Structure-based prediction of protein–protein binding affinity with consideration of allosteric effect

A structure-based benchmark for protein-protein binding affinity

(2011) Panagiotis L. Kastritis et al.   PROTEIN SCIENCE

A Systematic Study of the Energetics Involved in Structural Changes upon Association and Connectivity in Protein Interaction Networks

(2011) Amelie Stein et al.   STRUCTURE

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

Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations

(2010) D. J. Cole et al.   EPL

Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark

(2010) Panagiotis L. Kastritis et al.   JOURNAL OF PROTEOME RESEARCH

Calculation of the free energy of association for protein complexes

(2010) Nancy Horton et al.   PROTEIN SCIENCE

Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect

(2010) Chung-Jung Tsai et al.   PROTEIN SCIENCE

Docking and 3D-QSAR studies of influenza neuraminidase inhibitors using three-dimensional holographic vector of atomic interaction field analysis

(2009) Jiaying Sun et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Free energy calculations of glycosaminoglycan–protein interactions

(2009) Neha S Gandhi et al.   GLYCOBIOLOGY

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

Low-Resolution Structures of Transient Protein−Protein Complexes Using Small-Angle X-ray Scattering

(2009) Jascha Blobel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Quantitative prediction of protein-protein binding affinity with a potential of mean force considering volume correction

(2009) Yu Su et al.   PROTEIN SCIENCE

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

In silico quantitative prediction of peptides binding affinity to human MHC molecule: an intuitive quantitative structure–activity relationship approach

(2008) F. Tian et al.   AMINO ACIDS

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

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

Recent Advances in QSAR and Their Applications in Predicting the Activities of Chemical Molecules, Peptides and Proteins for Drug Design

(2008) Qi-Shi Du et al.   CURRENT PROTEIN & PEPTIDE SCIENCE

2D depiction of nonbonding interactions for protein complexes

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

Applying Novel Three-Dimensional Holographic Vector of Atomic Interaction Field to QSAR Studies of Artemisinin Derivatives

(2007) Yanrong Ren et al.   Quantitative structure-activity relationships & combinatorial science