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■ Abbreviation / Long Form : MD / molecular dynamics

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Total Number of Papers: 10929
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Abbreviation:   MD  (>> Co-occurring Abbreviation)
Long Form:   molecular dynamics
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No. Year Title Co-occurring Abbreviation
2020 A novel cathepsin L inhibitor prevents the progression of idiopathic pulmonary fibrosis. SAR
2020 A solvent-solute cooperative mechanism for symmetry-breaking charge transfer. BA, SBCT, TF
2020 A study of starch-urea-water mixtures with a combination of molecular dynamics simulation and traditional characterization methods. ---
2020 A survey of algorithms for transforming molecular dynamics data into metadata for in situ analytics based on machine learning methods. ---
2020 Adaptive Markov state model estimation using short reseeding trajectories. MSM
2020 Adiabatic-Molecular Dynamics Generalized Vertical Hessian Approach: A Mixed Quantum Classical Method To Compute Electronic Spectra of Flexible Molecules in the Condensed Phase. ---
2020 Adsorption behavior of beta-cyclodextrin onto gold nanoparticles. AuNP, beta-CD, CDs
2020 Alteration of the groove width of DNA induced by the multimodal hydrogen bonding of denaturants with DNA bases in its grooves affects their stability. GdmCl
2020 AMBER Force Field Parameters for Cobalt-Containing Biological Systems: A Systematic Derivation Study. ---
10  2020 Analysis of membrane permeability due to synergistic effect of controlled shock wave and electric field application. DPPC
11  2020 Arenobufagin, isolated from toad venom, inhibited epithelial-to-mesenchymal transition and suppressed migration and invasion of lung cancer cells via targeting IKKbeta/NFkappaB signal cascade. Arg, HE
12  2020 Asymmetric ligand binding in homodimeric Enterobacter cloacae nitroreductase yields the Michaelis complex for nitroaromatic substrates. NR, p-NBA
13  2020 Atomistic probing of aptameric binding of CD19 outer membrane domain reveals an "aptamer walking" mechanism. ---
14  2020 Balanced Amino-Acid-Specific Molecular Dynamics Force Field for the Realistic Simulation of Both Folded and Disordered Proteins. IDPs
15  2020 Binding mechanism of spinosine and venenatine molecules with p300 HAT enzyme: Molecular screening, molecular dynamics and free-energy analysis. HAT, HDAC
16  2020 Biological evaluation and molecular dynamics simulation of water-soluble fullerene derivative C60[C(COOH)2]3. DPPH, HSA, ROS
17  2020 Biophysical characterization of p53 core domain aggregates. p53C
18  2020 Building better enzymes: Molecular basis of improved non-natural nucleobase incorporation by an evolved DNA polymerase. WT
19  2020 C13 - a new empirical force field to characterize the mechanical behavior of carbyne chains. ---
20  2020 Capturing Structural Transitions in Surfactant Adsorption Isotherms at Solid/Solution Interfaces. CMC, CSAC, MTT, SDS
21  2020 Characterization and In Silico Analysis of The Structural Features of G-CSF Derived from Lysates of Escherichia coli. DTT, G-CSF, G-CSFR, PDB, rh-G-CSF
22  2020 Characterization of protein interaction surface on fatty acyl selectivity of starter condensation domain in lipopeptide biosynthesis. NRPSs
23  2020 Charge-based interactions of antimicrobial peptides and general drugs with lipid bilayers. AMPs, CDs, ES, MAAs, vdW
24  2020 Closest-Packing Water Monolayer Stably Intercalated in Phyllosilicate Minerals under High Pressure. HB, vdW
25  2020 Comparative study of stability and transport of molecules through cyclic peptide nanotube and aquaporin: a molecular dynamics simulation approach. AQP2, CPN
26  2020 Computer-Aided Design of Nanoparticles for Transdermal Drug Delivery. NPs, SC
27  2020 Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations. CCFS, TOM
28  2020 Conformational flexibility of GRASPs and their constituent PDZ subdomains reveals structural basis of their promiscuous interactome. GRASP, PDZ
29  2020 Considerations for Docking of Selective Angiotensin-Converting Enzyme Inhibitors. ACE, IFPs, PDB, QSAR
30  2020 Controlled Manipulation and Multiscale Modeling of Suspended Silicon Nanostructures under Site-Specific Ion Irradiation. Si
31  2020 Counterion-Mediated Crossing of the Cyanine Limit in Crystals and Fluid Solution - Bond Length Alternation and Spectral Broadening Unveiled by Quantum Chemistry. DFT, QM/MM
32  2020 Cyanine dyes with tail length asymmetry enhance photoselection: Amultiscale study on DiD probes in a liquid disordered membrane. ---
