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Abbreviation : TI
Long Form : thermodynamic integration
No. Year Title Co-occurring Abbreviation
2020 Prediction of octanol-water partition coefficients for the SAMPL6-[Formula: see text] molecules using molecular dynamics simulations with OPLS-AA, AMBER and CHARMM force fields. FEP, RMSE
2019 Alchemical Free-Energy Calculations by Multiple-Replica lamda-Dynamics: The Conveyor Belt Thermodynamic Integration Scheme. CB, CBTI, HRE/HRP, lamda-LEUS, lamdaD, MD
2019 AMPA Receptor Noncompetitive Inhibitors Occupy a Promiscuous Binding Site. MD, PMP
2019 Atomic insights into the effects of pathological mutants through the disruption of hydrophobic core in the prion protein. T-REMD
2019 Binding Free Energies of Conformationally Disordered Peptides Through Extensive Sampling and End-Point Methods. FEP, LIE, MD, MM/GBSA
2019 Calculate protein-ligand 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
2019 Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods. BAR, MD, MM, QM/MM
2019 Hydration of Aromatic Heterocycles as an Adversary of pi-Stacking. GIST
2019 Rapid and accurate structure-based 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. DE-MCMC, MCMC, TIDE
12  2019 Understanding Structure-Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations. HAT, SAR
13  2018 Comparison of free-energy methods using a tripeptide-water 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 data-driven analysis based on the binding free energy at the atomic level. QoIs
18  2018 Saturation Mutagenesis by Efficient Free-Energy Calculation. OSP, TPF
19  2018 Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode 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 2,4,6-trinitrotoluene catalyzed by pentaerythritol tetranitrate reductase: molecular dynamics simulations. EVB, FMN, MD, PETNR, TNT
22  2017 Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge. HREM-BAR
23  2017 Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. BAR
24  2017 Accuracy Test of the OPLS-AA Force Field for Calculating Free Energies of Mixing and Comparison with PAC-MAC. PAC-MAC, 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 direct-path non-equilibrium thermodynamic integration. ---
31  2017 Using force-based 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 enoyl-ACP reductase (FabI) benzimidazole inhibitors. MD
35  2016 Extended Thermodynamic Integration: Efficient Prediction of Lambda Derivatives at Nonsimulated Points. ---
36  2016 Maier-Saupe 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 (RE-EDS): A robust method to estimate multiple free-energy differences from a single simulation. EDS, MD, RE-EDS, RE-EDS
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 HIV-1 Protease Based on Thermodynamic Integration and MM-PBSA Methods. APV, MM-PBSA, PR
41  2015 Crystal-liquid interfacial free energy of hard spheres via a thermodynamic integration scheme. ---
42  2015 Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. COSMO-RS, QSPR
43  2015 Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach. IT-TI, 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 free-energy calculations of residue mutations in a tripeptide: TI versus lamda-LEUS. 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 lamda-local-elevation umbrella-sampling (lamda-LEUS) simulations via slow growth. lamda-LEUS, lamdaD, LEUS, SGMG
52  2014 Crystal-liquid interfacial free energy via thermodynamic integration. ---
53  2014 Free energy calculations to estimate ligand-binding affinities in structure-based drug design. FEP, LIE, MM, QM, SG
54  2014 Local Elevation Umbrella Sampling Applied to the Calculation of Alchemical Free-Energy Changes via lamda-Dynamics: The lamda-LEUS 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 ligand-binding domain: combining experimental and computational methods unravels differences in driving forces. ITC, OSP
58  2013 A Comparative Molecular Dynamics, MM-PBSA and Thermodynamic Integration Study of Saquinavir Complexes with Wild-Type HIV-1 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 alcohol-based molecules. GB, PB, PCM, SMD
62  2013 Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand 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: MM-PBSA vs TI. ASM, MM-PBSA
65  2013 Free-energy 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 Host-Guest Binding Free Energy Calculations. MD
68  2013 pH-triggered conformational switching of the diphtheria toxin T-domain: the roles of N-terminal histidines. MD
69  2013 Rational Design of Particle Mesh Ewald Compatible Lennard-Jones 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 V-ATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation. MD, V-ATPase
72  2012 Calculation of the relative free energy of oxidation of Azurin at pH 5 and pH 9. RE-TI
73  2012 Develop and test a solvent accessible surface area-based model in conformational entropy calculations. BSAS, HTS, MM-PBSA, 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 two-phase thermodynamic model. DOS, LJ
77  2012 Testing recent charge-on-spring type polarizable water models. I. Melting temperature and ice properties. COS, Ih
78  2011 Accurate determination of the Gibbs energy of Cu-Zr 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 HSMD-TI Method: The FKBP12-L8 Complex. DAM, DDM, HSMD, PME
81  2011 Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors. EDS
82  2011 Improved Binding Free Energy Predictions from Single-Reference 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 semi-closed 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 pi-Helices. EDS
86  2011 Relative stability of the open and closed conformations of the active site loop of streptavidin. AMBER, HSMD
87  2011 Soft-core potentials in thermodynamic integration: comparing one- and two-step transformations. ---
88  2010 Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange. HREX, SR-TI
89  2010 Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins. HSMD-TI, loop
90  2010 Molecular dynamics simulations of nonpolarizable inorganic salt solution interfaces: NaCl, NaBr, and NaI in transferable intermolecular potential 4-point with charge dependent polarizability (TIP4P-QDP) water. ---
91  2010 Nonpolar Solvation Free Energies of Protein-Ligand 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 Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs. GA
95  2009 Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir. IT-TI, PVR
96  2009 The self-referential method for linear rigid bodies: application to hard and Lennard-Jones 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 squalene-hopene cyclase. SHC, SSP
99  2007 Binding free energy prediction in strongly hydrophobic biomolecular systems. PMF
100  2007 Computational alanine scanning mutagenesis--an improved methodological approach. FEP, MM-PBSA