Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules

No abstract is available for this paper.

• Publication year

  2003

• Venue

  Bioinform.

• Publication date

  2003-09-22

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btg247PMID 14512347
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Methods for Prediction of Peptide Binding to MHC Molecules: A Comparative Study

  2002cited by this paper
• Numerical recipes in C

  2002cited by this paper
• Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201.

  2002cited by this paper
• Producing nature's gene-chips: the generation of peptides for display by MHC class I molecules.

  2002cited by this paper
• Structure‐based prediction of binding peptides to MHC class I molecules: Application to a broad range of MHC alleles

  2000cited by this paper
• Relating Amino Acid Sequence to Phenotype: Analysis of Peptide‐Binding Data

  2000influential reference
• An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries

  2000cited by this paper
• Specific and general HLA-DR binding motifs: comparison of algorithms.

  2000cited by this paper
• SYFPEITHI: database for MHC ligands and peptide motifs

  1999cited by this paper
• Consistency in structural energetics of protein folding and peptide recognition

  1997cited by this paper
• Two complementary methods for predicting peptides binding major histocompatibility complex molecules.

  1997cited by this paper
• The use of the area under the ROC curve in the evaluation of machine learning algorithms

  1997cited by this paper
• Application of Genetic Search in Derivation of Matrix Models of Peptide Binding to MHC Molecules

  1997cited by this paper
• Chemistry of peptides associated with MHC class I and class II molecules.

  1995cited by this paper
• Fine tuning of peptide binding to HLA-B*3501 molecules by nonanchor residues.

  1995cited by this paper
• Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains.

  1994influential reference
• Effect of conformational flexibility and solvation on receptor-ligand binding free energies.

  1994cited by this paper
• Precise prediction of major histocompatibility complex class II-peptide interaction based on peptide side chain scanning

  1994cited by this paper
• Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules.

  1993cited by this paper
• Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis.

  1989cited by this paper

• Multimodal learning on heterogeneous subgraphs and LLMs representation for MHC-peptide binding affinity prediction.

  2026cites this paper
• SiaScoreNet: a siamese neural network-based model integrating prediction scores for HLA-peptide interaction prediction

  2025influential citation
• Comparison of different substitution matrices for distance based T-cell receptor epitope predictions using tcrdist3

  2025cites this paper
• ConvNeXt-MHC: improving MHC–peptide affinity prediction by structure-derived degenerate coding and the ConvNeXt model

  2024cites this paper
• Energy landscapes of peptide-MHC binding

  2024influential citation
• Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens

  2023cites this paper
• Peptides of a Feather: How Computation Is Taking Peptide Therapeutics under Its Wing

  2023cites this paper
• State of the art in epitope mapping and opportunities in COVID-19

  2023cites this paper
• Unsupervised Mining of HLA-I Peptidomes Reveals New Binding Motifs and Potential False Positives in the Community Database

  2022cites this paper
• Unsupervised mining of HLA-I peptidomes reveals new binding motifs and substantial false positives in community database

  2021cites this paper
• Development of synthetic antigen vaccines for COVID-19

  2021cites this paper
• Immuno-informatics approach for B-cell and T-cell epitope based peptide vaccine design against novel COVID-19 virus

  2021cites this paper
• Proteasome-Generated cis-Spliced Peptides and Their Potential Role in CD8+ T Cell Tolerance

  2021cites this paper
• Immunoinformatics: Predicting Peptide-MHC Binding.

  2020cites this paper
• MHC-restricted phosphopeptide antigens: preclinical validation and first-in-humans clinical trial in participants with high-risk melanoma

  2020cites this paper
• IConMHC: a deep learning convolutional neural network model to predict peptide and MHC-I binding affinity

  2020cites this paper
• T Cell Epitope Predictions.

  2020influential citation
• The role of immunoinformatics in the development of T-cell peptide-based vaccines against Mycobacterium tuberculosis

  2020cites this paper
• In silico design of influenza a virus artificial epitope-based T-cell antigens and the evaluation of their immunogenicity in mice

  2020cites this paper
• In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives

  2020influential citation
• Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes.

