PRODUCTS: BIOINFORMATICS (DEC 2005/JAN 2006)
New generation drug discovery software enters market
Quantum Pharmaceuticals is issuing its first commercial release of research software that is expected to speed up pharma R&D. Quantum 3.1 is a suite of drug discovery software for Linux and Windows designed to enhance stages of drug discovery workflows, such as target identification, drug hit identification, lead identification and lead optimisation.
The Quantum software was developed by applying quantum and molecular physics instead of statistical scoring-function-like and QSAR-like methods.
Its benefit is precision of molecular modelling and calculations. Researchers can calculate the IC50 of protein-ligand and protein-protein complexes, perform ligand docking, perform virtual screening of small-molecule libraries, analyse large-scale protein movements, perform de novo drug design and calculate the solvation energy and solubility.
Quantum 3.1 also helps detect potential moderate-to-serious adverse activity, additional unexpected activity and broad relative selectivity for a library of compounds by screening them against several hundred ADME/TOX-associated proteins.
Its Mutagenesis module provides an interface for changing the protein sequence at specific sites through alterations to its amino acids and predicts changes in the bioactivity after mutations.
The free demo version can be downloaded from Quantum’s website.
PathwayLab provides computational systems biology environment
Wolfram Research is distributing PathwayLab – a new in silico systems biology software – developed by InNetics AB. This Mathematica application package provides facilities for modelling, documentation, computational analysis, and information management of biochemical pathways and networks.
Biochemical pathways and networks are graphical representations of complex biochemical reaction schemes. These include signalling pathways, metabolic pathways, and gene regulatory networks. A simple example of a metabolic pathway is the conversion of glucose into pyruvate and usable energy.
With PathwayLab, a model of a pathway can be created using a simple drag-and-drop graphical user interface. The interface includes graphical building blocks for specifying biochemical entities as well as reaction and control mechanisms. The result can be used to document and communicate the model, but more importantly it is a mathematical model that can be analysed computationally. With Mathematica, the pathway model – a system of coupled nonlinear differential equations – can be directly simulated, and the simulation result can be further analysed, including visualisation of the output.
By analysing a model, one can effectively do computer, or in silico, experiments, reducing the need for or guiding the choice of wet-lab experiments and thus accelerating the process of drug discovery.
Entelechon’s gene optimisation software hits the market
A new software package for gene optimisation is now available from Entelechon. Leto is an application dedicated to the optimisation of DNA sequences for maximum expression. After a beta test phase of two months, many valuable suggestions from beta testers have lead to important improvements of the application, which is now publicly available.
Leto features a sophisticated graphical user interface for designing and optimising DNA sequences both interactively and automatically. At the core of Leto is a genetic algorithm that integrates a large set of optimisation parameters, such as codon usage, mRNA secondary structure, splice site detection, or GC content.
Leto integrates with a highly customisable bioinformatics framework, GeneSynthetic (GS 3.0). This integration makes available to Leto the powerful LISP libraries of GS 3.0, so that users can adapt the mechanics of Leto to their specific needs.