Protein peptide docking

Protein–Peptide Docking

INQUIRY

The interactions between proteins and peptides play essential

functional roles in living organisms and they can be found in a

variety of signaling pathways involved in cellular localization,

immune response or protein expression and degradation.

Erroneous protein-peptide interactions are associated with a

number of diseases (e.g., cancer, autoimmune diseases). The

understanding of protein-peptide interactions is critical for targeted

drug design and their structural characterization is a hot subject of

current experimental and theoretical research.

Profacgen makes use of state-of-the-art docking software tools to

model protein–peptide interactions and to predict the complex

structure. The general modeling procedure is divided into two

stages: (1) a global search is performed to predict the binding site

at the protein receptor surface; (2) a flexible local docking method

is used to fit the peptide structure into the known binding site.

These two steps take into consideration the significant

conformational changes upon binding of the two components. The

peptide folding process is explicitly simulated in the docking

protocol. When experimental or predicted data on binding site

residues are available, such information can be used to constrain

the docking to local regions of the protein surface. Finally, the

best-scored structures are clustered, ranked and representatives of

the largest clusters are selected for high resolution structural

refinement before being presented to the customer.

Protein–peptide docking process

Protein–peptide docking process

Profacgen employs computational docking techniques to search all

possible binding modes in the translational and rotational space

between a protein receptor and its peptide binding partner. Given a

protein receptor structure and a peptide sequence, we predict the

structure of protein–peptide complex, starting from random

conformations and positions of the peptide. This is an important

means for understanding the physicochemical forces that underlie

macromolecular interactions and a valuable tool for modeling

protein–peptide complex structures at the atomic level.

Furthermore, the precise understanding of these interactions will

facilitate the rational design of potentially therapeutic peptide.

Features

Simulation of conformational changes in protein–peptide

interactions

Solvated docking protocol allowing explicit inclusion of interfacial

water molecules

Clustering to find highly populated clusters of low-energy

conformations

Support modified amino acids in proteins and peptides

High-resolution structural refinement for peptide-protein

complexes

No prior knowledge of the binding site or the peptide

conformation required

Peptide conformation allowed to be fully flexible

Identification of hot-spot residues and prediction of binding

affinity

Flexible extensions with upstream and downstream modeling

protocols

We provide the service in a customizable fashion to suit our

customers’ specific research goals. Please do not hesitate to

contact us for more details about our protein–peptide docking

service.