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■ Abbreviation / Long Form : MD / molecular dynamics simulations

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Total Number of Papers: 179
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Abbreviation:   MD  (>> Co-occurring Abbreviation)
Long Form:   molecular dynamics simulations
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No. Year Title Co-occurring Abbreviation
1  2020 Effect of hydrophobic and hydrogen bonding interactions on the potency of ss-alanine analogs of G-protein coupled glucagon receptor inhibitors. GCGRs, HOMO, LUMO, MM/GBSA
2  2020 Replica exchange dissipative particle dynamics method on threadlike micellar aqueous solutions. DPD, REDPD, REM
3  2019 A structure-activity relationship study of Forkhead Domain Inhibitors (FDI): The importance of halogen binding interactions. DBD, FDI, FDI-6, FOXM1
4  2019 Arylamide as Potential Selective Inhibitor for Matrix Metalloproteinase 9 (MMP9): Design, Synthesis, Biological Evaluation, and Molecular Modeling. MMP9
5  2019 Discovery of novel acylhydrazone neuraminidase inhibitors. NA, OC
6  2019 Discovery of selective farnesoid X receptor agonists for the treatment of hyperlipidemia from traditional Chinese medicine based on virtual screening and in vitro validation. FXR, TCM, TCMD
7  2019 Effect of Hydroxyapatite Surface on BMP-2 Biological Properties by Docking and Molecular Simulation Approaches. BMP-2, HAP, SMD
8  2019 Heparin-reduced graphene oxide nanocomposites for curcumin delivery: in vitro, in vivo and molecular dynamics simulation study. ADH, CUR, GBNMs, GO, rGO, UFH
9  2019 Mechanism of Sulfate Activation Catalyzed by ATP Sulfurylase - Magnesium Inhibits the Activity. APS, ATPS, SRB
10  2019 Molecular design of antioxidant lubricating oil additives via QSPR and analysis dynamic simulation method. SAPS, ZDDP
11  2019 Molecular simulation of thin liquid films: Thermal fluctuations and instability. STF
12  2019 Multiscale Simulation on Product Distribution from Pyrolysis of Styrene-Butadiene Rubber. DFT
13  2019 Probing the binding mechanism of capecitabine to human serum albumin using spectrometric methods, molecular modeling, and chemometrics approach. CAP, HSA, MCR-ALS
14  2019 Resolving solution conformations of the model semi-flexible polyelectrolyte homogalacturonan using molecular dynamics simulations and small-angle x-ray scattering. SAXS
15  2019 Scalar activity induced phase separation and liquid-solid transition in a Lennard-Jones system. MBWR
16  2019 Stabilization of a Highly Concentrated Colloidal Suspension of Pristine Metallic Nanoparticles. NPs
17  2019 Structural Analysis and Dynamic Processes of the Transmembrane Segment Inside Different Micellar Environments-Implications for the TM4 Fragment of the Bilitranslocase Protein. BTL, NMR, SDS, TM
18  2019 Structural and free energy landscape of novel mutations in ribosomal protein S1 (rpsA) associated with pyrazinamide resistance. Mtb, MTs, pncAWT, POA, PZA, PZase, TB
19  2019 Structural dynamics behind variants in pyrazinamidase and pyrazinamide resistance. anti-TB, Mtb, MTs, POA, PZA, PZase, RMSD, RMSF, WT
20  2019 Structural insights into DNA-stabilized silver clusters. AUC, ssDNA
21  2019 Structure-based identification of novel sirtuin inhibitors against triple negative breast cancer: An in silico and in vitro study. PDIs, SIRTs, TNBC
22  2018 A Molecular Dynamics-Quantum Mechanics Theoretical Study of DNA-Mediated Charge Transport in Hydrated Ionic Liquids. CT, IL
23  2018 Ab Initio Prediction of NMR Spin Relaxation Parameters from Molecular Dynamics Simulations. ---
24  2018 Bare surface of gold nanoparticle induces inflammation through unfolding of plasma fibrinogen. NPs
25  2018 Effect of Electron Donating Functional Groups on Corrosion Inhibition of J55 Steel in a Sweet Corrosive Environment: Experimental, Density Functional Theory, and Molecular Dynamic Simulation. DFT, XPS
26  2018 Insights into the interaction and binding mode of a set of antifungal azoles as inhibitors of potential fungal enzyme-based targets. CoMFA
27  2018 Investigation of 15-hydroxyprostaglandin dehydrogenase catalytic reaction mechanism by molecular dynamics simulations. ---
28  2018 Multilevel Molecular Modeling Approach for a Rational Design of Ionic Current Sensors for Nanofluidics. CNT
