PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein–Peptide and Protein–Protein Binding Affinity

Computational Assessment of Protein–Protein Binding Affinity by Reverse Engineering the Energetics in Protein Complexes

(2021) Bo Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Computational modeling and experimental validation of the EPI-X4/CXCR4 complex allows rational design of small peptide antagonists

(2021) Pandian Sokkar et al.   Communications Biology

Antibody-protein binding and conformational changes: identifying allosteric signalling pathways to engineer a better effector response

(2020) Mohammed M. Al Qaraghuli et al.   Scientific Reports

Proteome-wide Prediction of Lysine Methylation Leads to Identification of H2BK43 Methylation and Outlines the Potential Methyllysine Proteome

(2020) Kyle K. Biggar et al.   Cell Reports

Microtiter plate-based antibody-competition assay to determine binding affinities and plasma/blood stability of CXCR4 ligands

(2020) Mirja Harms et al.   Scientific Reports

ISLAND: in-silico proteins binding affinity prediction using sequence information

(2020) Wajid Arshad Abbasi et al.   BioData Mining

An optimized derivative of an endogenous CXCR4 antagonist prevents atopic dermatitis and airway inflammation

(2020) Mirja Harms et al.   Acta Pharmaceutica Sinica B

PPI-Detect: A support vector machine model for sequence-based prediction of protein-protein interactions

(2019) Sandra Romero-Molina et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery

(2019) Xin Yang et al.   CHEMICAL REVIEWS

ProtDCal‐Suite: A web server for the numerical codification and functional analysis of proteins

(2019) Sandra Romero‐Molina et al.   PROTEIN SCIENCE

SSIPe: accurately estimating protein–protein binding affinity change upon mutations using evolutionary profiles in combination with an optimized physical energy function

(2019) Xiaoqiang Huang et al.   BIOINFORMATICS

Selecting training sets for support vector machines: a review

(2018) Jakub Nalepa et al.   ARTIFICIAL INTELLIGENCE REVIEW

SKEMPI 2.0: An updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation

(2018) Justina Jankauskaitė et al.   BIOINFORMATICS

Structure-based design for binding peptides in anti-cancer therapy

(2018) Sheng-Hung Wang et al.   BIOMATERIALS

Therapeutic peptides: Historical perspectives, current development trends, and future directions

(2018) Jolene L. Lau et al.   BIOORGANIC & MEDICINAL CHEMISTRY

KDEEP: Protein–Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

(2018) José Jiménez et al.   Journal of Chemical Information and Modeling

Learning protein binding affinity using privileged information

(2018) Wajid Arshad Abbasi et al.   BMC BIOINFORMATICS

Influence of Varying Training Set Composition and Size on Support Vector Machine-Based Prediction of Active Compounds

(2017) Raquel Rodríguez-Pérez et al.   Journal of Chemical Information and Modeling

NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data

(2017) Vanessa Jurtz et al.   JOURNAL OF IMMUNOLOGY

The Current State of Peptide Drug Discovery: Back to the Future?

(2017) Antoine Henninot et al.   JOURNAL OF MEDICINAL CHEMISTRY

Systematic Identification of Machine-Learning Models Aimed to Classify Critical Residues for Protein Function from Protein Structure

(2017) Ricardo Corral-Corral et al.   MOLECULES

Novel “extended sequons” of human N-glycosylation sites improve the precision of qualitative predictions: an alignment-free study of pattern recognition using ProtDCal protein features

(2016) Yasser B. Ruiz-Blanco et al.   AMINO ACIDS

PRODIGY: a web server for predicting the binding affinity of protein–protein complexes

(2016) Li C. Xue et al.   BIOINFORMATICS

First Multitarget Chemo-Bioinformatic Model To Enable the Discovery of Antibacterial Peptides against Multiple Gram-Positive Pathogens

(2016) Alejandro Speck-Planche et al.   Journal of Chemical Information and Modeling

Enabling the Discovery and Virtual Screening of Potent and Safe Antimicrobial Peptides. Simultaneous Prediction of Antibacterial Activity and Cytotoxicity

(2016) Valeria V. Kleandrova et al.   ACS Combinatorial Science

ProtDCal: A program to compute general-purpose-numerical descriptors for sequences and 3D-structures of proteins

(2015) Yasser B Ruiz-Blanco et al.   BMC BIOINFORMATICS

The Relative Importance of Domain Applicability Metrics for Estimating Prediction Errors in QSAR Varies with Training Set Diversity

(2015) Robert P. Sheridan   Journal of Chemical Information and Modeling

Discovery and Characterization of an Endogenous CXCR4 Antagonist

(2015) Onofrio Zirafi et al.   Cell Reports

Contacts-based prediction of binding affinity in protein–protein complexes

(2015) Anna Vangone et al.   eLife

Diversity and Inter-Connections in the CXCR4 Chemokine Receptor/Ligand Family: Molecular Perspectives

(2015) Lukas Pawig et al.   Frontiers in Immunology

Constraining Cyclic Peptides To Mimic Protein Structure Motifs

(2014) Timothy A. Hill et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Protein–protein binding affinity prediction from amino acid sequence

(2014) K. Yugandhar et al.   BIOINFORMATICS

Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface

(2014) Panagiotis L. Kastritis et al.   JOURNAL OF MOLECULAR BIOLOGY

Improving ranking of models for protein complexes with side chain modeling and atomic potentials

(2013) Shruthi Viswanath et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

(2012) Jianyi Yang et al.   NUCLEIC ACIDS RESEARCH

Protein–protein binding affinity prediction on a diverse set of structures

(2011) Iain H. Moal et al.   BIOINFORMATICS

Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein−Protein Docking

(2011) Carles Pons et al.   Journal of Chemical Information and Modeling

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

(2010) Pedro J. Ballester et al.   BIOINFORMATICS

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

Calculation of the free energy of association for protein complexes

(2010) Nancy Horton et al.   PROTEIN SCIENCE

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

(2009) Yu Su et al.   PROTEIN SCIENCE

PIE—Efficient filters and coarse grained potentials for unbound protein–protein docking

(2009) D. V. S. Ravikant et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Small Molecule Protein–Protein Interaction Inhibitors as CNS Therapeutic Agents: Current Progress and Future Hurdles

(2008) Levi L Blazer et al.   NEUROPSYCHOPHARMACOLOGY

A combination of rescoring and refinement significantly improves protein docking performance

(2008) Brian Pierce et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Consensus scoring for enriching near-native structures from protein-protein docking decoys

(2008) Shide Liang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS