biostudies-literaturePatro RBMBFNIAID NIH HHSInnovative Medicine InitiativeNHGRI NIH HHSNational Institutes of HealthState of Mecklenburg-Vorpommern MV-ExcellenceNational Science Foundation155https://www.ebi.ac.uk/biostudies/studies/S-EPMC4826543biostudies-literatureUnknown17<h4>Background</h4>Understanding the interactions between antibodies and the linear epitopes that they recognize is an important task in the study of immunological diseases. We present a novel computational method for the design of linear epitopes of specified binding affinity to Intravenous Immunoglobulin (IVIg).<h4>Results</h4>We show that the method, called Pythia-design can accurately design peptides with both high-binding affinity and low binding affinity to IVIg. To show this, we experimentally constructed and tested the computationally constructed designs. We further show experimentally that these designed peptides are more accurate that those produced by a recent method for the same task. Pythia-design is based on combining random walks with an ensemble of probabilistic support vecBMC bioinformaticsA computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.PMC4826543IMI/115006R21AI0853760313692BAI085376R21 AI085376R01HG0071040315450G0315450D125608708121110313692AR01 HG007104R21 HG006913HG006913UR090120849899UR08051R21HG0069131053918Thiesen HJPatro RBarbarini NPrill RJSaez-Rodriguez JLorenz PTiengo ANorel RSteinbeck FLustrek MKingsford CBellazzi RZiems BStolovitzky GfalseA computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.<h4>Background</h4>Understanding the interactions between antibodies and the linear epitopes that they recognize is an important task in the study of immunological diseases. We present a novel computational method for the design of linear epitopes of specified binding affinity to Intravenous Immunoglobulin (IVIg).<h4>Results</h4>We show that the method, called Pythia-design can accurately design peptides with both high-binding affinity and low binding affinity to IVIg. To show this, we experimentally constructed and tested the computationally constructed designs. We further show experimentally that these designed peptides are more accurate that those produced by a recent method for the same task. Pythia-design is based on combining random walks with an ensemble of probabilistic support vec2016-01-01T00:00:00Z2016 Apr2026-07-15T16:33:45.323Z2026-07-07T03:08:24.438ZS-EPMC48265432705989610.1186/s12859-016-1008-7