33  2020 Data on A parametric temperature dependent potential for beta-PbF2: A numerical investigation by molecular dynamics. ---
34  2020 Dependences of Formation and Transition of the Surface Condensation Mode on Wettability and Temperature Difference. DWC, FWC, NC
35  2020 Design of potential IKK-betainhibitors using molecular docking and molecular dynamics techniques for their anti-cancer potential. IKK-beta
36  2020 Determination of the Free Energies of Mixing of Organic Solutions through a Combined Molecular Dynamics and Bayesian Statistics Approach. ---
37  2020 Development of the FMO/RI-MP2 Fully Analytic Gradient Using a Hybrid Distributed/Shared Memory Programming Model. ESP, FMO, GDDI, RI
38  2020 Discovery of novel nonpeptide small-molecule NRP1 antagonists: Virtual screening, molecular simulation and structural modification. VEGF
39  2020 DNA fragment translocation through the lipid membrane assisted by carbon nanotube. CNTs
40  2020 Do Molecular Dynamics Force Fields Capture Conformational Dynamics of Alanine in Water? PPII
41  2020 Dynamical reweighting methods for Markov models. MSMs
42  2020 Effect of a dirhamnolipid biosurfactant on the structure and phase behaviour of dimyristoylphosphatidylserine model membranes. diRL, DMPS, DSC, FTIR
43  2020 Effect of Polymer Concentration on the Structure and Dynamics of Short Poly(N,N-dimethylaminoethyl methacrylate) in Aqueous Solution: A Combined Experimental and Molecular Dynamics Study. PDMAEMA
44  2020 Effect of scale inhibitors on the structure and morphology of CaCO3 crystal electrochemically deposited on TA1 alloy. EIS, HEDP, PAA, PBTCA, Rct, SEM, XRD
45  2020 Effect of Transmembrane Electric Field on GM1 Containing DMPC-Cholesterol Monolayer: A Computational Study. Chol, DMPC, GM1
46  2020 Effects of the Van der Waals Force on the Vibration of Typical Multi-layered Two-dimensional Nanostructures. BP, MLBN, MLBP, MLGS, SPM, TMLTNs
47  2020 Elucidation the binding mechanism of Nelumbo nucifera-derived isoquinoline alkaloids as Rho-kinase 1 inhibitors by molecular docking and dynamic simulation. BBIs, SM, TBI, VSMCs
48  2020 Enhancement of thermo-mechanical stability for nanocomposites containing plasma treated carbon nanotubes with an experimental study and molecular dynamics simulations. CNTs, ICP-CNT, MSF-CNT
49  2020 Enhancing thermostability of a psychrophilic alpha-amylase by the structural energy optimization in the trajectories of molecular dynamics simulations. WT
50  2020 Ensemble-Based Molecular Simulation of Chemical Reactions under Vibrational Nonequilibrium. ---
51  2020 Evaluation of binding and antagonism/downregulation of brilanestrant molecule in estrogen receptor-alpha via quantum mechanics/molecular mechanics, molecular dynamics and binding free energy calculations. BRI, RMSD, RMSF, SERDs
52  2020 Evidence for an egg-box-like structure in iron(ii)-polygalacturonate hydrogels: a combined EXAFS and molecular dynamics simulation study. EXAFS
53  2020 Experimental investigation and molecular dynamics simulation of the binding of ellagic acid to bovine liver catalase: Activation study and interaction mechanism. ATR-FTIR, ELA, UV-vis
54  2020 Exploring the Activation Mechanism of a Metabotropic Glutamate Receptor Homodimer via Molecular Dynamics Simulation. PSN, TMDs
55  2020 Exploring the binding modes of cordycepin to human adenosine deaminase 1 (ADA1) compared to adenosine and 2'-deoxyadenosine. ADA1, Ade, DEO, LF
56  2020 Exploring the different states of wild-type T-cell receptor and mutant conformational changes towards understanding the antigen recognition. CDR, MHC, TCR
57  2020 Exploring the role of the membrane bilayer in the recognition of candesartan by its GPCR AT1 receptor. RAAS
58  2020 ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution. FF, MM, PDB, QM
59  2020 Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations. AFM, HS
60  2020 Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach. CG, TrV
61  2020 Growth Mechanism of Gold Nanorods: the Effect of Tip-Surface Curvature As Revealed by Molecular Dynamics Simulations. CTAB
62  2020 Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations. IDPs
63  2020 High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. EPR, PELDOR/DEER
64  2020 How does the novel T315L mutation of breakpoint cluster region-abelson (BCR-ABL) kinase confer resistance to ponatinib: a comparative molecular dynamics simulation study. Abl, ALL, bcr, BCR-ABL, TKIs, WT
65  2020 Hybrid Kinetic Monte Carlo/Molecular Dynamics Simulations of Bond Scissions in Proteins. KIMMDY
