Surfing the Protein-Protein Interaction Surface Using Docking Methods: Application to the Design of PPI Inhibitors

Alternative modulation of protein–protein interactions by small molecules

(2015) Gerhard Fischer et al.   CURRENT OPINION IN BIOTECHNOLOGY

Computational and biophysical approaches to protein–protein interaction inhibition of Plasmodium falciparum AMA1/RON2 complex

(2015) Emilie Pihan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Recent advances in virtual screening for drug discovery

(2015) Chung-Hang Leung et al.   METHODS

Flexibility and small pockets at protein–protein interfaces: New insights into druggability

(2015) Harry Jubb et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

In silico design of low molecular weight protein–protein interaction inhibitors: Overall concept and recent advances

(2015) Mélaine A. Kuenemann et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Protein models docking benchmark 2

(2015) Ivan Anishchenko et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Comparison of weak affinity chromatography and surface plasmon resonance in determining affinity of small molecules

(2014) Minh-Dao Duong-Thi et al.   ANALYTICAL BIOCHEMISTRY

CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts

(2014) E. Chermak et al.   BIOINFORMATICS

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

Scoring docking conformations using predicted protein interfaces

(2014) Reyhaneh Esmaielbeiki et al.   BMC BIOINFORMATICS

Novel Peptidomimetics for Inhibition of HER2:HER3 Heterodimerization in HER2-Positive Breast Cancer

(2014) Shanthi Kanthala et al.   Chemical Biology & Drug Design

Chemokine Receptor CCR5 Antagonist Maraviroc: Medicinal Chemistry and Clinical Applications

(2014) Guoyan Xu et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Udock, the interactive docking entertainment system

(2014) Guillaume Levieux et al.   FARADAY DISCUSSIONS

Challenges and opportunities in targeting the menin–MLL interaction

(2014) Tomasz Cierpicki et al.   Future Medicinal Chemistry

Structure-based design of small-molecule protein–protein interaction modulators: the story so far

(2014) Federico Falchi et al.   Future Medicinal Chemistry

HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein–Protein Interaction Inhibitors

(2014) Panagiotis L. Kastritis et al.   Journal of Chemical Information and Modeling

Combining Ligand- and Structure-Based Approaches for the Discovery of New Inhibitors of the EPHA2–ephrin-A1 Interaction

(2014) Daniele Pala et al.   Journal of Chemical Information and Modeling

Structure-Guided Design and Optimization of Small Molecules Targeting the Protein–Protein Interaction between the von Hippel–Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities

(2014) Carles Galdeano et al.   JOURNAL OF MEDICINAL CHEMISTRY

Small-Molecule Inhibitors of the MDM2–p53 Protein–Protein Interaction (MDM2 Inhibitors) in Clinical Trials for Cancer Treatment

(2014) Yujun Zhao et al.   JOURNAL OF MEDICINAL CHEMISTRY

Identification of an Atg8-Atg3 Protein–Protein Interaction Inhibitor from the Medicines for Malaria Venture Malaria Box Active in Blood and Liver Stage Plasmodium falciparum Parasites

(2014) Adelaide U.P. Hain et al.   JOURNAL OF MEDICINAL CHEMISTRY

Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design

(2014) Sam Grinter et al.   MOLECULES

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

PredHS: a web server for predicting protein–protein interaction hot spots by using structural neighborhood properties

(2014) Lei Deng et al.   NUCLEIC ACIDS RESEARCH

Targeting Protein-Protein Interaction by Small Molecules

(2013) Lingyan Jin et al.   Annual Review of Pharmacology and Toxicology

Specificity and affinity quantification of protein-protein interactions

(2013) Z. Yan et al.   BIOINFORMATICS

SwarmDock: a server for flexible protein–protein docking

(2013) Mieczyslaw Torchala et al.   BIOINFORMATICS

pyDockWEB: a web server for rigid-body protein–protein docking using electrostatics and desolvation scoring

(2013) Brian Jiménez-García et al.   BIOINFORMATICS

Small-molecule inhibition of the uPAR·uPA interaction: Synthesis, biochemical, cellular, in vivo pharmacokinetics and efficacy studies in breast cancer metastasis

(2013) Timmy Mani et al.   BIOORGANIC & MEDICINAL CHEMISTRY

Structure-activity relationships of peptidomimetics that inhibit PPI of HER2-HER3

(2013) Shanthi Kanthala et al.   BIOPOLYMERS

Immunosuppression by Co-stimulatory Molecules: Inhibition of CD2-CD48/CD58 Interaction by Peptides from CD2 to Suppress Progression of Collagen-induced Arthritis in Mice

(2013) Ameya Gokhale et al.   Chemical Biology & Drug Design

Protein–protein interaction networks: the puzzling riches

(2013) Shoshana J Wodak et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

From Protein-Protein Interactions to Rational Drug Design: Are Computational Methods Up to the Challenge?

