Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein–Protein Binding Affinity upon Mutation
نویسندگان
چکیده
منابع مشابه
Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation
Advances in sequencing have led to a rapid accumulation of mutations, some of which are associated with diseases. However, to draw mechanistic conclusions, a biochemical understanding of these mutations is necessary. For coding mutations, accurate prediction of significant changes in either the stability of proteins or their affinity to their binding partners is required. Traditional methods ha...
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Computational methods have traditionally struggled to predict the effect of mutations in antibody-antigen complexes on binding affinity. This has limited their usefulness during antibody engineering and development, and their ability to predict biologically relevant escape mutations. Here we present mCSM-AB, a user-friendly web server for accurately predicting antibody-antigen affinity changes ...
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Identifying the contributions to thermodynamic stability of capsids is of fundamental and practical importance. Here we use simulation to assess how mutations affect the stability of lumazine synthase from the hyperthermophile Aquifex aeolicus, a T = 1 icosahedral capsid; in the simulations the icosahedral symmetry of the capsid is preserved by simulating a single pentamer and imposing crystal ...
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MOTIVATION Mutations in human genome are mainly through single nucleotide polymorphism, some of which can affect stability and function of proteins, causing human diseases. Several methods have been proposed to predict the effect of mutations on protein stability; but most require features from experimental structure. Given the fast progress in protein structure prediction, this work explores t...
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Voltage-gated Ca2+ channels select Ca2+ over competing, more abundant ions by means of a high affinity binding site in the pore. The maximum off rate from this site is approximately 1,000x slower than observed Ca2+ current. Various theories that explain how high Ca2+ current can pass through such a sticky pore all assume that flux occurs from a condition in which the pore's affinity for Ca2+ tr...
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ژورنال
عنوان ژورنال: The Journal of Physical Chemistry B
سال: 2018
ISSN: 1520-6106,1520-5207
DOI: 10.1021/acs.jpcb.7b11367