Search Results for "dna"

The oxDNA code has been moved to https://github.com/lorenzo-rovigatti/oxDNA, please go there for new releases.

The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data.

...The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Skin sensitisation reactivity domain -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) -Structural alerts associated with covalent protein binding and DNA binding. - Ames mutagenicity Toxtree provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java), with the use of The Chemistry Development Kit.

The Gecko Hamaker open-source software project is a full implementation of the fully retarded Lifshitz formulations for isotropic and anisotropic plane-plane and cylinder-cylinder interactions with intervening interlayer materials, planar systems of up to 99 layers, and graded interfaces for the modeling of grain boundaries or other continuously changing systems, accompanied by a database of material optical properties spectra. The machine-readable optical property database is available...

RAINIER: Rapid Automated Inference of Nucleic-Acid Interaction Energy using Refinement RAINIER is a protein simulator that can predict the interface structure of DNA- and RNA-binding proteins, using statistical and physical techniques.

MeltDNA Tool For Prediction of DNA Duplex Hybridization & Melting Thermodynamics (delta G°, delta H° and delta S° ,Tm,Ta Prediction)