About: Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software

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About: Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software Goto Sponge NotDistinct Permalink

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scholarly article by Sereina Riniker et al published 24 November 2011 in Journal of Physical Chemistry

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rdf:type	Item
description	wetenschappelijk artikel (nl) наукова стаття, опублікована в листопаді 2011 (uk) article scientifique publié en 2011 (fr) im November 2011 veröffentlichter wissenschaftlicher Artikel (de) scholarly article by Sereina Riniker et al published 24 November 2011 in Journal of Physical Chemistry (en)
publication date	wds:Q57235428-37E69909-2F2C-46E0-9F9E-E53A7770C573
publication date	2011-11-24 00:00:00Z (xsd:dateTime)
language of work or name	wds:Q57235428-2A07EBAF-15B1-4BE0-976B-42143E11224C
language of work or name	English
author name string	wds:Q57235428-842D833A-CA16-41BF-8E2A-5FDBF0A8BF32 wds:Q57235428-A2564C33-A03D-4A55-92BF-8CD5C854F3CA wds:Q57235428-EC2655A3-4C3A-46FD-800D-6958B7C49565
author name string	Denise Steiner Clara D. Christ Halvor S. Hansen
rdfs:label	Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software (en) Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software (nl)
skos:prefLabel	Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software (en) Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software (nl)
name	Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software (en) Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software (nl)
author	wds:Q57235428-6C8588D8-EA27-4CBD-B9FD-3A4B3F22D40F wds:Q57235428-AAD7D5BB-8500-40AC-85C2-6A2A0006D043 wds:Q57235428-D1CC40CB-75EC-4FE4-80E3-4000D8664F36 wds:Q57235428-FF958C78-0DC5-4131-9DA5-B4A4E86EE14F
author	Chris Oostenbrink Wilfred F van Gunsteren Sereina Riniker Philippe H Hünenberger
title	wds:Q57235428-6EBAB13E-D2CF-4CD0-BC9A-A6AA6BC07F74
title	Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software (en)
page(s)	wds:Q57235428-B4105D77-9006-410E-9204-86781E1E9ED0
page(s)	13570-13577
instance of	wds:Q57235428-E31FAA1E-90D3-4026-B98E-3B4DB3785512
instance of	scholarly article
main subject	wds:Q57235428-13477B26-CB54-469D-9A4C-689D0A3FB5BD
main subject	software
PubMed ID	wds:Q57235428-7D363ADC-5BA5-4BA7-80D5-B03A1F46D872
PubMed ID	http://rdf.ncbi.nlm.nih.gov/pubchem/reference/22039957
PubMed ID	22039957
published in	wds:Q57235428-9DA412EF-F404-44BE-9DAA-1796CD3177BB
published in	Journal of Physical Chemistry B
issue	wds:Q57235428-F1380B25-198F-4A69-927F-64AB13A33CC0
volume	wds:Q57235428-FB08B21C-CEE1-417A-9D10-6D76AA30BF51
issue	46
volume	115
number of pages	wds:Q57235428-B4682B63-0F27-49BE-824C-8D8D21158AE4
number of pages	8 (xsd:decimal)
DOI	wds:Q57235428-9B9ECCC6-65A5-40E7-A9D3-62839753C00C
DOI	http://dx.doi.org/10.1021/JP204303A
DOI	10.1021/JP204303A
is about of	https://www.wikidata.org/wiki/Special:EntityData/Q57235428
is cites work of	Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A. Rationalization of stereospecific binding of propranolol to cytochrome P450 2D6 by free energy calculations Free enthalpies of replacing water molecules in protein binding pockets Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions On the thermodynamics of carbon nanotube single-file water loading: free energy, energy and entropy calculations. Refinement of the application of the GROMOS 54A7 force field to β-peptides Calculation of the relative free energy of oxidation of Azurin at pH 5 and pH 9. Mixing coarse-grained and fine-grained water in molecular dynamics simulations of a single system Replica exchange enveloping distribution sampling (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons Binding free energy, energy and entropy calculations using simple model systems Free-energy differences between states with different conformational ensembles Structural consequences of hereditary spastic paraplegia disease-related mutations in kinesin On the use of one-step perturbation to investigate the dependence of NOE-derived atom-atom distance bound violations of peptides upon a variation of force-field parameters. Enhanced conformational sampling using enveloping distribution sampling On the choice of a reference state for one-step perturbation calculations between polar and nonpolar molecules in a polar environment A comparison of pathway-independent and pathway-dependent methods in the calculation of conformational free enthalpy differences From dimers to collective dipoles: Structure and dynamics of methanol/ethanol partition by narrow carbon nanotubes. Influence of variation of a side chain on the folding equilibrium of a β-peptide: limitations of one-step perturbation
is cites work of	wds:Q28820935-75E1BBC3-1FFE-4611-87B4-11184A71B93B wds:Q47862201-30709B1A-7ED7-4957-A715-448B28B40A98 wds:Q57235415-F0325CD6-6ABC-499D-BF7F-EF8DF8EA1881 wds:Q48544964-05495030-C638-40D1-9928-E6A3C7F9AE20 wds:Q45345552-CEC96E37-995C-4EDD-9C18-68B1E4963F83 wds:Q43590057-D9DA6F01-1AED-48E3-9E08-DE1F2A8CCE38 wds:Q44944853-6DB7C6AE-9443-4D89-A08B-61A30371D918 wds:Q39840296-752DFEDF-F40C-4C37-BEDC-60CF3A10CDCB wds:Q34481459-5F3C40B1-CB60-43F6-9A3D-96705DE1A4FF wds:Q41894330-D845D57A-1C39-47A3-83D3-497667D1DE63 wds:Q45747310-5BCF4BA5-E209-42C8-AC92-FD9B7184331A wds:Q39722131-ACB56CD2-8D22-4C56-8819-F52AE3A0E51C wds:Q40652965-7A279B6A-6142-4CC4-BE5F-120AD554FD4C wds:Q51115239-3805564E-0404-4A2B-816F-63D5783787DD wds:Q36174475-F18B83B1-630A-4D65-B919-6078837014BC wds:Q46226471-FBE82D0A-A13A-4E39-A4A2-6F22D2B80D37 wds:Q48520852-402363F7-9995-4ECA-B596-81EC2FF2F41B wds:Q57235419-3CA575F4-3C78-4D33-85E5-A5D68BD93309 wds:Q58005479-06799779-C0A5-4D99-AEF7-89C8C0E65356 wds:Q58115990-90F20E03-FCA4-4CBD-AD8D-8C8CC8DCD682

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