
[Related PubMed/MEDLINE] Total Number of Papers: 118



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Abbreviation 
: TI 
Long Form 
: thermodynamic integration 

No. 
Year 
Title 
Cooccurring Abbreviation 
1 
2020 
Prediction of octanolwater partition coefficients for the SAMPL6[Formula: see text] molecules using molecular dynamics simulations with OPLSAA, AMBER and CHARMM force fields. 
FEP, RMSE 
2 
2019 
Alchemical FreeEnergy Calculations by MultipleReplica lamdaDynamics: The Conveyor Belt Thermodynamic Integration Scheme. 
CB, CBTI, HRE/HRP, lamdaLEUS, lamdaD, MD 
3 
2019 
AMPA Receptor Noncompetitive Inhibitors Occupy a Promiscuous Binding Site. 
MD, PMP 
4 
2019 
Atomic insights into the effects of pathological mutants through the disruption of hydrophobic core in the prion protein. 
TREMD 
5 
2019 
Binding Free Energies of Conformationally Disordered Peptides Through Extensive Sampling and EndPoint Methods. 
FEP, LIE, MD, MM/GBSA 
6 
2019 
Calculate proteinligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3. 
CADD, CatS, ELIE, FEP, GC3, LIE, MM/PBSA 
7 
2019 
Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines ForceMatched Reference Potential and Bennett's Acceptance Ratio Methods. 
BAR, MD, MM, QM/MM 
8 
2019 
Hydration of Aromatic Heterocycles as an Adversary of piStacking. 
GIST 
9 
2019 
Rapid and accurate structurebased therapeutic peptide design using GPU accelerated thermodynamic integration. 
 
10 
2019 
Robust Free Energy Perturbation Protocols for Creating Molecules in Solution. 
BAR, FEP, MC, MD 
11 
2019 
Thermodynamic integration via differential evolution: A method for estimating marginal likelihoods. 
DEMCMC, MCMC, TIDE 
12 
2019 
Understanding StructureActivity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations. 
HAT, SAR 
13 
2018 
Comparison of freeenergy methods using a tripeptidewater model system. 
BAR, EDS 
14 
2018 
Computational characterization of the selective inhibition of human norepinephrine and serotonin transporters by an escitalopram scaffold. 
hNET and hSERT, MATs 
15 
2018 
Extraction of Gd3+ and UO22+ Ions Using Polystyrene Grafted Dibenzo Crown Ether (DB18C6) with Octanol and Nitrobenzene: A Molecular Dynamics Study. 
DBCE, MD, NB, OCT 
16 
2018 
Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package. 
AFE, GPUs, MD 
17 
2018 
Features of interactions responsible for antifungal activity against resistant type cytochrome bc1: A datadriven analysis based on the binding free energy at the atomic level. 
QoIs 
18 
2018 
Saturation Mutagenesis by Efficient FreeEnergy Calculation. 
OSP, TPF 
19 
2018 
SingleIon Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and SingleElectrode Potential of Aqueous Li+ Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. 
DFT 
20 
2018 
Structure, Dynamics, and Hydration Free Energy of Carbon Dioxide in Aqueous Solution: A Quantum Mechanical/Molecular Mechanics Molecular Dynamics Thermodynamic Integration (QM/MM MD TI) Simulation Study. 
QM/MM 
21 
2018 
Understanding the hydrogen transfer mechanism for the biodegradation of 2,4,6trinitrotoluene catalyzed by pentaerythritol tetranitrate reductase: molecular dynamics simulations. 
EVB, FMN, MD, PETNR, TNT 
22 
2017 
Absolute binding free energies for octaacids and guests in SAMPL5 : Evaluating binding free energies for octaacid and guest complexes in the SAMPL5 blind challenge. 
HREMBAR 
23 
2017 
Absolute binding free energy calculations of CBClip hostguest systems in the SAMPL5 blind challenge. 
BAR 
24 
2017 
Accuracy Test of the OPLSAA Force Field for Calculating Free Energies of Mixing and Comparison with PACMAC. 
PACMAC, RMSE 
25 
2017 
Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor. 
McMD 
26 
2017 
Capillary fluctuations of surface steps: An atomistic simulation study for the model Cu(111) system. 
MD 
27 
2017 
Comparative Assessment of Computational Methods for Free Energy Calculations of Ionic Hydration. 
ERmod, GAFF, GB, HFEs, PB, SD, SMD 
28 
2017 
Fast and Reliable Thermodynamic Approach for Determining the Protonation State of the Asp Dyad. 
 
29 
2017 
Investigation of the bindings of a class of inhibitors with GSK3beta kinase using thermodynamic integration MD simulation and kinase assay. 
 
30 
2017 
Targeting Bayes factors with directpath nonequilibrium thermodynamic integration. 
 
