In Silico Protein Structure Service

Homology modeling based protein structure will provide basic information about its biological function. Knowing the tertiary structure can help efficiently design therapeutic drugs that specifically bind to protein targets. CD ComputaBio provides corresponding protein sequencing analysis, protein structure modeling and protein structure prediction services. Our protein structure related service has proven to be very useful for understanding the biochemical basis of physiological events at different stages of drug development (even in different fields such as materials science).

Figure 1 Monoclonal antibody drug protein modeling

• Sequence Analysis

Protein sequence is obtained from NCBI, then further used for complete protein sequence analysis (structural and functional annotation) and model building comparative modeling approach. Software tools, such as ExPASy ProtParam, are utilized to analyze protein sequences, structures and physicochemical properties of protein model, like molecular weight, theoretical isoelectric point (pI), amino acid composition, atomic composition, extinction co-efficient, half-life, aliphatic index, instability index and grand average of hydropathicity index (GRAVY). In silico protein analysis can also predict protein folding behavior and structure from amino acid sequences.

• Secondary Structure Prediction

Methods, like SOPMA and GORIV, are conducted to predict the percentage composition of all the secondary structure present in particular protein, including Alpha Helix, 310 Helix, Pi Helix, Beta Bridge, Extended Strand, Beta Turn, Bend Region, Random Coil, Sequence Length, Ambiguous States, and Other States.

• Homology Modeling

The modeling of the 3-dimensional structure of the protein is done using by homology modeling programs Swiss model. Template was searched using Swiss model template library. The templates with highest quality have been selected for model building. Models are built based on the target template alignment model quality. Model quality was estimating assessing the QMEAN score. QMEAN is a composite scoring function for both the estimation of the global quality of the entire model as well as for the local per-residue analysis of different regions within a model.

• Protein Optimization and Design

In silico protein optimization technology offers a quick and less costly approach. By modifying and optimizing the amino acid sequence of a protein, one could explore the structure-activity relationships (SAR) and using them control protein properties and eventually modify them in a desired way. We can also use the gained information to rationally predict and design new optimized variants. E.g. the main aim of peptide cutter is to design a protein that is easily digestible in the human gastrointestinal tract and thus in silico digestibility was performed using relative tools.

Services items

In silico protein structure analysis helps scientists and pharmaceutical companies to investigate the chemical kinetics for drug research and discovery, e.g. studies in protein aggregation diseases. Our expert team can model biochemical pathways related to the causes of diseases, like protein folding diseases, in order to control and prevent disease progression.