66  2020 Identification of a novel binding mechanism of Quinoline based molecules with lactate dehydrogenase of Plasmodium falciparum. MM-PBSA, Pf
67  2020 Identification of new potent A1 adenosine receptor antagonists using a multistage virtual screening approach. AR, RF
68  2020 Identification of novel Nrf2/Keap1 pathway mutations in pediatric acute lymphoblastic leukemia. ALL, Keap1, NF-kappaB, Nrf2, ROS
69  2020 Implementation of Geometry-Dependent Charge Flux into the Polarizable AMOEBA+ Potential. FFs, GDCF
70  2020 Implicit Micelle Model for Membrane Proteins Using Superellipsoid Approximation. APP, IMIC
71  2020 Improved Cation Binding to Lipid Bilayers with Negatively Charged POPS by Effective Inclusion of Electronic Polarization. ECC, POPS, PS
72  2020 Improved Modeling of Cation-pi and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins. FFs, QM
73  2020 Improved SMTB-Q model applied to oxygen migration and pressure phase transitions in UO2. IO, VO
74  2020 In Silico identification of hydantoin derivatives: a novel natural prolyl hydroxylase inhibitor. AD, HIF, KPLS, MM-GBSA, PHD
75  2020 Influence of the ion size on the stability of the smectic phase of ionic liquid crystals. DSC
76  2020 Inhibition of CD44 sensitizes cisplatin-resistance and affects Wnt/beta-catenin signaling in HNSCC cells. CSC, THIQ
77  2020 Insight into Speciation and Electrochemistry of Uranyl Ions in Deep Eutectic Solvents. ChCl, DES
78  2020 Insights from molecular dynamics simulations and steered molecular dynamics simulations to exploit new trends of the interaction between HIF-1alpha and p300. HIF-1, PPIs
79  2020 Insights into channel modulation mechanism of RYR1 mutants using Ca2+ imaging and molecular dynamics. MH, NTD
80  2020 Insights into the Binding Recognition and Susceptibility of Tofacitinib toward Janus Kinases. JAKs
81  2020 Interactions of a multifunctional di-triazole derivative with Alzheimer's Abeta42 monomer and Abeta42 protofibril: a systematic molecular dynamics study. AD, CHC, MM-PBSA, MTDL, ROS
82  2020 Interfacial Adhesion of Polylactic Acid on Cellulose Surface: A Molecular Dynamics Study. ---
83  2020 Inverted Binding of Non-natural Substrates in Strictosidine Synthase Leads to a Switch of Stereochemical Outcome in Enzyme-Catalyzed Pictet-Spengler Reactions. STR, THBC
84  2020 Investigating the interactions of the first 17 amino acid residues of Huntingtin with lipid vesicles using mass spectrometry and molecular dynamics. DOPC, ESI-MS, PC, PE, POPC, POPE
85  2020 Investigation of binding mechanism and downregulation of elacestrant for wild and L536S mutant estrogen receptor-alpha through molecular dynamics simulation and binding free energy analysis. ELA, SERDs
86  2020 Investigation of guanidinium chloride-induced unfolding pathway of sphingosine kinase 1. GdmCl, SphK1
87  2020 Investigations of Albumin-Insulin Detemir Complexes Using Molecular Dynamics Simulations and Free Energy Calculations. DLS, MM-PBSA
88  2020 Ligand-induced disorder-to-order transitions characterized by structural proteomics and molecular dynamics simulations. ---
89  2020 Liquid crystal ordering of nucleic acids. bp, dsDNA, dsRNA, LC, NAs, PMF, RCs, US
90  2020 Low-temperature dependence on the THz spectrum of CL-20/TNT energetic cocrystal by molecular dynamics simulations. THz
91  2020 Material Analysis and Molecular Dynamics Simulation for Cavitation Erosion and Corrosion Suppression in Water Hydraulic Valves. PTFE
92  2020 MD simulations reveal alternate conformations of the oxyanion hole in the Zika virus NS2B/NS3 protease. ZIKV
93  2020 MDMS: Software Facilitating Performing Molecular Dynamics Simulations. MDMS
94  2020 Mechanisms of ATP to cAMP Conversion Catalyzed by the Mammalian Adenylyl Cyclase: A Role of Magnesium Coordination Shells and Proton Wires. ATP, cAMP, ES, QM/MM
95  2020 Microscopic Study of Proton Kinetic Energy Anomaly for Nanoconfined Water. DINS, SWCNTs, VDOS
96  2020 Microsecond-timescale simulations suggest 5-HT-mediated preactivation of the 5-HT3A serotonin receptor. 5-HT, 5-HT3A, ECD, pLGICs, TMD
97  2020 Modeling amino-acid side chain infrared spectra: the case of carboxylic residues. IR, PMM
98  2020 Molecular Basis for Metabolic Regioselectivity and Mechanism of Cytochrome P450s toward Carcinogenic 4-(Methylnitrosamino)-(3-pyridyl)-1-butanone. DFT
99  2020 Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarization. Smac, XIAP
100  2020 Molecular characterization of the outer membrane of Pseudomonas aeruginosa. AA, CG, LPS, OM