31 
2017 
Using forcebased adaptive resolution simulations to calculate solvation free energies of amino acid sidechain analogues. 
AdResS 
32 
2016 
Determination of the protonation state of the Asp dyad: conventional molecular dynamics versus thermodynamic integration. 
MD 
33 
2016 
Estimating the Number of Subpopulations (K) in Structured Populations. 
 
34 
2016 
Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoylACP reductase (FabI) benzimidazole inhibitors. 
MD 
35 
2016 
Extended Thermodynamic Integration: Efficient Prediction of Lambda Derivatives at Nonsimulated Points. 
 
36 
2016 
MaierSaupe model of polymer nematics: Comparing free energies calculated with Self Consistent Field theory and Monte Carlo simulations. 
LC, MC, MS, SCF, WLC 
37 
2016 
Molecular Dynamics Analysis of Binding of Kinase Inhibitors to WT EGFR and the T790M Mutant. 
EGFR, MD, WT 
38 
2016 
Replica exchange enveloping distribution sampling (REEDS): A robust method to estimate multiple freeenergy differences from a single simulation. 
EDS, MD, REEDS, REEDS 
39 
2016 
The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrodinger FEP. 
 
40 
2015 
A Comparative Insight into Amprenavir Resistance of Mutations V32I, G48V, I50V, I54V, and I84V in HIV1 Protease Based on Thermodynamic Integration and MMPBSA Methods. 
APV, MMPBSA, PR 
41 
2015 
Crystalliquid interfacial free energy of hard spheres via a thermodynamic integration scheme. 
 
42 
2015 
Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. 
COSMORS, QSPR 
43 
2015 
Free Energy Calculations using a SwarmEnhanced Sampling Molecular Dynamics Approach. 
ITTI, sesMD, sesTI 
44 
2015 
Investigation of differences in the binding affinities of two analogous ligands for untagged and tagged p38 kinase using thermodynamic integration MD simulation. 
MD, REF 
45 
2015 
On the determination of phase boundaries via thermodynamic integration across coexistence regions. 
 
46 
2015 
Orthogonal sampling in freeenergy calculations of residue mutations in a tripeptide: TI versus lamdaLEUS. 
HR 
47 
2015 
Prediction of Surface and Bulk Partition of Nonionic Surfactants Using Free Energy Calculations. 
 
48 
2014 
Accuracy assessment and automation of free energy calculations for drug design. 
MBAR 
49 
2014 
Assessing the hydration free energy of a homologous series of polyols with classical and quantum mechanical solvation models. 
MD, PCM 
50 
2014 
Binding Free Energy Calculations for Lead Optimization: Assessment of Their Accuracy in an Industrial Drug Design Context. 
LIE 
51 
2014 
Communication: estimating the initial biasing potential for lamdalocalelevation umbrellasampling (lamdaLEUS) simulations via slow growth. 
lamdaLEUS, lamdaD, LEUS, SGMG 
52 
2014 
Crystalliquid interfacial free energy via thermodynamic integration. 
 
53 
2014 
Free energy calculations to estimate ligandbinding affinities in structurebased drug design. 
FEP, LIE, MM, QM, SG 
54 
2014 
Local Elevation Umbrella Sampling Applied to the Calculation of Alchemical FreeEnergy Changes via lamdaDynamics: The lamdaLEUS Scheme. 
lamdaD, LEUS, MD 
55 
2014 
Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field. 
CADD 
56 
2014 
Role of Deprotonation Free Energies in pKa Prediction and Molecule Ranking. 
 
57 
2014 
Thermodynamic characterization of new positive allosteric modulators binding to the glutamate receptor A2 ligandbinding domain: combining experimental and computational methods unravels differences in driving forces. 
ITC, OSP 
58 
2013 
A Comparative Molecular Dynamics, MMPBSA and Thermodynamic Integration Study of Saquinavir Complexes with WildType HIV1 PR and L10I, G48V, L63P, A71V, G73S, V82A and I84V Single Mutants. 
AIDS 
59 
2013 
A comparative study of methods to compute the free energy of an ordered assembly by molecular simulation. 
EC, FL, IH, OS, PR, SS 
60 
2013 
Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38alpha MAP kinase: a combined computational and experimental study. 
 
61 
2013 
Comparative assessment of computational methods for the determination of solvation free energies in alcoholbased molecules. 
GB, PB, PCM, SMD 
62 
2013 
Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative proteinligand binding free energies. 
 
