One of the most troublesome stages of Computer Aided Drug Design (CADD) process is analyzing huge amount of data provided by docking studies. Simple scoring functions alone can provide only shallow information about ligand-receptor interactions, since they do not distinguish neither residues nor single atoms. Very often a visual inspection is the only way to determine a binding mode. Here, we i...

In Corynebacterium glutamicum the LysE carrier protein exhibits the unique function of exporting L-lysine. We here analyze the membrane topology of LysE, a protein of 236 amino acyl residues, using PhoA- and LacZ-fusions. The amino-terminal end of LysE is located in the cytoplasm whereas the carboxy-terminal end is found in the periplasm. Although 6 hydrophobic domains were identified based on ...

BACKGROUND In the course of our whole-genome sequencing efforts, we have developed a pipeline for analyzing germline genomes from Mendelian types of cancer pedigrees (familial cancer variant prioritization pipeline, FCVPP). RESULTS The variant calling step distinguishes two types of genomic variants: single nucleotide variants (SNVs) and indels, which undergo technical quality control. Mendel...

The guided local search method has been successfully applied to a significant number of NP-hard optimization problems, producing results of similar caliber, if not better, compared to those obtained from algorithms specially designed for each singular optimization problem. Ranging from the familiar TSP and QAP to general function optimization problems, GLS sits atop many well-known algorithms s...

Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We assess the bioactivity and "drug-likeness" of a relatively small but structurally diverse dataset (containing >1,000 compounds) from African medicinal plants, which have been tested and proven a wide range of biological activit...

The new drug discovery is found to be a time consuming and costly process. Recently, a trend towards the use of in-silico computational chemistry and molecular modeling for computer aided drug design has gained significant momentum. This review is an investigation of the applications of different software in drug design. The modern drug discovery process is steadily becoming more information dr...

The deleterious genetic variants contributing to certain diseases may differ in terms of number and allele frequency from population to population depending on their evolutionary background. Here, we prioritize the deleterious variants from Pakistani population in manually curated gene list already reported to be associated with common, Mendelian, and congenital cardiovascular diseases (CVDs) u...

Staphylococcus aureus has gained much attention in the last decade as it is a major cause of the Urinary Tract Infection in Diabetic patients. The Extended Spectrum β-Lactamases (ESβL) producers are highly resistant to several conventional antibiotics. This limits the therapeutic options.Hence efforts are now taken to screen few medicinal plants, which are both economic and less toxic. Among th...

Computational assessment of the binding affinity of enzyme inhibitors prior to synthesis is an important component of computer-aided drug design (CADD) paradigms. The free energy perturbation (FEP) methodology is the most accurate means of estimating relative binding affinities between two inhibitors. However, due to its complexity and computation-intensive nature, practical applications are re...