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Protein-protein docking:
BioLuminate offers a state of the art protein-protein docking program, with modes for antibody and multimer docking.
Protein modeling:
BioLuminate contains a complete set of homology modeling and protein sequence analysis tools, including advanced loop predictions, annotation capabilities, chimeric model building, and interactive protein structure quality analysis.
Protein engineering:
BioLuminate generates protein aggregation propensity surfaces and performs residue-based property predictions including binding energy, thermal stability, solvent-accessible surface area, hydrophilicity, and hydrophobicity. In addition, cysteine scanning automatically identifies potential mutations that can result in disulfide bridges. Reactive hot spots prone to proteolysis, glycosylation, deamidation, and oxidation are also detected.
Antibody modeling:
BioLuminate offers an antibody-specific homology modeling workflow including automated prediction of CDR loops from sequence. BioLuminate includes a curated antibody database with tools to add in-house antibody structures.
Advanced simulations:
BioLuminate can access the full suite of Schrödinger simulation tools to perform advanced computational analyses such as helical stability/melting analysis from molecular dynamics (MD) simulations, free energy perturbation (FEP) calculation of binding affinity and protein stability, large-scale low-mode search for domain movement, and QM/MM prediction of binding site reactivity. Citations and Acknowledgements
Schrödinger Release 2020-1: BioLuminate, Schrödinger, LLC, New York, NY, 2020.
ö Zhu, K.; Day, T.; Warshaviak, D.; Murrett, C.; Friesner, R.; Pearlman, D., 'Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction,' Proteins, 2014, 82(8), 1646–1655
ö Salam, N.K.; Adzhigirey, M.; Sherman, W.; Pearlman, D.A., 'Structure-based approach to the prediction of disulfide bonds in proteins,' Protein Eng. Des. Sel., 2014, 27(10), 365-74
ö Beard, H.; Cholleti, A.; Pearlman, D.; Sherman, W.; Loving, K.A., 'Applying physics-based scoring to calculate free energies of binding for single amino acid mutations in protein-protein complexes,' PLoS ONE, 2013, 8(12), e82849
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