On the binding affinity of macromolecular interactions: daring to ask why proteins interact

Chemically Modified Peptides Targeting the PDZ Domain of GIPC as a Therapeutic Approach for Cancer

(2012) Chitta Ranjan Patra et al.   ACS Chemical Biology

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

(2012) David Ryan Koes et al.   BIOINFORMATICS

Role of the Biomolecular Energy Gap in Protein Design, Structure, and Evolution

(2012) Sarel J. Fleishman et al.   CELL

The Amyloid State of Proteins in Human Diseases

(2012) David Eisenberg et al.   CELL

Computational Prediction of Protein Hot Spot Residues

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

Small-Molecule Inhibitors of Protein-Protein Interactions: How to Mimic a Protein Partner

(2012) David C. Fry   CURRENT PHARMACEUTICAL DESIGN

Synergistic Applications of MD and NMR for the Study of Biological Systems

(2012) Olivier Fisette et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Inhibition of Amyloid Formation

(2012) Torleif Härd et al.   JOURNAL OF MOLECULAR BIOLOGY

Magnitude and Molecular Origin of Water Slowdown Next to a Protein

(2012) Fabio Sterpone et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Evolution of oligomeric state through geometric coupling of protein interfaces

(2012) T. Perica et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Templates are available to model nearly all complexes of structurally characterized proteins

(2012) P. J. Kundrotas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cellular solid-state nuclear magnetic resonance spectroscopy

(2012) M. Renault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prediction of protein-protein binding free energies

(2012) Thom Vreven et al.   PROTEIN SCIENCE

Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods

(2012) T. Scott Chen et al.   PROTEIN SCIENCE

Arbitrary protein−protein docking targets biologically relevant interfaces

(2012) Juliette Martin et al.   BMC Biophysics

Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding

(2012) Iain H. Moal et al.   PLoS Computational Biology

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

(2011) Iain H. Moal et al.   BIOINFORMATICS

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

(2011) George R Bickerton et al.   BMC BIOINFORMATICS

Autophagy: Renovation of Cells and Tissues

(2011) Noboru Mizushima et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

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

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

Challenges for the prediction of macromolecular interactions

(2011) Mark N Wass et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

(2011) R. Bryn Fenwick et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

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

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

Combining computational modeling with sparse and low-resolution data

(2011) Michael Habeck et al.   JOURNAL OF STRUCTURAL BIOLOGY

Insights on the Role of (Dis)order from Protein–Protein Interaction Linear Free-Energy Relationships

(2011) Meher K. Prakash   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings

(2011) Nikolaos G. Sgourakis et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

A De Novo Protein Binding Pair By Computational Design and Directed Evolution

(2011) John Karanicolas et al.   MOLECULAR CELL

Towards the prediction of protein interaction partners using physical docking

(2011) M. N. Wass et al.   Molecular Systems Biology

Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation

(2011) Stuart A. Sievers et al.   NATURE

Site-resolved measurement of water-protein interactions by solution NMR

(2011) Nathaniel V Nucci et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Bound Water at Protein-Protein Interfaces: Partners, Roles and Hydrophobic Bubbles as a Conserved Motif

(2011) Mostafa H. Ahmed et al.   PLoS One

Computational design of a symmetric homodimer using  -strand assembly

(2011) P. B. Stranges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accessing protein conformational ensembles using room-temperature X-ray crystallography

(2011) J. S. Fraser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase

(2011) D. Cardinale et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transient protein-protein interactions

(2011) S. E. Acuner Ozbabacan et al.   PROTEIN ENGINEERING DESIGN & SELECTION

A structure-based benchmark for protein-protein binding affinity

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

Quantitative use of chemical shifts for the modeling of protein complexes

(2011) Dirk Stratmann et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Nuclease colicins and their immunity proteins

(2011) Grigorios Papadakos et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition

(2011) Jeff Wereszczynski et al.   QUARTERLY REVIEWS OF BIOPHYSICS

From Computational Design to a Protein That Binds

(2011) B. S. Der et al.   SCIENCE

Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces

(2011) G. Grigoryan et al.   SCIENCE

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Cancer Immunoediting: Integrating Immunity's Roles in Cancer Suppression and Promotion

(2011) R. D. Schreiber et al.   SCIENCE

Automated Prediction of Protein Association Rate Constants

(2011) Sanbo Qin et al.   STRUCTURE

Adhesive water networks facilitate binding of protein interfaces

(2011) Mazen Ahmad et al.   Nature Communications

Prediction of protein binding sites and hot spots

(2011) Juan Fernández-Recio   Wiley Interdisciplinary Reviews-Computational Molecular Science

