Protein Modeling and Bioinformatics

Protein Structure Database
CCG has created a searchable database of over 13,000 protein structures from the Protein Data Bank. Each structure was imported using CCG’s PDB reader which corrects many of the errors commonly found in protein structure files. A graphical browser allows for searches on header, title, compound, het groups, resolution, date and experimental technique

Fold Identification
CCG has created a searchable database of structural families of proteins by exhaustively and iteratively clustering the Protein Data Bank. Incorporating rigorous sequence-to-family alignment, secondary structure prediction, hydrophobic fitness and Z-scoring, the search procedure outputs reliable homologues with a minimum of false positives. 

Multiple Alignment
CCG’s unique technology for simultaneous multiple sequence and structure alignment supports arbitrary constraints on residues, predicted secondary structure weighting and no pre-set limits on the number of proteins. The resulting alignment is a true multiple alignment and global superposition with no "master" sequence. 

Consensus Features
Geometric criteria are used to rapidly determine the structurally conserved features in a family of proteins including conserved waters. Separate criteria are used for the backbone, side chains and waters. A consensus structure can be output for use as a homology modeling template. 

Structure Prediction
Homology modeling techniques are used to build complete high-quality 3D structures of proteins from a template. Environment units such as bound ligands and conserved waters can be used in the template. A rotamer library is used to place side chain atoms. Multiple models are built and ranked with a statistical assessment of model quality. 

Protein Mechanics and Dynamics
Proteins structures can be refined using either AMBER ’89, ’94, MMFF94 or Engh-Huber parameters augmented with an implicit solvent model. Atom tethers, restraints and chiral constraints are supported. Molecular dynamics can be performed in either the NVE, NVT, NPT or NPH ensembles. 

Stereochemical Quality
Statistical measures (derived from x-ray crystal structures) of bond lengths, angles, backbone dihedrals and non-bonded contacts are used to assess the overall stereochemical quality of a protein structure. A graphical interface allows for the identification and visualization of outliers. 

Contact Analysis
Stabilizing contacts such as hydrogen bonds, salt bridges, hydrophobic contacts and disulfide bonds are often implicated in protein function. A graphical interface allows for the determination of important contacts that are often undetected in sequence alignments.