ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files

Additional file 2. Recreated 3D geometry optimized structures of 29 molecules as visualized in the original program (Gauss View)

ChemTextMiner: An open source tool kit for mining medical literature abstracts

Text mining involves recognizing patterns from a wealth of information hidden latent in unstructured text and deducing explicit relationships among data entities by using data mining tools. Text mining of Biomedical literature is essential for building biological network connecting genes, proteins, drugs, therapeutic categories, side effects etc. related to diseases of interest. We present an approach for textmining biomedical literature mostly in terms of not so obvious hidden relationships and build biological network applied for the textmining of important human diseases like MTB, Malaria, Alzheimer and Diabetes. The methods, tools and data used for building biological networks using a distributed computing environment previously used for ChemXtreme[1] and ChemStar[2] applications are also described

Nanoparticle Size and Heat Pipe Angle Impact on the Thermal Effectiveness of a Cylindrical Screen Mesh Heat Pipe

This study examines the effects of particle size and heat pipe angle on the thermal effectiveness of a cylindrical screen mesh heat pipe using silver nanoparticles (Ag) as the test substance. The experiment investigates three different particle sizes (30 nm, 50 nm, and 80 nm) and four different heat pipe angles (0°, 45°, 60°, and 90°) on the heat transmission characteristics of the heat pipe. The results show that the thermal conductivity of the heat pipe increased with an increase in heat pipe angle for all particle sizes, with the highest thermal conductivity attained at a 90° heat pipe angle. Furthermore, the thermal resistance of the heat pipe decreased as the particle size decreased for all heat pipe angles. The thermal conductivity measurements of the particle sizes—30, 50, and 80 nm—were 250 W/mK, 200 W/mK, and 150 W/mK, respectively. The heat transfer coefficient values for particle sizes 30 nm, 50 nm, and 80 nm were 5500 W/m2K, 4500 W/m2K, and 3500 W/m2K, respectively. The heat transfer coefficient increased with increased heat pipe angle for all particle sizes, with the highest heat transfer coefficient obtained at a 90° heat pipe angle. The addition of Ag nanoparticles at a volume concentration of 1% reduced the thermal resistance of the heat pipe, resulting in improved heat transfer performance. At a heat load of 150 W, the thermal resistance decreased from 0.016 °C/W without nanoparticles to 0.012 °C/W with 30 nm nanoparticles, 0.013 °C/W with 50 nm nanoparticles, and 0.014 °C/W with 80 nm nanoparticles. This study also found that the heat transfer coefficient increased with increased heat pipe angle for all particle sizes, with the highest heat transfer coefficient obtained at a 90° heat pipe angle

MOESM4 of ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files

Additional file 4. Sample input file containing co-ordinates of molecules separated by comma delimiter

MOESM5 of ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files

Additional file 5. Instruction for compilation of chemengine source code available online and operation manual

Comprehensive molecular docking and dynamic simulations for drug repurposing of clinical drugs against multiple cancer kinase targets

Drug repurposing is a method to identify novel therapeutic agents from the existing drugs and clinical compounds. In the present comprehensive work, molecular docking, virtual screening and dynamics simulations were carried out for ten cancer types viz breast, colon, central nervous system, leukaemia, melanoma, ovarian, prostate, renal and lung (non-small and small cell) against validated eighteen kinase targets. The study aims to understand the action of chemotherapy drugs mechanism through binding interactions against selected targets via comparative docking simulations with the state-art molecular modelling suits such as MOE, Cresset–Flare, AutoDock Vina, GOLD and GLIDE. Chemotherapeutic drugs (n = 112) were shortlisted from standard drug databases with appropriate chemoinformatic filters. Based on docking studies it was revealed that leucovorin, nilotinib, ellence, thalomid and carfilzomib drugs possessed potential against other cancer targets. A library was built to enumerate novel molecules based on the scaffold and functional groups extracted from known drugs and clinical compounds. Twenty novel molecules were prioritised further based on drug-like attributes. These were cross docked against 1MQ4 Aurora-A Protein Kinase for prostate cancer and 4UYA Mitogen-activated protein kinase for renal cancer. All docking programs yielded similar results but interestingly AutoDock Vina yielded the lowest RMSD with the native ligand. To further validate the final docking results at atomistic level, molecular dynamics simulations were performed to ascertain the stability of the protein–ligand complex. The study enables repurposing of drugs and lead identification by employing a host of structure and ligand based virtual screening tools and techniques. Communicated by Ramaswamy H. Sarma</p

Alterations in seedling vigour and antioxidant enzyme activities in Catharanthus roseus under seed priming with native diazotrophs

An experiment was conducted on Catharanthus roseus to study the effect of seed treatments with native diazotrophs on its seedling growth and antioxidant enzyme activities. The treatments had significant influence on various seedling parameters. There is no significant influence on dry matter production with the diazotrophs, Azospirillum and Azotobacter. However, the vital seedling parameters such as germination percentage and vigour index were improved. Azotobacter treatment influenced maximum of 50% germination, whereas Azospirillum and Azotobacter were on par with C. roseus with respect to their vigour index. There was significant difference in the population of total diazotrophs. Azospirillum and Azotobacter between rhizosphere and non-rhizosphere soils of C. roseus had the same trend and were observed at various locations of the study. The activities of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POX) and catalase (CAT) were increased to a significant extent due to the treatment with diazotrophs