Drug–protein binding: a critical review of analytical tools

(2010) Karine Vuignier et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Global Dynamics of Proteins: Bridging Between Structure and Function

(2010) Ivet Bahar et al.   Annual Review of Biophysics

Absolute Protein-Protein Association Rate Constants from Flexible, Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association

(2010) Tamara Frembgen-Kesner et al.   BIOPHYSICAL JOURNAL

From Induced Fit to Conformational Selection: A Continuum of Binding Mechanism Controlled by the Timescale of Conformational Transitions

(2010) Huan-Xiang Zhou   BIOPHYSICAL JOURNAL

Accounting for conformational changes during protein–protein docking

(2010) Martin Zacharias   CURRENT OPINION IN STRUCTURAL BIOLOGY

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

(2010) Adrian H Elcock   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Using peptides to study protein–protein interactions

(2010) Hadar Benyamini et al.   Future Medicinal Chemistry

Computational Design of a PAK1 Binding Protein

(2010) Ramesh K. Jha et al.   JOURNAL OF MOLECULAR BIOLOGY

Structural Characterization of Protein–Protein Complexes by Integrating Computational Docking with Small-angle Scattering Data

(2010) Carles Pons et al.   JOURNAL OF MOLECULAR BIOLOGY

The Subunit Interfaces of Weakly Associated Homodimeric Proteins

(2010) Sucharita Dey 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

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

(2010) Michelle L Stewart 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

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

(2010) Raphaël Bourgeas et al.   PLoS One

Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires

(2010) G. Reddy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

(2010) T. Ando et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Structure-based thermodynamic analysis of the dissociation of protein phosphatase-1 catalytic subunit and microcystin-LR docked complexes

(2010) Pierre Lavigne et al.   PROTEIN SCIENCE

Calculation of the free energy of association for protein complexes

(2010) Nancy Horton et al.   PROTEIN SCIENCE

Docking by structural similarity at protein-protein interfaces

(2010) Rohita Sinha et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

How different from random are docking predictions when ranked by scoring functions?

(2010) Elisenda Feliu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting kinetic constants of protein-protein interactions based on structural properties

(2010) Hongjun Bai et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Docking and scoring protein interactions: CAPRI 2009

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein-protein docking benchmark version 4.0

(2010) Howook Hwang et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Blind predictions of protein interfaces by docking calculations in CAPRI

(2010) Marc F. Lensink et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Transient Protein-Protein Interactions: Structural, Functional, and Network Properties

(2010) James R. Perkins et al.   STRUCTURE

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2009) J. Li et al.   BIOINFORMATICS

Fruitful and Futile Encounters along the Association Reaction between Proteins

(2009) Michal Harel et al.   BIOPHYSICAL JOURNAL

Common Crowding Agents Have Only a Small Effect on Protein-Protein Interactions

(2009) Yael Phillip et al.   BIOPHYSICAL JOURNAL

Defining the Human Deubiquitinating Enzyme Interaction Landscape

(2009) Mathew E. Sowa et al.   CELL

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

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

Fundamental Aspects of Protein−Protein Association Kinetics

(2009) G. Schreiber et al.   CHEMICAL REVIEWS

Inhibition of protein–protein interactions using designed molecules

(2009) Andrew J. Wilson   CHEMICAL SOCIETY REVIEWS

The road less traveled: modulating signal transduction enzymes by inhibiting their protein–protein interactions

(2009) Michelle R Arkin et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Convergence and combination of methods in protein–protein docking

(2009) Sandor Vajda et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Interaction between the Transactivation Domain of p53 and PC4 Exemplifies Acidic Activation Domains as Single-stranded DNA Mimics

(2009) Sridharan Rajagopalan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Empirical estimation of the energetic contribution of individual interface residues in structures of protein–protein complexes

(2009) Mainak Guharoy et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Design of protein-interaction specificity gives selective bZIP-binding peptides

(2009) Gevorg Grigoryan et al.   NATURE

Protein structure determination in living cells by in-cell NMR spectroscopy

(2009) Daisuke Sakakibara et al.   NATURE

Computer-aided design of functional protein interactions

(2009) Daniel J Mandell et al.   Nature Chemical Biology

Cell cycle kinases as therapeutic targets for cancer

(2009) Silvia Lapenna et al.   NATURE REVIEWS DRUG DISCOVERY

Subcellular targeting strategies for drug design and delivery

(2009) Lawrence Rajendran et al.   NATURE REVIEWS DRUG DISCOVERY

Conformational selection or induced fit: A flux description of reaction mechanism

(2009) G. G. Hammes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

(2009) T. Wlodarski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast screening of protein surfaces using geometric invariant fingerprints

