a chemical library genera…
View article: Additional file 3 of Profiling and analysis of chemical compounds using pointwise mutual information
Additional file 3 of Profiling and analysis of chemical compounds using pointwise mutual information Open
Additional file 3. Compound sets used for synthetic accessibility classification (TMC and TCP test sets). Manually curated test set (TMC) consists of 40 HS compounds manually selected from scientific papers and of 30 ES sets, each of them …
View article: Additional file 1 of Profiling and analysis of chemical compounds using pointwise mutual information
Additional file 1 of Profiling and analysis of chemical compounds using pointwise mutual information Open
Additional file 1. Compound sets used for synthetic accessibility analysis (nonpher - 693 353 HS compounds, zinc_random – 693 353 ES compounds, savi - 610 245 ES compounds, scubidoo – 999 749 ES compounds) including excessively complex (i.…
View article: Profiling and analysis of chemical compounds using pointwise mutual information
Profiling and analysis of chemical compounds using pointwise mutual information Open
Pointwise mutual information (PMI) is a measure of association used in information theory. In this paper, PMI is used to characterize several publicly available databases (DrugBank, ChEMBL, PubChem and ZINC) in terms of association strengt…
View article: Counterfeit benzodiazepines—A phantom menace
Counterfeit benzodiazepines—A phantom menace Open
The high-profile case of fentanyl-laced counterfeit Xanax pills linked to multiple severe intoxications and a documented fatality in the San Francisco area may represent just the tip of the benzo black market iceberg.1, 2 Fentanyl as well …
View article: SYBA: Bayesian estimation of synthetic accessibility of organic compounds
SYBA: Bayesian estimation of synthetic accessibility of organic compounds Open
SYBA (SYnthetic Bayesian Accessibility) is a fragment-based method for the rapid classification of organic compounds as easy- (ES) or hard-to-synthesize (HS). It is based on a Bernoulli naïve Bayes classifier that is used to assign SYBA sc…
View article: SYBA: Bayesian estimation of synthetic accessibility of organic compounds
SYBA: Bayesian estimation of synthetic accessibility of organic compounds Open
SYBA (SYnthetic Bayesian Accessibility) is a fragment-based method for the rapid classification of organic compounds as easy- (ES) or hard-to-synthesize (HS). It is based on a Bernoulli naïve Bayes classifier that is used to assign SYBA sc…
View article: SYBA: Bayesian estimation of synthetic accessibility of organic compounds
SYBA: Bayesian estimation of synthetic accessibility of organic compounds Open
SYBA (SYnthetic Bayesian Accessibility) is a fragment-based method for the rapid classification of organic compounds as easy- (ES) or hard-to-synthesize (HS). It is based on a Bernoulli naïve Bayes classifier that is used to assign SYBA sc…
View article: SYBA: Bayesian estimation of synthetic accessibility of organic compounds
SYBA: Bayesian estimation of synthetic accessibility of organic compounds Open
SYBA (SYnthetic Bayesian Accessibility) is a fragment based method for the rapid classification of organic compounds as easy- (ES) or hard-to-synthesize (HS). SYBA is based on the Bayesian analysis of the frequency of molecular fragments i…
View article: Additional file 3 of SYBA: Bayesian estimation of synthetic accessibility of organic compounds
Additional file 3 of SYBA: Bayesian estimation of synthetic accessibility of organic compounds Open
Additional file 3. Manually curated test set (TMC). It consists of 40 HS compounds manually selected from scientific papers and of 30 ES sets, each of them contains 40 compounds selected from the ZINC15 database.
View article: Additional file 4 of SYBA: Bayesian estimation of synthetic accessibility of organic compounds
Additional file 4 of SYBA: Bayesian estimation of synthetic accessibility of organic compounds Open
Additional file 4. Computationally picked test set (TCP). It consists of 3 581 HS compounds that were obtained from the GDB-17 database complemented by the same number of compounds randomly selected from the ZINC15 database.
View article: Additional file 1 of SYBA: Bayesian estimation of synthetic accessibility of organic compounds
Additional file 1 of SYBA: Bayesian estimation of synthetic accessibility of organic compounds Open
Additional file 1. Training set S. It consists of 693 353 ES compounds selected from the ZINC15 database and of 693 353 ES compounds generated by Nonpher.