63 
2013 
Comparison of two simulation methods to compute solvation free energies and partition coefficients. 
AA, AAD, EE, OPLS, SPC/E 
64 
2013 
Computational Alanine Scanning Mutagenesis: MMPBSA vs TI. 
ASM, MMPBSA 
65 
2013 
Freeenergy differences between states with different conformational ensembles. 
GTP, LE/US, OSP 
66 
2013 
Molecular modeling of the green leaf volatile methyl salicylate on atmospheric air/water interfaces. 
GLV, MD, MeSA, PMF, SOAs 
67 
2013 
On the Role of Dewetting Transitions in HostGuest Binding Free Energy Calculations. 
MD 
68 
2013 
pHtriggered conformational switching of the diphtheria toxin Tdomain: the roles of Nterminal histidines. 
MD 
69 
2013 
Rational Design of Particle Mesh Ewald Compatible LennardJones Parameters for +2 Metal Cations in Explicit Solvent. 
CNs, HFEs, IOD, LJ, MD, PME 
70 
2012 
Alchemical Free Energy Differences in Flexible Molecules from Thermodynamic Integration or Free Energy Perturbation Combined with Driven Adiabatic Dynamics. 
dAFED, FEP 
71 
2012 
Calculating the Na⁺ translocating VATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation. 
MD, VATPase 
72 
2012 
Calculation of the relative free energy of oxidation of Azurin at pH 5 and pH 9. 
RETI 
73 
2012 
Develop and test a solvent accessible surface areabased model in conformational entropy calculations. 
BSAS, HTS, MMPBSA, NMA, SAS, WSAS 
74 
2012 
Development of a methodology to compute solvation free energies on the basis of the theory of energy representation for solutions represented with a polarizable force field. 
ER 
75 
2012 
Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors. 
LIE, LRA, OSP, TPF 
76 
2012 
Rapid determination of entropy and free energy of mixtures from molecular dynamics simulations with the twophase thermodynamic model. 
DOS, LJ 
77 
2012 
Testing recent chargeonspring type polarizable water models. I. Melting temperature and ice properties. 
COS, Ih 
78 
2011 
Accurate determination of the Gibbs energy of CuZr melts using the thermodynamic integration method in Monte Carlo simulations. 
MCS 
79 
2011 
Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA. 
 
80 
2011 
Calculation of the Absolute Free Energy of Binding and Related Entropies with the HSMDTI Method: The FKBP12L8 Complex. 
DAM, DDM, HSMD, PME 
81 
2011 
Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine Nmethyltransferase inhibitors. 
EDS 
82 
2011 
Improved Binding Free Energy Predictions from SingleReference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. 
HREX, SR 
83 
2011 
Improving marginal likelihood estimation for Bayesian phylogenetic model selection. 
HM, SS 
84 
2011 
Induced fit or conformational selection? The role of the semiclosed state in the maltose binding protein. 
ABF, aMD, CS, IF, MBP 
85 
2011 
On the Use of Enveloping Distribution Sampling (EDS) to Compute Free Enthalpy Differences between Different Conformational States of Molecules: Application to 310, alpha, and piHelices. 
EDS 
86 
2011 
Relative stability of the open and closed conformations of the active site loop of streptavidin. 
AMBER, HSMD 
87 
2011 
Softcore potentials in thermodynamic integration: comparing one and twostep transformations. 
 
88 
2010 
Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. 
HREX, SRTI 
89 
2010 
Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins. 
HSMDTI, loop 
90 
2010 
Molecular dynamics simulations of nonpolarizable inorganic salt solution interfaces: NaCl, NaBr, and NaI in transferable intermolecular potential 4point with charge dependent polarizability (TIP4PQDP) water. 
 
91 
2010 
Nonpolar Solvation Free Energies of ProteinLigand Complexes. 
MM/GBSA, PCM, SASA 
92 
2010 
Unveiling the unfolding pathway of FALS associated G37R SOD1 mutant: a computational study. 
CTMD, FALS, SMD, WT 
93 
2009 
Applying linear interaction energy method for binding affinity calculations of podophyllotoxin analogues with tubulin using continuum solvent model and prediction of cytotoxic activity. 
FEP, LIE, RMSE, SGB 
94 
2009 
Effects of Restrained Sampling Space and Nonplanar Amino Groups on FreeEnergy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs. 
GA 
95 
2009 
IndependentTrajectories ThermodynamicIntegration FreeEnergy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. 
ITTI, PVR 
96 
2009 
The selfreferential method for linear rigid bodies: application to hard and LennardJones dumbbells. 
SR 
97 
2008 
Calculating chemically accurate redox potentials for engineered flavoproteins from classical molecular dynamics free energy simulations. 
ET, FAD, FMN, MDFES 
98 
2008 
Computational study of the mechanism and the relative free energies of binding of anticholesteremic inhibitors to squalenehopene cyclase. 
SHC, SSP 
99 
2007 
Binding free energy prediction in strongly hydrophobic biomolecular systems. 
PMF 
100 
2007 
Computational alanine scanning mutagenesisan improved methodological approach. 
FEP, MMPBSA 
