Some relevant Published databases

We have listed several relevant databases with short introductions and links with their active or dead mood to make it more convenient and easier for researchers, our aim in giving the database's dead mood is to ensure that researchers may still get knowledge from the articles.


The Center for Computational Structural Biology (CCSB) currently comprises four highly synergistic and independently funded research laboratories focusing on a variety of aspect of modelling and simulating structural biology ranging from biomolecular visualization, computation and design, spanning from atomic structure and interactions to the mesoscale structure of living cells. It was created in 2018 as a successor of the Molecular Graphics Laboratory (MGL), founded by Arthur Olson in 1981. Over the years we have developed several freely-available software tools including AutoDock, Python Molecular Viewer, and CellPACK. Current applications include the design and virtual screening of covalent inhibitors of HIV-1 proteins, docking and binding energy prediction of small molecules and peptides to flexible biomolecular targets, and modeling of subcellular structures such as bacterial nucleoids and secretory vesicles.



A large number of protein-protein interactions are mediated by the binding of protein and peptide fragments. The determination of protein-polypeptide interactions is of great significance for the development of peptide drugs. Peptides have been involved in the docking progress since they often cover a relatively larger surface area when binding to the `hot-spots` on the surface of a protein target. Therefore, peptide molecules can interact with target proteins with high specificity and biologically relevant affinity, and can be utilized as therapeutic and diagnostic tools. However, protein-peptide interactions are often associated with large-scale conformational changes that are difficult to study since the secondary structure of short peptides is not always well defined. Molecular docking provides a reasonable starting point to identify candidate molecules on the basis of their binding affinities to a target of interest.



Due to its complex nature, accurately modeling a protein-protein docking interaction can often prove to be very challenging. NovaDock molecular docking software offers the ability to predict protein-protein docking interactions for any two binding partners utilizing SwarmDock, one of the top algorithms validated in the CAPRI blind docking experiment. Utilizing the SwarmDock algorithm, NovaDock explores protein flexibility when docking, resulting in more accurate predictions. Simply provide your ligand and receptor PDB or structure files, proposing specific residue contacts between the binding partners if desired. NovaDock will then predict the three-dimensional structure of the macromolecular complex and provide energy score, cluster size, and number of ligand contacts for each model for analysis in Protean 3D.



Creative BioMart's strong expertise in protein structure enables us to accelerate your project by providing protein structure prediction and assessment services, including structural modeling and structural assessment. This service can help us accurately understand the 3D structural information of proteins and the interactions between proteins and proteins (or other molecules), which are very important for research in biology, medicine and pharmacy.



Understanding compound selectivity is vital when designing novel pharmaceuticals. The extent of on- and off-target effects, or potential polypharmacology, informs modifications to develop safe and effective drugs.