29  2018 Spectroscopy and molecular dynamics simulation study on the interaction of sunset yellow food additive with pepsin. SY
30  2018 Structural and thermodynamic characterization of endo-1,3-beta-glucanase: Insights into the substrate recognition mechanism. ---
31  2018 Tannerella forsythia Tfo belongs to Porphyromonas gingivalis HmuY-like family of proteins but differs in heme-binding properties. ---
32  2018 The design of high affinity human PD-1 mutants by using molecular dynamics simulations (MD). ---
33  2018 The Interaction Modes of Haloimidazolium Salts in Solution. ITC, QM/MM
34  2018 Understanding the inhibitory mechanism of BIT225 drug against p7 viroporin using computational study. ER, HCV, HMA, IS, TM
35  2018 Universal Relationship between Molecular Structure and Crystal Structure in Peptoid Polymers and Prevalence of the cis Backbone Conformation. ---
36  2018 V-Shaped Molecular Configuration of Wax Esters of Jojoba Oil in a Langmuir Film Model. JO, WEs
37  2018 Vasoinhibin comprises a three-helix bundle and its antiangiogenic domain is located within the first 79 residues. PRL
38  2018 X-Ray diffraction and resonance shear measurement of nano-confined ionic liquids. ILs, RSM
39  2017 A theoretical and experimental study of calcium, iron, zinc, cadmium, and sodium ions absorption by aspartame. ---
40  2017 Are induced fit protein conformational changes caused by ligand-binding predictable? A molecular dynamics investigation. ---
41  2017 Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model. EET, SH, TDDFT
42  2017 Computational design of cyclic peptides for the customized oriented immobilization of globular proteins. beta 2m
43  2017 Expression of recombinant SnRK1 in E. coli. Characterization of adenine nucleotide binding to the SnRK1.1/AKINbetagamma-beta3 complex. ---
44  2017 Interactions of the Calcite {10.4} Surface with Organic Compounds: Structure and Behaviour at Mineral - Organic Interfaces. XRR
45  2017 Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics. KMC
46  2017 Ligand recognition properties of the vasopressin V2 receptor studied under QSAR and molecular modeling strategies. QSAR, V2R
47  2017 MD simulations and multivariate studies for modeling the antileishmanial activity of peptides. ---
48  2017 Molecular Dynamics Simulation of a RNA Aptasensor. ---
49  2017 Observation of the unexpected morphology of graphene wrinkle on copper substrate. AFM, CVD
50  2017 Qualitative and quantitative simulation of androgen receptor antagonists: A case study of polybrominated diphenyl ethers. AR, PBDEs, QSAR
51  2017 Salt Bridge Formation between the I-BAR Domain and Lipids Increases Lipid Density and Membrane Curvature. I-BAR
52  2017 Solute Partitioning in Micelles: Combining Molecular Dynamics Simulations, COSMOmic, and Experiments. CTAB, SDS, TX-114
53  2017 Spectroscopic Observation and Molecular Dynamics Simulation of Ga Surface Segregation in Liquid Pd-Ga Alloys. ---
54  2017 Structural insights into type I and type II of nsp4 porcine reproductive and respiratory syndrome virus (nsp4 PRRSV) by molecular dynamics simulations. PCA, PRRSV
55  2017 Structured Ionomer Thin Films at Water Interface: Molecular Dynamics Simulation Insight. ---
56  2017 UV-activated ZnO films on a flexible substrate for room temperature O2 and H2O sensing. KPFM, LAMMPS
57  2016 Ab initio calculation of thermodynamic potentials and entropies for superionic water. bcc, DFT, fcc
58  2016 Atomistic resolution structure and dynamics of lipid bilayers in simulations and experiments. ---
59  2016 BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. ---
60  2016 Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures. QM/MM
61  2016 Classical investigation of long-range coherence in biological systems. ---
62  2016 Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations. GCM
63  2016 Effect of flavonols on wine astringency and their interaction with human saliva. ---
64  2016 Hydrodynamic Radius Fluctuations in Model DNA-Grafted Nanoparticles. NPs, Rh, ssDNA
65  2016 Molecular simulation study of the specific combination between four kinds of phthalic acid esters and human serum albumin. HSA, PAEs
66  2016 Probing the binding of Cu(2+) ions to a fragment of the Abeta(1-42) polypeptide using fluorescence spectroscopy, isothermal titration calorimetry and molecular dynamics simulations. ITC, MES
