BioMedCAChe
Features
Protein Sequence Editor
An important tool in homology modeling, the new sequence editor allows researchers to build, align, visualise in 3D, edit, mutate and analyse 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.
New Automated Sequence Alignment
Exact sequence alignment using the Needleman-Wunsch algorithm with BLOSUM50 weights and sequence matching speeds identification of active sites.
New Surfaces Identify 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.
New command selects conserved residues
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 visualise which portions of the protein are conserved.
4X Greater Accuracy for Heats of Formation and Metals
The semiempirical PM5 method within MOPAC 2002 provides 4X greater accuracy than competing packages for predicting heats of formation.
Homology Modeling
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.