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

Molecular mechanics and dynamics: numerical tools to sample the configuration space

(2014) Matteo Masetti   Frontiers in Bioscience-Landmark

Protein–protein interactions as druggable targets: recent technological advances

(2013) Alicia P Higueruelo et al.   CURRENT OPINION IN PHARMACOLOGY

DOT2: Macromolecular docking with improved biophysical models

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

BH3 Mimetics: Status of the Field and New Developments

(2013) C. Billard   MOLECULAR CANCER THERAPEUTICS

Small-molecule inhibitor starting points learned from protein–protein interaction inhibitor structure

(2012) David Ryan Koes et al.   BIOINFORMATICS

Searching for the Holy Grail; protein–protein interaction analysis and modulation

(2012) Xavier Morelli et al.   EMBO REPORTS

Features of protein–protein interactions that translate into potent inhibitors: topology, surface area and affinity

(2012) Matthew C. Smith et al.   EXPERT REVIEWS IN MOLECULAR MEDICINE

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

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

How Good Are State-of-the-Art Docking Tools in Predicting Ligand Binding Modes in Protein–Protein Interfaces?

(2012) Dennis M. Krüger et al.   Journal of Chemical Information and Modeling

ZINC: A Free Tool to Discover Chemistry for Biology

(2012) John J. Irwin et al.   Journal of Chemical Information and Modeling

Protein–protein interaction inhibitors get into the groove

(2012) Asher Mullard   NATURE REVIEWS DRUG DISCOVERY

PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure

(2012) D. R. Koes et al.   NUCLEIC ACIDS RESEARCH

Enabling Large-Scale Design, Synthesis and Validation of Small Molecule Protein-Protein Antagonists

(2012) David Koes et al.   PLoS One

Targeting Multiple Conformations Leads to Small Molecule Inhibitors of the uPAR·uPA Protein–Protein Interaction That Block Cancer Cell Invasion

(2011) May Khanna et al.   ACS Chemical Biology

Immunosuppressive Small Molecule Discovered by Structure-Based Virtual Screening for Inhibitors of Protein-Protein Interactions

(2011) Tim Geppert et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Computational techniques are valuable tools for the discovery of protein–protein interaction inhibitors: The 14-3-3σ case

(2011) Valentina Corradi et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins

(2011) Daniel B Roche et al.   BMC BIOINFORMATICS

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

(2011) Tim Geppert et al.   CHEMISTRY & BIOLOGY

Pharmacophore Modelling: A Forty Year Old Approach and its Modern Synergies

(2011) F. Caporuscio et al.   CURRENT MEDICINAL CHEMISTRY

Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches

(2011) P. Tuffery et al.   Journal of the Royal Society Interface

Femtosecond X-ray protein nanocrystallography

(2011) Henry N. Chapman et al.   NATURE

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins

(2011) Kuan Pern Tan et al.   NUCLEIC ACIDS RESEARCH

Disabling the mitotic spindle and tumor growth by targeting a cavity-induced allosteric site of survivin

(2011) A Berezov et al.   ONCOGENE

Inhibitors of Helicobacter pylori Protease HtrA Found by ‘Virtual Ligand’ Screening Combat Bacterial Invasion of Epithelia

(2011) Martin Löwer et al.   PLoS One

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

(2011) Stefano Lise et al.   PLoS One

Application of a novel in silico high-throughput screen to identify selective inhibitors for protein–protein interactions

(2010) Catherine Joce et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Identification of the first non-peptidic small molecule inhibitor of the c-Abl/14-3-3 protein–protein interactions able to drive sensitive and Imatinib-resistant leukemia cells to apoptosis

(2010) Valentina Corradi et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Pattern Recognition Receptors and Inflammation

(2010) Osamu Takeuchi et al.   CELL

Targeting protein–protein interactions for therapeutic intervention: a challenge for the future

(2010) Giovanna Zinzalla et al.   Future Medicinal Chemistry

Targeting the BH3 Domain Mediated Protein−Protein Interaction of Bcl-xL through Virtual Screening

(2010) Prasenjit Mukherjee et al.   Journal of Chemical Information and Modeling

Structure-based Design of Novel Small-Molecule Inhibitors of Plasmodium falciparum

(2010) Sandhya Kortagere et al.   Journal of Chemical Information and Modeling

Rational design of small-molecule inhibitors of the LEDGF/p75-integrase interaction and HIV replication

(2010) Frauke Christ et al.   Nature Chemical Biology

ANCHOR: a web server and database for analysis of protein-protein interaction binding pockets for drug discovery

(2010) L. M. C. Meireles et al.   NUCLEIC ACIDS RESEARCH

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

(2009) José Ignacio Garzon et al.   BIOINFORMATICS

EasyMIFs and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures

(2009) Dario Ghersi et al.   BIOINFORMATICS

A dynamic target-based pharmacophoric model mapping the CD4 binding site on HIV-1 gp120 to identify new inhibitors of gp120–CD4 protein–protein interactions

(2009) Fabiana Caporuscio et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Rationalizing the chemical space of protein–protein interaction inhibitors

(2009) Olivier Sperandio et al.   DRUG DISCOVERY TODAY

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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

Three-Dimensional Pharmacophore Methods in Drug Discovery

(2009) Andrew R. Leach et al.   JOURNAL OF MEDICINAL CHEMISTRY

f POP: footprinting functional pockets of proteins by comparative spatial patterns

(2009) Yan Yuan Tseng et al.   NUCLEIC ACIDS RESEARCH

PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces

(2009) Salam A. Assi et al.   NUCLEIC ACIDS RESEARCH

MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction

(2009) Bingding Huang   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A novel and efficient tool for locating and characterizing protein cavities and binding sites

(2009) Ashutosh Tripathi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

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 Molecule Inhibitors Targeting HIV-1 Reverse Transcriptase Dimerization

(2008) Dina Grohmann et al.   CHEMBIOCHEM

In Silico-In Vitro Screening of Protein-Protein Interactions: Towards the Next Generation of Therapeutics

(2008) Bruno Villoutreix et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores

(2008) Caterina Barillari et al.   Journal of Chemical Information and Modeling

New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome

(2008) George Nicola et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Modulation of biomolecular interactions with complex-binding small molecules

(2008) Zheng Cai et al.   METHODS

The RosettaDock server for local protein-protein docking

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

VIROLOGY: HIV Gets By With a Lot of Help From Human Host

(2008) J. Cohen   SCIENCE

PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins

(2007) Yeturu Kalidas et al.   JOURNAL OF STRUCTURAL BIOLOGY

Efficient docking of peptides to proteins without prior knowledge of the binding site

(2002) Csaba Hetényi et al.   PROTEIN SCIENCE