Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia
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July 2014 |
Tumor neoantigens: building a framework for personalized cancer immunotherapy
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August 2015 |
Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer
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July 2017 |
An immunogenic personal neoantigen vaccine for patients with melanoma
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July 2017 |
The Role of Neoantigens in Cancer Immunotherapy
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August 2021 |
Personal Neoantigen Cancer Vaccines: A Road Not Fully Paved
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December 2020 |
An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection
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February 2021 |
Mass spectrometry–driven exploration reveals nuances of neoepitope-driven tumor rejection
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July 2019 |
NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data
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October 2017 |
Predicting MHC-peptide binding affinity by differential boundary tree
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July 2021 |
Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction
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December 2017 |
DeepSeqPan, a novel deep convolutional neural network model for pan-specific class I HLA-peptide binding affinity prediction
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January 2019 |
Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting
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February 2021 |
Structural dissimilarity from self drives neoepitope escape from immune tolerance
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August 2020 |
Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity
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September 2014 |
Hepatitis C virus-cross-reactive TCR gene-modified T cells: a model for immunotherapy against diseases with genomic instability
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February 2016 |
T cell receptor cross-reactivity expanded by dramatic peptide–MHC adaptability
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September 2018 |
Improving T Cell Receptor On-Target Specificity via Structure-Guided Design
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February 2019 |
Structure Based Prediction of Neoantigen Immunogenicity
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August 2019 |
Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy
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October 2017 |
Characterization of CD8 + T-cell responses to non-anchor-type HLA class I neoantigens with single amino-acid substitutions
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January 2021 |
APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations
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March 2019 |
Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens
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November 2020 |
HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy
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September 2020 |
DockTope: a Web-based tool for automated pMHC-I modelling
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December 2015 |
Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests
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July 2020 |
GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking
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September 2017 |
General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept
- Antunes, Dinler A.; Devaurs, Didier; Moll, Mark
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BCB '18: 9th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics
https://doi.org/10.1145/3233547.3233719
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conference
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August 2018 |
Accurate prediction of protein structures and interactions using a three-track neural network
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journal
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July 2021 |
Highly accurate protein structure prediction with AlphaFold
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journal
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July 2021 |
Systematic Comparison of Amber and Rosetta Energy Functions for Protein Structure Evaluation
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journal
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September 2018 |
Ranking predicted protein structures with support vector regression
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journal
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November 2007 |
Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening: Machine-learning SFs to improve structure-based binding affinity prediction and virtual screening
- Ain, Qurrat Ul; Aleksandrova, Antoniya; Roessler, Florian D.
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Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 5, Issue 6
https://doi.org/10.1002/wcms.1225
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August 2015 |
Four Small Puzzles That Rosetta Doesn't Solve
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May 2011 |
Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy
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October 2020 |
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences
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journal
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November 2020 |
Features and development of Coot
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March 2010 |
Structures of MART-126/27–35 Peptide/HLA-A2 Complexes Reveal a Remarkable Disconnect between Antigen Structural Homology and T Cell Recognition
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October 2007 |
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
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January 2010 |
Practically Useful: What the R osetta Protein Modeling Suite Can Do for You
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April 2010 |
Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta
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January 2015 |
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
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May 2017 |
Loss of T Cell Antigen Recognition Arising from Changes in Peptide and Major Histocompatibility Complex Protein Flexibility: IMPLICATIONS FOR VACCINE DESIGN
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September 2011 |
Progress and challenges in high-resolution refinement of protein structure models
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February 2005 |
Two Different T Cell Receptors use Different Thermodynamic Strategies to Recognize the Same Peptide/MHC Ligand
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February 2005 |
[20] Processing of X-ray diffraction data collected in oscillation mode
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January 1997 |
Towards automated crystallographic structure refinement with phenix.refine
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March 2012 |
Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics
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January 2011 |
MolProbity : all-atom structure validation for macromolecular crystallography
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December 2009 |
A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations
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January 2018 |
Peptide-Binding Groove Contraction Linked to the Lack of T Cell Response: Using Complex Structure and Energy To Identify Neoantigens
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August 2018 |
Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes
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November 1998 |
Modeling the structure of bound peptide ligands to major histocompatibility complex
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September 2004 |
Sub-angstrom modeling of complexes between flexible peptides and globular proteins
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January 2010 |
Computing the Structure of Bound Peptides
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December 1993 |
Free energy mapping of class I MHC molecules and structural determination of bound peptides
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July 1996 |
Predicting Binding Affinities of Protein Ligands from Three-Dimensional Models: Application to Peptide Binding to Class I Major Histocompatibility Proteins
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November 1999 |
Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens
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November 2013 |
Structural Prediction of Peptides Bound to MHC Class I
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February 2006 |
DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations
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July 2006 |
Improvements to Robotics-Inspired Conformational Sampling in Rosetta
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May 2013 |
Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules
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May 1991 |
When the Lowest Energy Does Not Induce Native Structures: Parallel Minimization of Multi-Energy Values by Hybridizing Searching Intelligences
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September 2012 |
A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming
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October 2007 |
What is a support vector machine?
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December 2006 |
Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models
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March 2006 |
A Molecular Switch Abrogates Glycoprotein 100 (gp100) T-cell Receptor (TCR) Targeting of a Human Melanoma Antigen
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April 2016 |
An in silico—in vitro Pipeline Identifying an HLA-A*02:01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients
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journal
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November 2019 |
Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen
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journal
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June 2020 |
The presentation of SARS-CoV-2 peptides by the common HLA-A∗02:01 molecule
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journal
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February 2021 |
Targeting of cancer neoantigens with donor-derived T cell receptor repertoires
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journal
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May 2016 |
Conversion of a T Cell Antagonist into an Agonist by Repairing a Defect in the TCR/Peptide/MHC Interface
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journal
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October 2000 |
Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner
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January 2021 |
Molecular dynamics simulations of macromolecular crystals
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journal
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November 2018 |
The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands
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journal
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November 2018 |
Gapped sequence alignment using artificial neural networks: application to the MHC class I system
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journal
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October 2015 |