Characterization of PDZ domain–peptide interactions using an integrated protocol of QM/MM, PB/SA, and CFEA analyses

Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses

(2010) Feifei Tian et al.   AMINO ACIDS

Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor

(2010) Kshatresh Dutta Dubey et al.   JOURNAL OF BIOLOGICAL PHYSICS

A physical model for PDZ-domain/peptide interactions

(2010) Kristian Kaufmann et al.   JOURNAL OF MOLECULAR MODELING

Gaussian process: an alternative approach for QSAM modeling of peptides

(2009) Peng Zhou et al.   AMINO ACIDS

QM/MM Study of Epitope Peptides Binding to HLA-A*0201: The Roles of Anchor Residues and Water

(2009) Yuanchao Li et al.   Chemical Biology & Drug Design

Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach

(2009) Marius Retegan et al.   Journal of Chemical Information and Modeling

Fluorine Bonding — How Does It Work In Protein−Ligand Interactions?

(2009) Peng Zhou et al.   Journal of Chemical Information and Modeling

Comprehensive comparison of eight statistical modelling methods used in quantitative structure–retention relationship studies for liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome

(2009) Peng Zhou et al.   JOURNAL OF CHROMATOGRAPHY A

Improved prediction of protein side-chain conformations with SCWRL4

(2009) Georgii G. Krivov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-Peptide Interactions Adopt the Same Structural Motifs as Monomeric Protein Folds

(2009) Peter Vanhee et al.   STRUCTURE

Modeling and prediction of binding affinities between the human amphiphysin SH3 domain and its peptide ligands using genetic algorithm-Gaussian processes

(2008) Peng Zhou et al.   BIOPOLYMERS

Peptide-mediated interactions in biological systems: new discoveries and applications

(2008) Evangelia Petsalaki et al.   CURRENT OPINION IN BIOTECHNOLOGY

2D depiction of nonbonding interactions for protein complexes

(2008) Peng Zhou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Characterization of Domain–Peptide Interaction Interface: A Case Study on the Amphiphysin-1 SH3 Domain

(2008) Tingjun Hou et al.   JOURNAL OF MOLECULAR BIOLOGY

Atoms-in-Molecules Dual Parameter Analysis of Weak to Strong Interactions: Behaviors of Electronic Energy Densities versus Laplacian of Electron Densities at Bond Critical Points

(2008) Waro Nakanishi et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Predicting PDZ domain–peptide interactions from primary sequences

(2008) Jiunn R Chen et al.   NATURE BIOTECHNOLOGY

Side chain substitution benchmark for peptide/MHC interaction

(2008) Bernhard Knapp et al.   PROTEIN SCIENCE

Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins

(2008) Peng Zhou et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Specificity Map for the PDZ Domain Family

(2008) Raffi Tonikian et al.   PLOS BIOLOGY