In vitro secondary pharmacology assays are an important tool for predicting clinical adverse drug reactions (ADRs) of investigational drugs. We created the Secondary Pharmacology Database (SPD) by testing 1958 drugs using 200 assays to validate target-AD
Eliminating the duplicates and proteins of residue length less than 30, we have got a non redundant database of 80,592. We developed a search algorithm FIND-SIM to find similar primary sequence substrings in a query protein and target proteins. Some examples of full secondary structure matches...
Our goal was to develop a computer program that can describe an RNA structural element of any complexity and then search any nucleotide sequence database, including the complete prokaryotic and eukaryotic genomes, for these structural elements. Here we describe in detail a new computational motif ...
importance of this interaction to the Residue propensity. The propensities of a residue to occur at i and i + 1 positions were calculated as the ratio of the percentage of occurrence of that particular residue at either of these positions to its percentage in the whole database. ...
Analysis of proteins in nr database of NCBI using these class specific profiles has revealed several interesting examples, namely, C-MT domains in NRPS modules, N-MT domains with significant homology to C-MT proteins, and presence of NRPS/PKS MTs in association with other catalytic domains. ...
In the following sections, the conducted research is described and its findings are discussed, including open issues for future research. 1.4. Method The literature search was done using ACM database (https://dl.acm.org) using keywords “parallel programming education.” The search yielded 166 ...
(DNNs). Both algorithms formulate RNA secondary structure prediction as multiple binary classification problems that predict whether each pair of nucleotides forms a base pair or not, using a deep neural network trained with a large amount of training data. As with the other machine learning-based...
a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagr...
In cases where a fully annotated BGC was available but not deposited in a public database, the relevant information was obtained directly from the corresponding genome sequence. The assessment of homology and similarity between two or more BGCs was performed using Clinker, which is based on the ...
Entrez Gene is a gene-specific database (NCBI National Center for Biotechnology Information) located on the US National Institutes of Health Campus in Bethesda, MD, USA. Entrez Gene produces unique Gene ID (integers) as stable identifiers for a subset of model organisms for genes. It detects ...