(2013) Edgar D. Coelho et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Novel toll-like receptor 4 (TLR4) antagonists identified by structure- and ligand-based virtual screening

(2013) Urban Švajger et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Design, synthesis and characterization of peptidomimetic conjugate of BODIPY targeting HER2 protein extracellular domain

(2013) Sashikanth Banappagari et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Recent applications of isotopic labeling for protein NMR in drug discovery

(2013) Hidekazu Hiroaki   Expert Opinion on Drug Discovery

Structural Basis and Targeting of the Interaction between Fibroblast Growth Factor-inducible 14 and Tumor Necrosis Factor-like Weak Inducer of Apoptosis

(2013) Harshil Dhruv et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Characterization and Structure of the Vaccinia Virus NF-κB Antagonist A46

(2013) Sofiya Fedosyuk et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DOT2: Macromolecular docking with improved biophysical models

(2013) Victoria A. Roberts et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

iPfam: a database of protein family and domain interactions found in the Protein Data Bank

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

(2013) Sandra Orchard et al.   NUCLEIC ACIDS RESEARCH

KBDOCK 2013: a spatial classification of 3D protein domain family interactions

(2013) Anisah W. Ghoorah et al.   NUCLEIC ACIDS RESEARCH

3did: a catalog of domain-based interactions of known three-dimensional structure

(2013) Roberto Mosca et al.   NUCLEIC ACIDS RESEARCH

Protein-protein interactions: General trends in the relationship between binding affinity and interfacial buried surface area

(2013) Jieming Chen et al.   PROTEIN SCIENCE

How good is automated protein docking?

(2013) Dima Kozakov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Design, synthesis and evaluation of N6-substituted 2-aminoadenosine-5′-N-methylcarboxamides as A3 adenosine receptor agonists

(2013) Shane M. Devine et al.   MedChemComm

Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein–Protein Interactions?

(2013) David M. Dias et al.   ACS Medicinal Chemistry Letters

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information

(2013) Anne Lopes et al.   PLoS Computational Biology

Small-Molecule Stabilization of Protein-Protein Interactions: An Underestimated Concept in Drug Discovery?

(2012) Philipp Thiel et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Cell-Dock: high-performance protein–protein docking

(2012) Carles Pons et al.   BIOINFORMATICS

Computational Prediction of Protein Hot Spot Residues

(2012) John Kenneth Morrow et al.   CURRENT PHARMACEUTICAL DESIGN

Identification of a Small Molecule That Modulates Platelet Glycoprotein Ib-von Willebrand Factor Interaction

(2012) Katleen Broos et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Conformationally Constrained Peptidomimetic Binds to the Extracellular Region of HER2 Protein

(2012) Sashikanth Banappagari et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Inhibition of protein–protein interaction of HER2–EGFR and HER2–HER3 by a rationally designed peptidomimetic

(2012) Sashikanth Banappagari et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Docking and scoring with ICM: the benchmarking results and strategies for improvement

(2012) Marco A. C. Neves et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Structural characterization and inhibition of the Plasmodium Atg8–Atg3 interaction

(2012) Adelaide U.P. Hain et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software

(2012) Michael Forster et al.   NUCLEIC ACIDS RESEARCH

2P2Idb: a structural database dedicated to orthosteric modulation of protein–protein interactions

(2012) Marie Jeanne Basse et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Multicomponent Synthesis of Diverse 1,4-Benzodiazepine Scaffolds

(2012) Yijun Huang et al.   ORGANIC LETTERS

ATTRACT-EM: A New Method for the Computational Assembly of Large Molecular Machines Using Cryo-EM Maps

(2012) Sjoerd J. de Vries et al.   PLoS One

Structural biology and drug discovery for protein–protein interactions

(2012) Harry Jubb et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Antithrombotic drug candidate ALX-0081 shows superior preclinical efficacy and safety compared with currently marketed antiplatelet drugs

(2011) H. Ulrichts et al.   BLOOD

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Minimalist and universal peptidomimetics

(2011) Eunhwa Ko et al.   CHEMICAL SOCIETY REVIEWS

Context-Based Identification of Protein-Protein Interfaces and “Hot-Spot” Residues

(2011) Tim Geppert et al.   CHEMISTRY & BIOLOGY

Chemical and structural lessons from recent successes in protein–protein interaction inhibition (2P2I)

(2011) Xavier Morelli et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Modulators of Protein-Protein Interactions – Novel Approaches in Targeting Protein Kinases and Other Pharmaceutically Relevant Biomolecules

(2011) Rechfeld Florian et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Medicinal chemistry for 2020

