title: MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions.
abstract: Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of impacts of variants on proteins. To address this need we introduce a new computational method MutaBind to evaluate the effects of sequence variants and disease mutations on protein interactions and calculate the quantitative changes in binding affinity. The MutaBind method uses molecular mechanics force fields, statistical potentials and fast side-chain optimization algorithms. The MutaBind server maps mutations on a structural protein complex, calculates the associated changes in binding affinity, determines the deleterious effect of a mutation, estimates the confidence of this prediction and produces a mutant structural model for download. MutaBind can be applied to a large number of problems, including determination of potential driver mutations in cancer and other diseases, elucidation of the effects of sequence variants on protein fitness in evolution and protein design. MutaBind is available at http://www.ncbi.nlm.nih.gov/projects/mutabind/.
authors.affiliation: National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Minghui
authors.initials: M
authors.lastname: Li
authors.affiliation: Institute Leloir Foundation, Buenos Aires, C1405BWE, Argentina.
authors.forename: Franco L
authors.initials: FL
authors.lastname: Simonetti
authors.affiliation: National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA.
authors.forename: Alexander
authors.initials: A
authors.lastname: Goncearenco
authors.affiliation: National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA panch@ncbi.nlm.nih.gov.
authors.forename: Anna R
authors.initials: AR
authors.lastname: Panchenko
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D066264:Datasets as Topic; D019143:Evolution, Molecular; D056084:Genetic Fitness; D006801:Humans; D020407:Internet; D056004:Molecular Dynamics Simulation; D009369:Neoplasms / Q000235:genetics; D011485:Protein Binding / Q000235:genetics; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps / Q000235:genetics*; D011506:Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012984:Software
chemical_list: D011506:Proteins