BioMedCAChe Speeds the Drug Discovery Process by Predicting Better Quality Leads
BioMedCAChe is the new computer-aided chemistry software package designed specifically for bio- and medicinal chemists. The package aids researchers in discovering structure-activity relationships, optimizing leads by maximizing activity, and improving the prediction of bioavailability. The power of the package enables researchers to predict properties of compounds that have never been made or properties that have never been measured. This prediction enables researchers to select those novel compounds for testing or synthesis that are most likely to be successful, saving valuable lab time and resources. BioMedCAChe also offers users the ability to devise ways to calculate molecular properties and calibrate them to experimental results.
BioMedCAChe allows researchers to optimize, dock, and model reactions of molecules with tens of thousands of atoms. BioMedCAChe imports and graphically displays PDB (Protein Data Bank) files with full information from the original files retained and accessible via the Project
Note: A recent JACS paper suggests that active sites in enzymes correlate with the position of the frontier molecular orbitals (calculated on the "solvated" protein with CAChe's MOPAC 2000 compute engine using the COSMO solvent model). See: Kazuki Ohno et al, J. Am. Chem. Soc. 2001, 123, 8161-8162. Effects of Hydration on the Electronic Structure of an Enzyme: Implications for Catalytic Function.
The ProjectLeader interface within BioMedCAChe lets researchers automate, store, and analyze predicted properties for whole libraries of compounds. Users can set up spreadsheets of molecules and the calculations they want to run, automating regression techniques to help determine ADME and QSAR/QSPR predictions of any property and allowing easy comparison among molecules. Researchers can load entire compound libraries and run “rule-of-five” calculations on them, screening for drug-like compounds automatically and tabulating results while they work in the lab.
Six new styles for displaying proteins as backbone ribbons are available in 6.0.
An important tool in homology modeling, the new sequence editor allows researchers to build, align, visualize in 3D, edit, mutate and analyze proteins. The integrated sequence view permits simultaneous viewing and manipulating of secondary and tertiary (3D) structures. An amino acid repository of structures enables researchers to easily build new proteins graphically by simply typing their residue code into the editor.
Exact sequence alignment using the Needleman-Wunsch algorithm with BLOSUM50 weights and sequence matching speeds identification of active sites.
The new accessible surface colors proteins by hydrophillic and hydrophobic properties. The new crevice surface colors maps deep crevices in a protein that might be good ligand binding sites. The new adjacent surface draws the active site pocket.
The new Select Conserved command quickly selects identical residues in aligned residues and simultaneously highlights the conserved residues on the 3D structure allowing you to visualize which portions of the protein are conserved.
The semiempirical PM5 method within MOPAC 2002 provides 4X greater accuracy than competing packages for predicting heats of formation.
Researchers can create 3D structures of proteins for which only the sequence is known from the known 3D structure of a similar protein. The new Find and Replace command in 6.0 speeds homology modeling.
Read how a University of Florida researcher used BioMedCAChe for homology modeling of MC4R.
Add non standard amino acids to the amino acid repository.
BioMedCAChe supports the building of crystal structures and displays protein crystal packing using the crystal information found in PDB file.
Automatically locate and label hydrogen bonds or atoms that are too close together and bump into one another in version 6.0.
New parameters and enhanced augmentation rules for bio-molecules increase the accuracy of mechanics calculations in 6.0.
Selection and many operations in 6.0 are ten times faster for large proteins.
Unlike most competitors, BioMedCAChe runs on Windows and provides fast visualization and analysis of molecules with tens of thousands of atoms.