  2019cites this paper
• Computational Immunogenetics

  2019cites this paper
• Peptide Presentation Is the Key to Immunotherapeutical Success

  2018cites this paper
• The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands

  2018cites this paper
• Predicting Antigen Presentation—What Could We Learn From a Million Peptides?

  2018cites this paper
• MAPS: Analyzing Peptide Binding Subsites in Major Histocompatibility Complexes

  2018cites this paper
• Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes

  2018cites this paper
• Whole genome duplications have provided teleosts with many roads to peptide loaded MHC class I molecules

  2018cites this paper
• GradDock: rapid simulation and tailored ranking functions for peptide‐MHC Class I docking

  2018cites this paper
• Artificial Epitope-Based Immunogens in HIV-Vaccine Design

  2018cites this paper
• MHC Informatics to Peptide Vaccine Design

  2018cites this paper
• Artificial Epitope-Based Immunogens in HIV-Vaccine Design

  2018cites this paper
• Current methods for the prediction of T‐cell epitopes

  2018cites this paper
• Fundamentals and Methods for T- and B-Cell Epitope Prediction

  2017cites this paper
• Development of a replication‐deficient adenoviral vector‐based vaccine candidate for the interception of HPV16‐ and HPV18‐induced infections and disease

  2017cites this paper
• A mechanistic model predicting cell surface presentation of peptides by MHC class I proteins, considering peptide competition, viral intracellular kinetics and host genotype factors

  2017cites this paper
• Advances in Therapeutic Cancer Vaccines.

  2016cites this paper
• Repertoire of Classical MHC Class I and Class II Molecules

  2016cites this paper
• Epitope prediction for MSP119 protein in Plasmodium yeolii using computational approaches

  2016cites this paper
• Predicting Peptide-MHC Binding Affinities with Imputed Training Data

  2016cites this paper
• Design and Evaluation of Optimized Artificial HIV-1 Poly-T Cell-Epitope Immunogens

  2015cites this paper
• Immunoinformatics and epitope prediction in the age of genomic medicine

  2015cites this paper
• T Cell Epitopes and Post-Translationally Modified Epitopes in Type 1 Diabetes

  2015cites this paper
• Novel approaches in polyepitope T-cell vaccine development against HIV-1

  2014cites this paper
• Customized Predictions of Peptide–MHC Binding and T-Cell Epitopes Using EPIMHC

  2014cites this paper
• Enzymatic Discovery of a HER-2/neu Epitope That Generates Cross-Reactive T Cells

  2013influential citation
• Identification and Enhancement of HLA-A2.1-Restricted CTL Epitopes in a New Human Cancer Antigen-POTE

  2013cites this paper
• Computational prediction of cleavage using proteasomal in vitro digestion and MHC I ligand data

  2013influential citation
• Integrating peptides' sequence and energy of contact residues information improves prediction of peptide and HLA-I binding with unknown alleles

  2013cites this paper
• A combination of epitope prediction and molecular docking allows for good identification of MHC class I restricted T-cell epitopes

  2013cites this paper
• Computational B cell vaccine design

  2013cites this paper
• Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

  2013cites this paper
• The immune epitope database: a historical retrospective of the first decade

  2012cites this paper
• Interpretable machine learning approaches in computational biology

  2012cites this paper
• Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire

  2012cites this paper
• That Generates Cross-Reactive T Cells Enzymatic Discovery of a HER-2/neu Epitope

  2012influential citation
• Residue analysis of a CTL epitope of SARS-CoV spike protein by IFN-gamma production and bioinformatics prediction

  2012cites this paper
• Immunoglobulin light chain, Blimp‐1 and cytochrome P4501B1 peptides as potential vaccines for AL amyloidosis

  2012cites this paper
• Predicting Binding-Peptide of HLA-I on Unknown Alleles by Integrating Sequence Information and Energies of Contact Residues

  2012cites this paper
• Computational Methods for Investigating Dendritic Cell Biology

  2011cites this paper
• Theoretische Untersuchungen zur MHC I Antigenpräsentation

  2011cites this paper
• Statistical Applications in Genetics and Molecular Biology Prediction of Genomewide Conserved Epitope Profiles of HIV-1 : Classifier Choice and Peptide Representation

  2011cites this paper
• Large-scale characterization of peptide-MHC binding landscapes with structural simulations

  2011cites this paper
• Intra- and Inter-clade Cross-reactivity by HIV-1 Gag Specific T-Cells Reveals Exclusive and Commonly Targeted Regions: Implications for Current Vaccine Trials

  2011cites this paper
• Nonparametric Combinatorial Sequence Models

  2011cites this paper
• Predicting peptide binding to Major Histocompatibility Complex molecules.