(2011) Seetharama D Satyanarayanajois et al.   Future Medicinal Chemistry

Conformationally Constrained Peptides from CD2 To Modulate Protein–Protein Interactions between CD2 and CD58

(2011) Ameya Gokhale et al.   JOURNAL OF MEDICINAL CHEMISTRY

Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology

(2011) Sarel J. Fleishman et al.   JOURNAL OF MOLECULAR BIOLOGY

MarkUs: a server to navigate sequence-structure-function space

(2011) M. Fischer et al.   NUCLEIC ACIDS RESEARCH

PRUNE and PROBE--two modular web services for protein-protein docking

(2011) P. Mitra et al.   NUCLEIC ACIDS RESEARCH

Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

(2011) Nir London et al.   NUCLEIC ACIDS RESEARCH

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins

(2011) B. A. Shoemaker et al.   NUCLEIC ACIDS RESEARCH

Predictions of Hot Spot Residues at Protein-Protein Interfaces Using Support Vector Machines

(2011) Stefano Lise et al.   PLoS One

Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library

(2011) Brian G. Pierce et al.   PLoS One

Binding ofPlasmodiummerozoite proteins RON2 and AMA1 triggers commitment to invasion

(2011) Prakash Srinivasan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrating atom-based and residue-based scoring functions for protein-protein docking

(2011) Thom Vreven et al.   PROTEIN SCIENCE

KFC2: A knowledge-based hot spot prediction method based on interface solvation, atomic density, and plasticity features

(2011) Xiaolei Zhu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

An overview of human protein databases and their application to functional proteomics in health and disease

(2011) YanQiong Zhang et al.   Science China-Life Sciences

Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination

(2011) Srayanta Mukherjee et al.   STRUCTURE

Structure–activity relationship of conformationally constrained peptidomimetics for antiproliferative activity in HER2-overexpressing breast cancer cell lines

(2011) Sashikanth Banappagari et al.   MedChemComm

Exploring NMR ensembles of calcium binding proteins: Perspectives to design inhibitors of protein-protein interactions

(2011) Adriana Isvoran et al.   BMC STRUCTURAL BIOLOGY

FILTREST3D: discrimination of structural models using restraints from experimental data

(2010) Michal J. Gajda et al.   BIOINFORMATICS

Ultra-fast FFT protein docking on graphics processors

(2010) David W. Ritchie et al.   BIOINFORMATICS

A Peptide from the Beta-strand Region of CD2 Protein that Inhibits Cell Adhesion and Suppresses Arthritis in a Mouse Model

(2010) Seetharama D. Satyanarayanajois et al.   Chemical Biology & Drug Design

Discovery of Modulators of Protein-Protein Interactions: Current Approaches and Limitations

(2010) Lidio M.C. Meireles et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Small-molecule protein-protein interaction inhibitors: Therapeutic potential in light of molecular size, chemical space, and ligand binding efficiency considerations

(2010) Peter Buchwald   IUBMB LIFE

Design of Potent Inhibitors of Human RAD51 Recombinase Based on BRC Motifs of BRCA2 Protein: Modeling and Experimental Validation of a Chimera Peptide

(2010) Julian Nomme et al.   JOURNAL OF MEDICINAL CHEMISTRY

Structure of the Complex between HER2 and an Antibody Paratope Formed by Side Chains from Tryptophan and Serine

(2010) Robert D. Fisher et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Virtual screening: an endless staircase?

(2010) Gisbert Schneider   NATURE REVIEWS DRUG DISCOVERY

DIMA 3.0: Domain Interaction Map

(2010) Q. Luo et al.   NUCLEIC ACIDS RESEARCH

3did: identification and classification of domain-based interactions of known three-dimensional structure

(2010) A. Stein et al.   NUCLEIC ACIDS RESEARCH

FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking

(2010) E. Mashiach et al.   NUCLEIC ACIDS RESEARCH

HotPoint: hot spot prediction server for protein interfaces

(2010) N. Tuncbag et al.   NUCLEIC ACIDS RESEARCH

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

(2010) D. Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Presaging Critical Residues in Protein interfaces-Web Server (PCRPi-W): A Web Server to Chart Hot Spots in Protein Interfaces

(2010) Joan Segura Mora et al.   PLoS One

Protein interface conservation across structure space

(2010) Q. C. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The β-d-Glucose Scaffold as a β-Turn Mimetic

(2009) Ralph F. Hirschmann et al.   ACCOUNTS OF CHEMICAL RESEARCH

FRODOCK: a new approach for fast rotational protein–protein docking

(2009) José Ignacio Garzon et al.   BIOINFORMATICS

Fragment-based identification of druggable ‘hot spots’ of proteins using Fourier domain correlation techniques