67  2016 Residue-based design of small molecule inhibitor for H1N1, H5N1 and H7N1 mutants. ---
68  2016 Simulating the Favorable Aggregation of Monolacunary Keggin Anions. ---
69  2016 The compatibility of Tacrine molecule with poly(n-butylcyanoacrylate) and Chitosan as efficient carriers for drug delivery: A molecular dynamics study. CNS, PBCA
70  2016 The discovery of novel and selective fatty acid binding protein 4 inhibitors by virtual screening and biological evaluation. LPS
71  2016 Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model. MSM, TBA
72  2016 What controls open-pore and residual currents in the first sensing zone of alpha-hemolysin nanopore? Combined experimental and theoretical study. alphaHL
73  2015 1-Butanol absorption in poly(styrene-divinylbenzene) ion exchange resins for catalysis. ---
74  2015 A molecular dynamics study of guest-host hydrogen bonding in alcohol clathrate hydrates. sH, sII
75  2015 Adaptation of Extremophilic Proteins with Temperature and Pressure: Evidence from Initiation Factor 6. IF6, QENS
76  2015 Confronting the complexity of CNT materials. CNT
77  2015 Extended structure of rat islet amyloid polypeptide in solution. hIAPP, IAPP, NMR, rIAPP, SAXS
78  2015 Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6. ---
79  2015 Investigation of ligand selectivity in CYP3A7 by molecular dynamics simulations. DHEA
80  2015 Ion Association in Hydrothermal Sodium Sulfate Solutions Studied by Modulated FT-IR-Raman Spectroscopy and Molecular Dynamics. SCWG, SCWO
81  2015 Molecular adhesion at clay nanocomposite interfaces depends on counterion hydration-molecular dynamics simulation of montmorillonite/xyloglucan. Mnt, XG
82  2015 Preferential sites for intramolecular glucosepane cross-link formation in type I collagen: A thermodynamic study. AGEs, ECM, MMP1
83  2015 Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins. CO, PCA
84  2015 Probing Origin of Binding Difference of inhibitors to MDM2 and MDMX by Polarizable Molecular Dynamics Simulation and QM/MM-GBSA Calculation. ---
85  2015 Surfactin at the Water/Air Interface and in Solution. ---
86  2015 The stability of amino-functionalized polyhedral oligomeric silsesquioxanes in water. POSS
87  2014 Conformational characterization of ipomotaosides and their recognition by COX-1 and 2. ---
88  2014 HIV-1 Tat membrane interactions probed using X-ray and neutron scattering, CD spectroscopy and MD simulations. DOPC, DOPE, DOPS, LAXS, Tat, WAXS
89  2014 Hydration Gibbs free energies of open and closed shell trivalent lanthanide and actinide cations from polarizable molecular dynamics. ---
90  2014 Identification of novel tyrosine kinase inhibitors for drug resistant T315I mutant BCR-ABL: a virtual screening and molecular dynamics simulations study. CML
91  2014 In Silico Insight into Potent of Anthocyanin Regulation of FKBP52 to Prevent Alzheimer's Disease. AD
92  2014 Molecular modeling study of the recognition mechanism and enantioseparation of 4-hydroxypropranolol by capillary electrophoresis using carboxymethyl-beta-cyclodextrin as the chiral selector. CE, CM-beta-CD, DFT, PM3
93  2014 Multiple scale dynamics in proteins probed at multiple time scales through fluctuations of NMR chemical shifts. ---
94  2014 Nanomechanics of beta-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods. AA, AFM, CG MD
95  2014 Vesicle structures from bolaamphiphilic biosurfactants: experimental and molecular dynamics simulation studies on the effect of unsaturation on sophorolipid self-assemblies. LNSL
96  2013 Competing specific interactions investigated by molecular dynamics: analysis of poly(p-dioxanone)/poly(vinylphenol) blends. FTIR, PPDO, PVPh, RDFs
97  2013 Conformational coupling between receptor and kinase binding sites through a conserved salt bridge in a signaling complex scaffold protein. CD
98  2013 Conformational flexibility of the ErbB2 ectodomain and trastuzumab antibody complex as revealed by molecular dynamics and principal component analysis. ErbB2-ECD, PCA
99  2013 Drug design for neuropathic pain regulation from traditional Chinese medicine. FLAT, MLR, SVM, TCM
100  2013 Identification of crucial amino acids in mouse aldehyde oxidase 3 that determine substrate specificity. AOX, mAOX3, XOR