  2011cites this paper
• Comparative analysis of epitope predictions: proposed library of putative vaccine candidates for HIV

  2011cites this paper
• Major histocompatibility complex class I binding predictions as a tool in epitope discovery

  2010cites this paper
• Using Gaussian Process with Test Rejection to Detect T-Cell Epitopes in Pathogen Genomes

  2010cites this paper
• Mutation-specific control of BCR-ABL T315I positive leukemia with a recombinant yeast-based therapeutic vaccine in a murine model.

  2010cites this paper
• Immunogenicity Assessment of Antibody Therapeutics

  2010cites this paper
• Effects of thymic selection of the T cell repertoire on HLA-class I associated control of HIV infection

  2010cites this paper
• MHC class I molecules exploit the low G+C content of pathogen genomes for enhanced presentation

  2010cites this paper
• T-Epitope Designer

  2009cites this paper
• Prediction of Peptides Binding to MHC Class I Alleles by Partial Periodic Pattern Mining

  2009cites this paper
• Towards in silico design of epitope-based vaccines

  2009cites this paper
• A Comparative Study of HLA Binding Affinity and Ligand Diversity: Implications for Generating Immunodominant CD8+ T Cell Responses1

  2009influential citation
• An Attempt to Improve the Quantitative Epitope Prediction by Modelling Alternative Binding Modes

  2009cites this paper
• Diverse recognition of conserved orthopoxvirus CD8+ T cell epitopes in vaccinated rhesus macaques.

  2009cites this paper
• Prediction of MHC-peptide binding: a systematic and comprehensive overview.

  2009cites this paper
• An introduction to epitope prediction methods and software

  2009cites this paper
• The shared tumor associated antigen cyclin‐A2 is recognized by high‐avidity T‐cells

  2009cites this paper
• Predicting affinity and specificity of antigenic peptide binding to major histocompatibility class I molecules.

  2009cites this paper
• Evolutionary approaches for predicting MHC peptide binding

  2009cites this paper
• Towardsin silicodesignof epitope-basedvaccines

  2009cites this paper
• Bioinformation Discovery: Data to Knowledge in Biology

  2009cites this paper
• Immune epitope database analysis resource (IEDB-AR)

  2008cites this paper
• Evaluation of knowledge based threading method for the prediction of peptides binding to MHC class I alleles

  2008cites this paper
• Cyclin D1–Specific Cytotoxic T Lymphocytes Are Present in the Repertoire of Cancer Patients: Implications for Cancer Immunotherapy

  2008cites this paper
• Evaluation of MHC class I peptide binding prediction servers: Applications for vaccine research

  2008cites this paper
• Improving peptide-MHC class I binding prediction for unbalanced datasets

  2008cites this paper
• A Hybrid Model for Prediction of Peptide Binding to MHC Molecules

  2008cites this paper
• Flanking p10 contribution and sequence bias in matrix based epitope prediction: revisiting the assumption of independent binding pockets

  2008cites this paper
• Computational discovery of vaccine targets

  2008cites this paper
• Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries

  2008cites this paper
• Prediction of peptide-MHC binding using profiles.

  2007cites this paper
• Immunoinformatics

  2007influential citation
• Structure-based prediction of MHC-peptide association: algorithm comparison and application to cancer vaccine design.

  2007cites this paper
• A detailed comparison of peptides presented by different HLA class I loci: an in silico approach

  2007cites this paper
• Strength in numbers: achieving greater accuracy in MHC-I binding prediction by combining the results from multiple prediction tools

  2007influential citation