by Elizabeth Swanberg | Jan 2, 2019 | Background, Bench
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by Elizabeth Swanberg | Jan 2, 2019 | Background, Background on Homology Modeling
CYRUS BENCH HOMOLOGY: A HIGHLY AUTOMATED, AUTOMATED, CLOUD-ENABLED, POWERFUL, AND USER-FRIENDLY HOMOLOGY MODELING PIPELINE USING ROSETTA-CM Lucas G. Nivón, Ryan Gomoto, and Yifan Song Author Affiliations: Cyrus Biotechnology, Inc. 500 Yale Ave. N. Seattle WA...
by Elizabeth Swanberg | Jan 2, 2019 | Rosetta
ROSETTA SAMPLING METHODS Rosetta uses its energy function to determine whether a conformation is favorable. Using this function, it can sample a wide range of conformations in order to optimize protein structure in terms of score. Rosetta uses several ways of sampling...
by Elizabeth Swanberg | Jan 2, 2019 | Structure Prediction, Tools
OVERVIEW HM Antibody is a structure prediction tool for the variable region of antibodies. The protocol assumes that your sequence is a naturally-occuring antibody, which means that there is a limit to how much your input can diverge from the norm. Often, users have...
by Elizabeth Swanberg | Dec 31, 2018 | FAQs
IMPROVED DDG, FREE ENERGY MUTATION CALCULATOR Our delta delta G (DDG) tool has been significantly improved in order to make better predictions of the stability of single point mutations. This method has been significantly changed in order address certain weaknesses in...
by Elizabeth Swanberg | Dec 31, 2018 | Introductory Workflows, Workflows
BACKGROUND A protein Position Specific Scoring Matrix (PSSM) takes the alignment of your protein to a list of homologs and counts the amino acids found at each position for the homologs. This is an easy way of measuring evolutionarily related mutations accepted at...
by Elizabeth Swanberg | Dec 31, 2018 | Analysis, Tools
BACKGROUND Immunogenicity is the propensity of a molecule to provoke a response by the immune system. In many cases this is the desired behavior of the immune system, recognizing foreign objects and targeting them for neutralization or removal. However immunogenicity...
by Elizabeth Swanberg | Dec 31, 2018 | Analysis, Tools
Delta Delta G (DDG) is a metric for predicting how a single point mutation will affect protein stability. DDG, often referred to as 𝚫𝚫G, is the change in the change in Gibbs free energy (double changes intended). DDG is a measure of the change in energy between the...
by Elizabeth Swanberg | Dec 31, 2018 | Actions, Tools
OVERVIEW The Replace Ligand tool allows you to swap a new ligand into a pocket in place of an existing ligand. This is useful when you want to dock a molecule that is similar to a ligand with a known binding conformation. Design and other modeling can then be carried...
