Prediction of CB[8] host–guest binding free energies in SAMPL6 using the double-decoupling method
Published 2018 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Prediction of CB[8] host–guest binding free energies in SAMPL6 using the double-decoupling method
Authors
Keywords
Binding free energy, Double-decoupling, Hamiltonian replica exchange, Bennett acceptance ratio, Umbrella sampling, Weighted histogram analysis
Journal
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
Volume -, Issue -, Pages -
Publisher
Springer Nature America, Inc
Online
2018-08-06
DOI
10.1007/s10822-018-0144-8
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Graph–Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions
- (2018) Kyungreem Han et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain
- (2017) Germano Heinzelmann et al. Journal of Chemical Theory and Computation
- Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations
- (2017) Bing Xie et al. Journal of Chemical Theory and Computation
- Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field
- (2017) Christian Margreitter et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition
- (2017) Eva Bilkova et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Overview of the SAMPL5 host–guest challenge: Are we doing better?
- (2016) Jian Yin et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association
- (2016) Jan Domański et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Solv-ccCA: Implicit Solvation and the Correlation Consistent Composite Approach for the Determination of pKa
- (2014) Amanda G. Riojas et al. Journal of Chemical Theory and Computation
- The SAMPL4 host–guest blind prediction challenge: an overview
- (2014) Hari S. Muddana et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
- (2013) Kelly L. Damm-Ganamet et al. Journal of Chemical Information and Modeling
- Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles
- (2013) James C. Gumbart et al. Journal of Chemical Theory and Computation
- GalaxyDock2: Protein-ligand docking using beta-complex and global optimization
- (2013) Woong-Hee Shin et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data
- (2013) Richard M. Venable et al. JOURNAL OF PHYSICAL CHEMISTRY B
- GalaxyDock: Protein–Ligand Docking with Flexible Protein Side-chains
- (2012) Woong-Hee Shin et al. Journal of Chemical Information and Modeling
- Revised AMBER Parameters for Bioorganic Phosphates
- (2012) T. Steinbrecher et al. Journal of Chemical Theory and Computation
- Blind prediction of host–guest binding affinities: a new SAMPL3 challenge
- (2012) Hari S. Muddana et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities
- (2012) L. Wang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Structure, dynamics, and hydration of POPC/POPS bilayers suspended in NaCl, KCl, and CsCl solutions
- (2011) Piotr Jurkiewicz et al. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
- A pseudopotential-based composite method: The relativistic pseudopotential correlation consistent composite approach for molecules containing 4d transition metals (Y–Cd)
- (2011) Marie L. Laury et al. JOURNAL OF CHEMICAL PHYSICS
- Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations
- (2010) Wei Jiang et al. Journal of Chemical Theory and Computation
- The SAMPL2 blind prediction challenge: introduction and overview
- (2010) Matthew T. Geballe et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Energy-consistent pseudopotentials and correlation consistent basis sets for the 5d elements Hf–Pt
- (2009) Detlev Figgen et al. JOURNAL OF CHEMICAL PHYSICS
- CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
- (2009) K. Vanommeslaeghe et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview
- (2009) J. Peter Guthrie JOURNAL OF PHYSICAL CHEMISTRY B
- Universal Solvation Model Based on Solute Electron Density and on a Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions
- (2009) Aleksandr V. Marenich et al. JOURNAL OF PHYSICAL CHEMISTRY B
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExplorePublish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn More