A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction
Human leukocyte antigen class I (HLA-I) molecules are encoded by major histocompatibility
complex (MHC) class I loci in humans. The binding and interaction between HLA-I …
complex (MHC) class I loci in humans. The binding and interaction between HLA-I …
MHC class II epitope predictive algorithms
Major histocompatibility complex class II (MHC‐II) molecules sample peptides from the
extracellular space, allowing the immune system to detect the presence of foreign microbes …
extracellular space, allowing the immune system to detect the presence of foreign microbes …
Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions
Peptide–protein interactions are among the most prevalent and important interactions in the
cell, but a large fraction of those interactions lack detailed structural characterization. The …
cell, but a large fraction of those interactions lack detailed structural characterization. The …
[HTML][HTML] NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence
Background Binding of peptides to Major Histocompatibility Complex (MHC) molecules is
the single most selective step in the recognition of pathogens by the cellular immune system …
the single most selective step in the recognition of pathogens by the cellular immune system …
Sub‐angstrom modeling of complexes between flexible peptides and globular proteins
A wide range of regulatory processes in the cell are mediated by flexible peptides that fold
upon binding to globular proteins. Computational efforts to model these interactions are …
upon binding to globular proteins. Computational efforts to model these interactions are …
Improved docking of polypeptides with Glide
I Tubert-Brohman, W Sherman… - Journal of chemical …, 2013 - ACS Publications
Predicting the binding mode of flexible polypeptides to proteins is an important task that falls
outside the domain of applicability of most small molecule and protein–protein docking tools …
outside the domain of applicability of most small molecule and protein–protein docking tools …
[HTML][HTML] Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking
Protein–peptide interactions play essential functional roles in living organisms and their
structural characterization is a hot subject of current experimental and theoretical research …
structural characterization is a hot subject of current experimental and theoretical research …
[HTML][HTML] A unified conformational selection and induced fit approach to protein-peptide docking
Protein-peptide interactions are vital for the cell. They mediate, inhibit or serve as structural
components in nearly 40% of all macromolecular interactions, and are often associated with …
components in nearly 40% of all macromolecular interactions, and are often associated with …
An ID2-dependent mechanism for VHL inactivation in cancer
Mechanisms that maintain cancer stem cells are crucial to tumour progression. The ID2
protein supports cancer hallmarks including the cancer stem cell state. HIFα transcription …
protein supports cancer hallmarks including the cancer stem cell state. HIFα transcription …
DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility
I Antes - Proteins: Structure, Function, and Bioinformatics, 2010 - Wiley Online Library
Molecular docking programs play an important role in drug development and many well‐
established methods exist. However, there are two situations for which the performance of …
established methods exist. However, there are two situations for which the performance of …