Biophysical and computational fragment-based approaches to targeting protein–protein interactions: applications in structure-guided drug discovery

Probing the druggability of protein–protein interactions: targeting the Notch1 receptor ankyrin domain using a fragment-based approach

(2012) Noha Abdel-Rahman et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Structural biology and drug discovery for protein–protein interactions

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

The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors

(2011) Yibin Xiang et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions

(2011) Nobuyoshi Sugaya et al.   BMC BIOINFORMATICS

Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database

(2011) George R Bickerton et al.   BMC BIOINFORMATICS

Fragment screening to predict druggability (ligandability) and lead discovery success

(2011) Fredrik N.B. Edfeldt et al.   DRUG DISCOVERY TODAY

Design and Synthesis of Imidazopyridine Analogues as Inhibitors of Phosphoinositide 3-Kinase Signaling and Angiogenesis

(2011) Okseon Kim et al.   JOURNAL OF MEDICINAL CHEMISTRY

Fragment Growing Induces Conformational Changes in Acetylcholine-Binding Protein: A Structural and Thermodynamic Analysis

(2011) Ewald Edink et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Interaction databases on the same page

(2011) Andrei L Turinsky et al.   NATURE BIOTECHNOLOGY

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

(2011) Stefano Lise et al.   PLoS One

Route to three-dimensional fragments using diversity-oriented synthesis

(2011) A. W. Hung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Screening for GPCR Ligands Using Surface Plasmon Resonance

(2011) Iva Navratilova et al.   ACS Medicinal Chemistry Letters

Systematic Analysis of Helical Protein Interfaces Reveals Targets for Synthetic Inhibitors

(2010) Andrea L. Jochim et al.   ACS Chemical Biology

Adding New Chemistries to the Genetic Code

(2010) Chang C. Liu et al.   Annual Review of Biochemistry

Treatment of systemic lupus erythematosus with epratuzumab

(2010) Pawel Traczewski et al.   BRITISH JOURNAL OF CLINICAL PHARMACOLOGY

A Stapled p53 Helix Overcomes HDMX-Mediated Suppression of p53

(2010) Federico Bernal et al.   CANCER CELL

Homodimeric Enzymes as Drug Targets

(2010) D. Cardinale et al.   CURRENT MEDICINAL CHEMISTRY

Structural biology in fragment-based drug design

(2010) Christopher W Murray et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Higher throughput calorimetry: opportunities, approaches and challenges

(2010) Francisco E Torres et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery

(2010) Stéphanie Pérot et al.   DRUG DISCOVERY TODAY

Beyond the Canonical 20 Amino Acids: Expanding the Genetic Lexicon

(2010) Travis S. Young et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Large-Scale Comparison of Four Binding Site Detection Algorithms

(2010) Peter Schmidtke et al.   Journal of Chemical Information and Modeling

Enthalpic Efficiency of Ligand Binding

(2010) György G. Ferenczy et al.   Journal of Chemical Information and Modeling

Fragment-Based Deconstruction of Bcl-xLInhibitors

(2010) Sarah Barelier et al.   JOURNAL OF MEDICINAL CHEMISTRY

Understanding and Predicting Druggability. A High-Throughput Method for Detection of Drug Binding Sites

(2010) Peter Schmidtke et al.   JOURNAL OF MEDICINAL CHEMISTRY

Identification and Characterization of Acidic Mammalian Chitinase Inhibitors

(2010) Derek C. Cole et al.   JOURNAL OF MEDICINAL CHEMISTRY

MK-2206, an Allosteric Akt Inhibitor, Enhances Antitumor Efficacy by Standard Chemotherapeutic Agents or Molecular Targeted Drugs In vitro and In vivo

(2010) H. Hirai et al.   MOLECULAR CANCER THERAPEUTICS

The MCL-1 BH3 helix is an exclusive MCL-1 inhibitor and apoptosis sensitizer

(2010) Michelle L Stewart et al.   Nature Chemical Biology

PCRPi - DB: a database of computationally annotated hot spots in protein interfaces

(2010) Joan Segura et al.   NUCLEIC ACIDS RESEARCH

DIMA 3.0: Domain Interaction Map

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

DOMINE: a comprehensive collection of known and predicted domain-domain interactions

(2010) Sailu Yellaboina 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

e-LEA3D: a computational-aided drug design web server

(2010) D. Douguet   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

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

Atomic Analysis of Protein-Protein Interfaces with Known Inhibitors: The 2P2I Database

