Coarse-grain modelling of protein–protein interactions
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December 2013 |
Protein–protein interactions: scoring schemes and binding affinity
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June 2017 |
Present and future challenges and limitations in protein-protein docking: Challenges in Protein-Protein Docking
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Protein-protein recognition: Crystal structural analysis of a barnase-barstar complex at 2.0-.ANG. resolution
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Initiating a watch list for Ebola virus antibody escape mutations
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January 2016 |
Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles
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July 2013 |
Molecular ‘time-machines’ to unravel key biological events for drug design: Molecular ‘time-machines’ for drug design
- Ganesan, Aravindhan; Coote, Michelle L.; Barakat, Khaled
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Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 7, Issue 4
https://doi.org/10.1002/wcms.1306
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May 2017 |
Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes
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December 2013 |
GROMACS: Fast, flexible, and free
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January 2005 |
Lipid-Modulated Sequence-Specific Association of Glycophorin A in Membranes
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July 2010 |
Comparative Protein Structure Modeling Using MODELLER
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June 2016 |
Coarse-Graining Methods for Computational Biology
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May 2013 |
Interplay between binding affinity and kinetics in protein-protein interactions: Affinity-Kinetics Correlation of PPIs
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April 2016 |
Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations
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August 2016 |
SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models
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August 2012 |
Toward Optimized Potential Functions for Protein–Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field
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August 2013 |
Comparison of multiple Amber force fields and development of improved protein backbone parameters
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November 2006 |
PLUMED 2: New feathers for an old bird
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February 2014 |
Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex.
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August 1989 |
Characterization of single-nucleotide polymorphisms in coding regions of human genes
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Another Coarse Grain Model for Aqueous Solvation: WAT FOUR?
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November 2010 |
UCSF Chimera?A visualization system for exploratory research and analysis
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January 2004 |
Prediction of Protein-Protein Interface Sequence Diversity Using Flexible Backbone Computational Protein Design
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December 2008 |
The Free Energy Landscape of Dimerization of a Membrane Protein, NanC
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January 2014 |
Perspective on the Martini model
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January 2013 |
Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark
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May 2010 |
X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor.
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October 1986 |
A knowledge-based forcefield for protein-protein interface design
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October 2007 |
Computational Design of Protein Interfaces with Receptor Flexibility
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January 2010 |
Canonical sampling through velocity rescaling
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January 2007 |
Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles
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October 2015 |
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
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June 1993 |
The FoldX web server: an online force field
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July 2005 |
Umbrella sampling: Umbrella sampling
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May 2011 |
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
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October 1992 |
BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations
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May 2013 |
The power of coarse graining in biomolecular simulations: The power of coarse graining in biomolecular simulations
- Ingólfsson, Helgi I.; Lopez, Cesar A.; Uusitalo, Jaakko J.
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Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 4, Issue 3
https://doi.org/10.1002/wcms.1169
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August 2013 |
Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes
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January 2010 |
Progress and challenges in predicting protein-protein interaction sites
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December 2008 |
Dimerization of the EphA1 Receptor Tyrosine Kinase Transmembrane Domain: Insights into the Mechanism of Receptor Activation
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October 2014 |
Polymorphic transitions in single crystals: A new molecular dynamics method
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December 1981 |
Comment on ‘protein–protein binding affinity prediction from amino acid sequence’
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October 2014 |
SIRAH: A Structurally Unbiased Coarse-Grained Force Field for Proteins with Aqueous Solvation and Long-Range Electrostatics
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January 2015 |
PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
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July 2004 |
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins
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November 2013 |
Enhanced sampling techniques in biomolecular simulations
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November 2015 |
Self-Association of Models of Transmembrane Domains of ErbB Receptors in a Lipid Bilayer
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December 2010 |
Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity
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March 2014 |
SIRAH tools: mapping, backmapping and visualization of coarse-grained models
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January 2016 |
Enhanced sampling techniques in molecular dynamics simulations of biological systems
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May 2015 |