Applications of Biskit Software

Biskit is a modular, object-oriented Python library for structural bioinformatics research. It facilitates the manipulation and analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories. For efficient handling of numbers, Biskit objects are tightly integrated with numpy (Numeric Python). Biskit provides a platform to quickly integrate external programs and new algorithms into complex workflows. Therefore, calculations are often delegated to established programs such as Xplor, Amber, Hex, DSSP, Fold-X, T-Coffee, TMAlign, and Modeller. Biskit also simplifies the parallelization of computation through PVM (Parallel Virtual Machine). Biskit is an open-source software. Our scientists use Biskit software to analyze protein macromolecular structures, protein complexes, and small molecule dynamics trajectories. At the same time, in order to meet the needs of customers, the software is used to automatically predict protein structures through homology modeling, as well as the possibility of predicting complex structures of proteins through flexible protein-protein docking.

Our Services Based on Biskit Software

Biskit is a software that facilitates research in structural bioinformatics and molecular modeling. Biskit also focuses on the integration of various structure-centric data and algorithms, including molecular dynamics simulations and protein-protein docking for sequence search and visualization. On the Biskit software platform, CD ComputaBio can provide customers with high-quality computational biology services.

• Analyze molecular structures, complexes and molecular dynamics trajectories
• Automatic conformal sampling
• Analyze the sequence of proteins
• Automatic homology modeling
• Search for homologous sequences and 3D structures (Blast)
• Multiple alignment (T-Coffee)
• Model building (Modeller)
• Cross-validation by rebuilding available templates
• Multiple model protein-protein (Cross) docking
• Quasi-harmonic entropy calculation
• Parallelize and automate your own structural bioinformatics workflow
• Flexible peptide docking
• Structure sampling with Xplor
• Structure sampling with Amber
• Clean the model (manually)
• Build topology (automatic)
• Prepare the folder and run MD
• Convert the amber result to a pickled Biskit. Ensemble Traj object
• Trajectory clustering
• Modelling validation
• Data visualize
• Electrostatic free energy of binding with DelPhi

The Features of Biskit Software

• Biskit seamlessly integrates with around 15 popular external programs such as Amber, Blast, Hex, Hmmer, Fold-X, Modeller, Prosa, Pymol, T-Coffee and Xplor.
• Biskit focuses on structure-centric integration of various data and algorithms.
• Many calculations are performed within the Biskit module itself.
• Biskit code is well documented.
• Almost every module in Biskit includes a dedicated test class that further explains its use and makes it easy for beginners to learn.

The Workflow of Biskit Software

Our Capabilities

Biskit is a set of programs for solving specific tasks, mainly used in bioinformatics research. Our scientists operate and analyze macromolecular structures, protein-ligand complexes, and molecular dynamics trajectories primarily on the Biskit software platform. Using Biskit's homology modeling module, our scientists can predict the structure of proteins, but also the structure of protein-protein docking complexes, analyzing docking binding pockets and key amino acids.