(2010) Raphaël Bourgeas et al.   PLoS One

Crystal Structure of Human AKT1 with an Allosteric Inhibitor Reveals a New Mode of Kinase Inhibition

(2010) Wen-I Wu et al.   PLoS One

New surface contacts formed upon reductive lysine methylation: Improving the probability of protein crystallization

(2010) Pawel Sledz et al.   PROTEIN SCIENCE

The Overlap of Small Molecule and Protein Binding Sites within Families of Protein Structures

(2010) Fred P. Davis et al.   PLoS Computational Biology

Application of Fragment Growing and Fragment Linking to the Discovery of Inhibitors ofMycobacterium tuberculosisPantothenate Synthetase

(2009) Alvin W. Hung et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

'Double water exclusion': a hypothesis refining the O-ring theory for the hot spots at protein interfaces

(2009) J. Li et al.   BIOINFORMATICS

Assessing the druggability of protein-protein interactions by a supervised machine-learning method

(2009) Nobuyoshi Sugaya et al.   BMC BIOINFORMATICS

Predicting protein-protein binding sites in membrane proteins

(2009) Andrew J Bordner   BMC BIOINFORMATICS

Fpocket: An open source platform for ligand pocket detection

(2009) Vincent Le Guilloux et al.   BMC BIOINFORMATICS

Identification of Allosteric PIF-Pocket Ligands for PDK1 using NMR-Based Fragment Screening and1H-15N TROSY Experiments

(2009) Brian J. Stockman et al.   Chemical Biology & Drug Design

AutoGrow: A Novel Algorithm for Protein Inhibitor Design

(2009) Jacob D. Durrant et al.   Chemical Biology & Drug Design

Atomic Interactions and Profile of Small Molecules Disrupting Protein-Protein Interfaces: the TIMBAL Database

(2009) Alícia P. Higueruelo et al.   Chemical Biology & Drug Design

Inhibition of protein–protein interactions using designed molecules

(2009) Andrew J. Wilson   CHEMICAL SOCIETY REVIEWS

Linking folding and binding

(2009) Peter E Wright et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The RNA aptamer disrupts protein-protein interaction between β-catenin and nuclear factor-κB p50 and regulates the expression of C-reactive protein

(2009) Yong Seok Choi et al.   FEBS LETTERS

Assessment of helical interfaces in protein–protein interactions

(2009) Andrea L. Jochim et al.   Molecular BioSystems

Structural interactomics: informatics approaches to aid the interpretation of genetic variation and the development of novel therapeutics

(2009) Semin Lee et al.   Molecular BioSystems

Direct inhibition of the NOTCH transcription factor complex

(2009) Raymond E. Moellering et al.   NATURE

Impact of linker strain and flexibility in the design of a fragment-based inhibitor

(2009) Suhman Chung et al.   Nature Chemical Biology

The role of dynamic conformational ensembles in biomolecular recognition

(2009) David D Boehr et al.   Nature Chemical Biology

The influence of lead discovery strategies on the properties of drug candidates

(2009) György M. Keserü et al.   NATURE REVIEWS DRUG DISCOVERY

The Negatome database: a reference set of non-interacting protein pairs

(2009) Pawel Smialowski et al.   NUCLEIC ACIDS RESEARCH

Trapping Moving Targets with Small Molecules

(2009) G. M. Lee et al.   SCIENCE

A Quantitative Model of Thermal Stabilization and Destabilization of Proteins by Ligands

(2008) Piotras Cimmperman et al.   BIOPHYSICAL JOURNAL

SCOWLP classification: Structural comparison and analysis of protein binding regions

(2008) Joan Teyra et al.   BMC BIOINFORMATICS

Shape Shifting Leads to Small-Molecule Allosteric Drug Discovery

(2008) Sarah H. Lawrence et al.   CHEMISTRY & BIOLOGY

Predicting druggable binding sites at the protein–protein interface

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

Fragment-Based de Novo Ligand Design by Multiobjective Evolutionary Optimization

(2008) Fabian Dey et al.   Journal of Chemical Information and Modeling

CONFIRM: connecting fragments found in receptor molecules

(2008) David C. Thompson et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Recent Developments in Fragment-Based Drug Discovery

(2008) Miles Congreve et al.   JOURNAL OF MEDICINAL CHEMISTRY

The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design

(2008) Tjelvar S.G. Olsson et al.   JOURNAL OF MOLECULAR BIOLOGY

An empirical framework for binary interactome mapping

(2008) Kavitha Venkatesan et al.   NATURE METHODS

Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures

(2008) Mizuki Morita et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

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