Druggable Binding Pocket Identification and Modeling
Dynamic Conformations Sampling of Structures
Dynamic Conformations Sampling of Structures is an aggressive conformational search method that combines backbone and sidechain minimization in a highly efficient manner. It is the core method for many Rosetta algorithms, including X-Ray structure refinement, protein structure prediction, protein design with high backbone flexibility, identification of alternative conformations of a protein, and more. This is first described in Tyka et al, JMB vol. 405 p. 607.
Allosteric Effects of Ligand Binding
Protein/Protein Docking
Protein / Protein Docking is a cloud-based implementation of the PIPER Fast Fourier Transform (FFT) based docking algorithm developed in Sandor Vajda’s laboratory. PIPER is one of the top performing tools for protein/protein docking with all atoms represented (Other tools in Rosetta offer various methods of “fuzzy” non-all-atom docking). It includes specialized modes for common use cases such as antibody/antigen docking and docking with distance restraints. By delivering this tool on the cloud, we are able to analyze large problems for you in parallel. “PIPER: An FFT-based protein docking program with pairwise potentials”.
Kozakov et al Proteins Structure Function and Bioinformatics vol. 65 p. 392.
Protein/Small Molecule Docking
Protein/Small Molecule Docking is the RosettaLigand protocol for ligand docking, first published in Meiler and Baker, Proteins 2006, vol. 65 p. 538 and with more recent improvements in (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132508). These methods are especially useful with constraints between the small molecule and the protein but can be used for classic small molecule docking as well, especially in combination with other Cyrus or Rosetta tools. These methods can perform docking with a fixed protein backbone or with backbone flexibility — Rosetta’s performance is particularly strong in situations requiring backbone flexibility