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Abbreviation : US
Long Form : umbrella sampling
No. Year Title Co-occurring Abbreviation
2020 Liquid crystal ordering of nucleic acids. bp, dsDNA, dsRNA, LC, MD, NAs, PMF, RCs
2020 Predicting Partition Coefficients of Neutral and Charged Solutes in the Mixed SLES-Fatty Acids Micellar System. CGenFF, MD, PMF, SLES
2019 Delineating Protein-Protein Curvilinear Dissociation Pathways and Energetics with Naive Multiple-Walker Umbrella Sampling Simulations. PMF
2019 Dynamic Docking of a Medium-Sized Molecule to Its Receptor by Multicanonical MD Simulations. McMD
2019 Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method. CTSK, DHQase, FXa, Hsp90, RMSEs
2019 Evaluation of Predicted Protein-Protein Complexes by Binding Free Energy Simulations. ---
2019 Insight into the selective binding mechanism of DNMT1 and DNMT3A inhibitors: a molecular simulation study. DNMTs, MD
2019 Insights Into the Resistance Mechanisms of Inhibitors to FLT3 F691L Mutation via an Integrated Computational Approach. aMDs, AML, DCC, FEL, FLT3, MD, PCA, SASA
2019 Interconversion of hydrated protons at the interface between liquid water and platinum. AIMD, HER
10  2019 Investigation of Molecular Details of Keap1-Nrf2 Inhibitors Using Molecular Dynamics and Umbrella Sampling Techniques. MD, PPI
11  2019 Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed? beta-CD, MAPK, PMF
12  2019 Prediction of AChE-ligand affinity using the umbrella sampling simulation. AChE, AD, BBB, PMF, RMSE
13  2018 Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation. AI, FE Profile, MBAR, QM/MM, SE, TP
14  2018 Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges. BAR, DDM, HREM, MAD, RMSD, WHAM
15  2018 Dimer Interface of the Human Serotonin Transporter and Effect of the Membrane Composition. hSERT, MD, TM12
16  2018 Efficient Computation of Free Energy Surfaces of Diels⁻Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level. AI, DA, FE, MBAR, QM/MM, SE, wTP
17  2018 Enhanced Molecular Dynamics Methods Applied to Drug Design Projects. aMD
18  2018 Importance of protein flexibility in molecular recognition: a case study on Type-I1/2 inhibitors of ALK. ALK, MD
19  2018 Insight into resistance mechanism of anaplastic lymphoma kinase to alectinib and JH-VIII-157-02 caused by G1202R solvent front mutation. ALK, MD, NSCLC
20  2018 Insights into Resistance Mechanisms of Inhibitors to Mps1 C604Y Mutation via a Comprehensive Molecular Modeling Study. aMD, MD
21  2018 Molecular Dynamics Simulations of Ion Selectivity in a Claudin-15 Paracellular Channel. PMF
22  2018 Molecular Mechanism Behind the Resistance of the G1202R-Mutated Anaplastic Lymphoma Kinase to the Approved Drug Ceritinib. ALK, ALKWT, aMD, DCCM, NSCLC, PCA
23  2018 Molecular Mechanism, Dynamics, and Energetics of Protein-Mediated Dinucleotide Flipping in a Mismatched DNA: A Computational Study of the RAD4-DNA Complex. MD, RAD4, XPC
24  2018 Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method. BAR, DDM, HREM, QM, RMSE, WHAM
25  2018 Protein-Ligand Dissociation Simulated by Parallel Cascade Selection Molecular Dynamics. MSM, PaCS-MD, SMD
26  2017 How Does the L884P Mutation Confer Resistance to Type-II Inhibitors of JAK2 Kinase: A Comprehensive Molecular Modeling Study. ALL, JAK2, MD, MPNs
27  2017 Insight into resistance mechanisms of AZD4547 and E3810 to FGFR1 gatekeeper mutation via theoretical study. FGFR1, MM/GBSA, PMF
28  2017 Theoretical studies on FGFR isoform selectivity of FGFR1/FGFR4 inhibitors by molecular dynamics simulations and free energy calculations. FGFRs, MD, MM/GBSA
29  2017 Umbrella sampling molecular dynamics simulations reveal concerted ion movement through G-quadruplex DNA channels. ABF, MD, PMF
30  2016 Effective Riemannian Diffusion Model for Conformational Dynamics of Biomolecular Systems. MFEP, PMF
31  2016 Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations. ---
32  2016 Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics. CVs, MTD, WHAM
33  2016 Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin. 4-BP, DHP, MD, PMF, SMD, UV-vis
34  2015 DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates. MD
35  2015 Exploring resistance mechanisms of HCV NS3/4A protease mutations to MK5172: insight from molecular dynamics simulations and free energy calculations. MD, MM/GBSA, WT
36  2015 Molybdenum carbide nanocatalysts at work in the in situ environment: a density functional tight-binding and quantum mechanical/molecular mechanical study. DFTB, MCNPs, MM, QM
37  2015 Simple, yet powerful methodologies for conformational sampling of proteins. cMD, FFM, MD, OFLOOD, PaCS-MD, TBSA, WHAM
38  2014 Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations. ---
39  2014 Efficient calculation of relative binding free energies by umbrella sampling perturbation. PMF
40  2014 Free energy predictions of ligand binding to an alpha-helix using steered molecular dynamics and umbrella sampling simulations. EGCG, MD, SMD
41  2014 Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers. GPA, NMR, REMD, TM
42  2014 REMD and umbrella sampling simulations to probe the energy barrier of the folding pathways of engrailed homeodomain. EnHD, REMD, WHAM
43  2014 Unbinding free energy of acetylcholinesterase bound oxime drugs along the gorge pathway from metadynamics-umbrella sampling investigation. PMF
44  2013 Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal. ---
45  2013 Overcoming dissipation in the calculation of standard binding free energies by ligand extraction. MD
46  2013 The liquid-liquid transition in supercooled ST2 water: a comparison between umbrella sampling and well-tempered metadynamics. WT-MetaD
47  2012 Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space. BAR, BAR-US, BOH-US
48  2012 Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer. H-REMD, PMF, RMSD
49  2011 Use of Umbrella Sampling to Calculate the Entrance/Exit Pathway for Z-Pro-Prolinal Inhibitor in Prolyl Oligopeptidase. POP, SMD, ZPP
50  2010 Ball-and-Stick Local Elevation Umbrella Sampling: Molecular Simulations Involving Enhanced Sampling within Conformational or Alchemical Subspaces of Low Internal Dimensionalities, Minimal Irrelevant Volumes, and Problem-Adapted Geometries. EDS, LE
51  2010 Dynamic ligand-induced-fit simulation via enhanced conformational samplings and ensemble dockings: a survivin example. CPC, HTS, MBAR, PMF, REMD
52  2010 Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling. BF, FB-LEUS, LE, LEUS, MD, poly-Val, polyAla, VD
53  2010 Using the local elevation method to construct optimized umbrella sampling potentials: calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water. LE, LEUS, MD
54  2009 Simulating the kinetics and thermodynamics of transitions via forward flux/umbrella sampling. FFS
55  2006 Structure and energetics of channel-forming protein-polysaccharide complexes inferred via computational statistical thermodynamics. alphaHL, beta-CD, TI, WHAM