Structural Bioinformatics

At Biotechvana we are pleased to offer our users advanced structural bioinformatics services focused on the study of proteins and biomolecular complexes using computational modeling, simulation, and design tools. Our analyses make it possible to explore the structure, function, and dynamics of proteins, as well as to optimize their properties through rational engineering and artificial intelligence approaches.

In the field of structural bioinformatics, we offer different types of analyses adapted to the goals of each project, including:

Protein Engineering and Design: optimization or de novo creation of proteins through structural redesign, AI-assisted prediction, and functional mutation analysis.
Molecular Modeling and Simulation: prediction of three-dimensional structures, structural refinement, stability analysis, and molecular dynamics simulations using advanced tools.
Biomolecular Interaction Studies: analysis of protein–ligand or protein–protein complexes, binding site prediction, complex simulation, and estimation of binding free energies.

Each project is approached in a personalized manner, adapting methods and tools to the type of protein, ligand, or molecular system of interest.

Protein Engineering and Design

This analysis supports the design or redesign of proteins with desired properties by evaluating variants through structure–function insights.

Preprocessing of structural and sequence data

Retrieval of protein sequences from databases (UniProt, PDB, AlphaFold DB, etc.).
Structure curation: removal of ligands, protonation, correction of missing residues, etc.

Computational Design and Modeling

Structural modeling (AlphaFold, OmegaFold, Swiss-Model…).
Model analysis and identification of functional regions.
De novo design or redesign of existing proteins (RFdiffusion, ProteinMPNN, LigandMPNN).
Molecular dynamics simulation to evaluate structural stability (AMBER, GROMACS...).

Molecular Modeling

This analysis enables reliable structural models, stability assessment, and extraction of functional properties for mechanistic and applied studies.

Model preparation and optimization

Prepare a clean, simulation-ready molecular model by correcting errors, assigning protonation states, and optimizing geometry.
Start by adding missing atoms and residues, fixing chain breaks, and choosing appropriate protonation states for ionizable groups at the target pH.
Apply an appropriate force field and perform energy minimization to remove steric clashes and relax strained bonds; this yields a low-energy starting structure suitable for further refinement or simulations.

Structural refinement

Improve local and global geometry using targeted refinement methods to better match experimental data or theoretical expectations.
Refinement can include loop modeling, side-chain rotamer optimization, and restrained minimization or short molecular dynamics to correct poorly modeled regions.

Stability and flexibility analysis

Assess how the structure behaves over time and which regions are rigid or mobile.
Use molecular dynamics (MD) simulations or normal mode analysis to sample conformational space and compute metrics such as RMSD, RMSF, and secondary-structure persistence.
Identify flexible loops, hinge regions, and stable cores.
Evaluate thermal stability, unfolding pathways, or the effect of mutations on dynamics to predict functional consequences.

Evaluation of structural and functional properties

Characterize features that relate structure to biological function and potential applications.
Analyze binding pockets, electrostatic surfaces, hydrogen-bond networks, and hydrophobic patches to infer ligandability and interaction hotspots.
Compute properties like solvent accessibility, pKa shifts, and predicted binding energies to support drug design, mutational studies, or interpretation of experimental results.

Protein–Protein and Protein–Ligand Interaction Studies

This analysis clarifies how biomolecules interact and with what affinity, supporting mechanistic interpretation, target prioritization, and experimental design.

Protein–ligand and protein–protein interaction analysis (AutoDock Vina, HADDOCK)

Identify and characterize how small molecules or other proteins bind to a target protein.
Use docking tools (AutoDock Vina, HADDOCK, etc.) to predict binding poses and prioritize likely interactions.
Inspect key contacts such as hydrogen bonds and hydrophobic interactions.
Map interaction hot spots.
Use the results to guide hypothesis generation for mutagenesis, inhibitor design, or experimental validation.

Molecular dynamics simulation of the complex

Simulate the time-dependent behavior of protein–ligand or protein–protein complexes to sample realistic conformations and dynamic interactions.
Run molecular dynamics simulations to observe conformational changes, solvent effects, and transient contacts.
Analyze trajectories to compute metrics such as RMSD, RMSF, and interaction lifetimes.
These simulations reveal mechanisms that are not evident from static models.

Binding free energy calculation (MM/PBSA, MM/GBSA)

Quantify binding strength using methods such as MM/PBSA or MM/GBSA to estimate relative or absolute binding free energies.
Calculate energetic contributions (electrostatics, van der Waals, solvation) from MD snapshots to prioritize ligands or mutations and rationalize observed affinities.

Stability and affinity evaluation of complexes

Evaluate complex stability and interaction affinity.
Combine structural analyses, MD-derived metrics, and free energy estimates to determine complex half-life, propensity for dissociation, and the effect of mutations or environmental changes on affinity.
These evaluations support design decisions and experimental strategies.

If you are interested in obtaining more information about the structural bioinformatics services we offer, please contact us at biotechvana@biotechvana.com. We will provide you with a quote for your study or, if you prefer, arrange a meeting with you and your team with no obligation.