By Schrodinger
Harness the structural biology revolution Unlock your protein target for high-precision, structure-based design We are in the midst of a revolution in structural biology, with a proliferation of available structures across protein classes now possible due to advances in cryo-EM and technologies such as AlphaFold. However, significant refinement and accurate ligand placement is required to use these models in physics-based simulations including docking and free energy perturbation. Schrödinger’s comprehensive suite of solutions for protein model refinement, ligand placement, and binding site analysis allows you to unlock a broader range of targets for structure-based design. CAPABILITIES Solutions to generate design-ready structures from a broad range of starting points Enable both on-targets and off-targets for rigorous structure-based design High resolution structures Prepare high resolution X-ray crystal or cryo-EM structures for structure-based design Quickly and reliably prepare high-quality, all-atom protein models suitable for physics-based simulations Predict the binding mode of novel ligands in existing structures at near experimental accuracy Understand competitor binding modes without needing to obtain an experimental structure for each series Low resolution structures Refine and validate low resolution X-ray crystal or cryo-EM structures Correct common structural problems and create reliable, all-atom protein models Dock ligands into ambiguous density, such as in cryo-EM structures, using a best-in-class force field to resolve uncertainty Place cofactors and solvent to convert low resolution models into complete, all-atom representations No structure Create and validate structures from homologous protein sequence or make use of available AlphaFold structures Harness the power of genomic data to easily create homology models of pharmaceutically relevant targets Reliably and accurately dock ligands into template-based homology models or AlphaFold structures Quantitatively validate structural models using known SAR and a highly accurate in silico binding affinity assay Identify and assess the druggability of protein binding sites Binding site identification Rapidly identify and rank a protein’s probable binding sites with confidence - SiteMap Cryptic pocket exploration Elucidate cryptic binding pockets and reveal binding hot spots using metadynamics accelerated sampling workflow for mixed solvent simulations - Desmond Hydration site analysis Discover new possibilities for ligand design by predicting the location and thermodynamic potential of hydration sites in the binding site - WaterMap