(2009) Ryan Brenke et al.   BIOINFORMATICS

Protein-protein docking using region-based 3D Zernike descriptors

(2009) Vishwesh Venkatraman et al.   BMC BIOINFORMATICS

Synthetic Inhibitors of Extended Helix-Protein Interactions Based on a Biphenyl 4,4′-Dicarboxamide Scaffold

(2009) Johanna M. Rodriguez et al.   CHEMBIOCHEM

Design, Synthesis, and Docking Studies of Peptidomimetics Based on HER2-Herceptin Binding Site with Potential Antiproliferative Activity Against Breast Cancer Cell lines

(2009) Seetharama Satyanarayanajois et al.   Chemical Biology & Drug Design

Inhibition of protein–protein interactions using designed molecules

(2009) Andrew J. Wilson   CHEMICAL SOCIETY REVIEWS

Rationalizing the chemical space of protein–protein interaction inhibitors

(2009) Olivier Sperandio et al.   DRUG DISCOVERY TODAY

$F^2$Dock: Fast Fourier Protein-Protein Docking

(2009) C L Bajaj et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Lipid G Protein-coupled Receptor Ligand Identification Using β-Arrestin PathHunter™ Assay

(2009) Hong Yin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Discovery of Small Molecule Inhibitors of Protein−Protein Interactions Using Combined Ligand and Target Score Normalization

(2009) Fergal P. Casey et al.   Journal of Chemical Information and Modeling

Empirical Scoring Functions for Advanced Protein−Ligand Docking with PLANTS

(2009) Oliver Korb et al.   Journal of Chemical Information and Modeling

Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

(2009) Jason B. Cross et al.   Journal of Chemical Information and Modeling

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Design of β-Hairpin Peptides for Modulation of Cell Adhesion by β-Turn Constraint

(2009) Sumana Giddu et al.   JOURNAL OF MEDICINAL CHEMISTRY

Stabilizers of the Max Homodimer Identified in Virtual Ligand Screening Inhibit Myc Function

(2009) H. Jiang et al.   MOLECULAR PHARMACOLOGY

Genetic variants at CD28, PRDM1 and CD2/CD58 are associated with rheumatoid arthritis risk

(2009) Soumya Raychaudhuri et al.   NATURE GENETICS

Inferred Biomolecular Interaction Server—a web server to analyze and predict protein interacting partners and binding sites

(2009) Benjamin A. Shoemaker et al.   NUCLEIC ACIDS RESEARCH

Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments

(2009) Roberto Mosca et al.   PLoS Computational Biology

Structure-Based View of Epidermal Growth Factor Receptor Regulation

(2008) Kathryn M. Ferguson   Annual Review of Biophysics

FunHunt: model selection based on energy landscape characteristics

(2008) Nir London et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

α-Helix mimetics as inhibitors of protein–protein interactions

(2008) Ishu Saraogi et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

3D-Garden: a system for modelling protein–protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm

(2008) Victor I. Lesk et al.   BIOINFORMATICS

Small molecular weight protein–protein interaction antagonists—an insurmountable challenge?

(2008) Alexander Dömling   CURRENT OPINION IN CHEMICAL BIOLOGY

Editorial [Hot topic: Cell Adhesion Molecules: Structure, Function, Drug Design, and Biomaterials (Executive Editor: Seetharama D. Satyanarayanajois)]

(2008) Seetharama Satyanarayanajois   CURRENT PHARMACEUTICAL DESIGN

Drug-Like Inhibitors of Protein-Protein Interactions: A Structural Examination of Effective Protein Mimicry

(2008) D. Fry   CURRENT PROTEIN & PEPTIDE SCIENCE

Predicting druggable binding sites at the protein–protein interface

(2008) Jonathan C. Fuller et al.   DRUG DISCOVERY TODAY

Lead generation: reality check on commonly held views

(2008) Nader Fotouhi et al.   Expert Opinion on Drug Discovery

The RosettaDock server for local protein-protein docking

(2008) S. Lyskov et al.   NUCLEIC ACIDS RESEARCH

FireDock: a web server for fast interaction refinement in molecular docking

(2008) E. Mashiach et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

PIPs: human protein-protein interaction prediction database

(2008) M. D. McDowall et al.   NUCLEIC ACIDS RESEARCH

Rhoptry neck protein RON2 forms a complex with microneme protein AMA1 in Plasmodium falciparum merozoites

(2008) Jun Cao et al.   PARASITOLOGY INTERNATIONAL

Estimating the size of the human interactome

(2008) M. P. H. Stumpf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The humanized anti-glycoprotein Ib monoclonal antibody h6B4-Fab is a potent and safe antithrombotic in a high shear arterial thrombosis model in baboons

(2008) Alexandre Fontayne et al.   THROMBOSIS AND HAEMOSTASIS

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

(2007) N Moitessier et al.   BRITISH JOURNAL OF PHARMACOLOGY