(2009) S. Yin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein design in biological networks: from manipulating the input to modifying the output

(2009) A. M. Van der Sloot et al.   PROTEIN ENGINEERING DESIGN & SELECTION

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

(2009) Yu Su et al.   PROTEIN SCIENCE

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

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

(2009) Roberto Mosca et al.   PLoS Computational Biology

Integrating Diverse Data for Structure Determination of Macromolecular Assemblies

(2008) Frank Alber et al.   Annual Review of Biochemistry

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou et al.   Annual Review of Biophysics

Small-Molecule Inhibitors of the MDM2-p53 Protein-Protein Interaction to Reactivate p53 Function: A Novel Approach for Cancer Therapy

(2008) Sanjeev Shangary et al.   Annual Review of Pharmacology and Toxicology

ProtorP: a protein-protein interaction analysis server

(2008) C. Reynolds et al.   BIOINFORMATICS

Development and validation of an empirical free energy function for calculating protein–protein binding free energy surfaces

(2008) Joseph Audie   BIOPHYSICAL CHEMISTRY

Computational chemistry approaches to drug discovery in signal transduction

(2008) Peter M. Fischer   Biotechnology Journal

Identification of hot-spot residues in protein-protein interactions by computational docking

(2008) Solène Grosdidier et al.   BMC BIOINFORMATICS

ABT-263: A Potent and Orally Bioavailable Bcl-2 Family Inhibitor

(2008) C. Tse et al.   CANCER RESEARCH

Principles of Protein−Protein Interactions: What are the Preferred Ways For Proteins To Interact?

(2008) Ozlem Keskin et al.   CHEMICAL REVIEWS

Water as a Biomolecule

(2008) Philip Ball   CHEMPHYSCHEM

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

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

Peptides as protein binding site mimetics

(2008) Jutta Eichler   CURRENT OPINION IN CHEMICAL BIOLOGY

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

(2008) Alexander Dömling   CURRENT OPINION IN CHEMICAL BIOLOGY

United we stand: combining structural methods

(2008) Nathan P Cowieson et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Multiscale methods for macromolecular simulations

(2008) Paul Sherwood et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Recent Progress and Future Directions in Protein-Protein Docking

(2008) David Ritchie   CURRENT PROTEIN & PEPTIDE SCIENCE

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

(2008) D. Fry   CURRENT PROTEIN & PEPTIDE SCIENCE

Homology-based modeling of 3D structures of protein–protein complexes using alignments of modified sequence profiles

(2008) Petras J. Kundrotas et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Computational Redesign of the SHV-1 β-Lactamase/β-Lactamase Inhibitor Protein Interface

(2008) Kimberly A. Reynolds et al.   JOURNAL OF MOLECULAR BIOLOGY

Identification of Protein Interaction Partners and Protein–Protein Interaction Sites

(2008) Sophie Sacquin-Mora et al.   JOURNAL OF MOLECULAR BIOLOGY

Computational Redesign of a Protein–Protein Interface for High Affinity and Binding Specificity Using Modular Architecture and Naturally Occurring Template Fragments

(2008) V. Potapov et al.   JOURNAL OF MOLECULAR BIOLOGY

Architectures and Functional Coverage of Protein–Protein Interfaces

(2008) Nurcan Tuncbag et al.   JOURNAL OF MOLECULAR BIOLOGY

Can Morphing Methods Predict Intermediate Structures?

(2008) Dahlia R. Weiss et al.   JOURNAL OF MOLECULAR BIOLOGY

A Novel Peptide Agonist of Formyl-Peptide Receptor-Like 1 (ALX) Displays Anti-Inflammatory and Cardioprotective Effects

(2008) I. Hecht et al.   JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS

BAX activation is initiated at a novel interaction site

(2008) Evripidis Gavathiotis et al.   NATURE

Assembly reflects evolution of protein complexes

(2008) Emmanuel D. Levy et al.   NATURE

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS

Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms

(2008) K.-i. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Selected-fit versus induced-fit protein binding: Kinetic differences and mutational analysis

(2008) Thomas R. Weikl et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein–protein interaction and quaternary structure

(2008) Joël Janin et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Alternative splicing: current perspectives

(2007) Eddo Kim et al.   BIOESSAYS

Water as an Active Constituent in Cell Biology

(2007) Philip Ball   CHEMICAL REVIEWS

Electrostatic rate enhancement and transient complex of protein–protein association

(2007) Ramzi Alsallaq et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Functional aspects of co-variant surface charges in an antibody fragment

(2002) Nicolas Hugo et al.   PROTEIN SCIENCE