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Abbreviation : MD
Long Form : molecular dynamics
No. Year Title Co-occurring Abbreviation
2021 Humidity effect on peeling of monolayer graphene and hexagonal boron nitride. h-BN
2021 Molecular Dynamics Simulations of Channelrhodopsin Chimera, C1C2. DOPC
2021 Molecular Simulations Guidelines for Biological Nanomaterials: From Peptides to Membranes. ---
2021 Pulling a folded polymer through a nanopore. ---
2021 Repurposing of existing FDA approved drugs for Neprilysin inhibition: An in-silico study. HTVS, IFD-SP, NEP, SP
2021 Studies in molecular modeling, in-vitro CDK2 inhibition and antimetastatic activity of some synthetic flavones. ---
2021 Use of a combination of the MD simulations and NMR spectroscopy to determine the regulatory mechanism of pulsed electric field (PEF) targeting at C-terminal histidine of VNAVLH. PEF
2020 "Register-shift" insulin analogs uncover constraints of proteotoxicity in protein evolution. IR
2020 2-Methyltetrol sulfate ester-initiated nucleation mechanism enhanced by common nucleation precursors: A theory study. DMA, MA, MTS, NPF, SA, TMA
10  2020 A 200 nanoseconds all-atom simulation of the pH-dependent EF loop transition in bovine beta-lactoglobulin. The role of the orientation of the E89 side chain. BLG, PDB
11  2020 A Benzene-Mapping Approach for Uncovering Cryptic Pockets in Membrane-Bound Proteins. DENV
12  2020 A boosted unbiased molecular dynamics method for predicting ligands binding mechanisms: Probing the binding pathway of dasatinib to Src-kinase. ---
13  2020 A case study of poly (aryl ether sulfone) hemodialysis membrane interactions with human blood: Molecular dynamics simulation and experimental analyses. ATR-FTIR, CKD, ESRD, hFg, HSA, SEM, SSNMR, TEM, TRF
14  2020 A Closer Look at Anandamide Interaction With TRPV1. AEA, TRPV1
15  2020 A coarse-grain force field based on quantum mechanics (CGq FF) for molecular dynamics simulation of poly(ethylene glycol)-block-poly(epsilon-caprolactone) (PEG-b-PCL) micelles. AA, NB, PCL, PEG, PEG-b-PCL, Rg
16  2020 A coarse-grained model of dimethyl sulfoxide for molecular dynamics simulations with lipid membranes. CG, DMSO
17  2020 A combined NMR, MD and DFT conformational analysis of 9-O-acetyl sialic acid-containing GM3 ganglioside glycan and its 9-N-acetyl mimic. DFT, GM3-glycan, NMR
18  2020 A comprehensive study of the thermal conductivity of the hard sphere fluid and solid by molecular dynamics simulation. ET, HS
19  2020 A computational approach to drug repurposing against SARS-CoV-2 RNA dependent RNA polymerase (RdRp). COVID-19, RdRp, SARS-CoV-2
20  2020 A computational approach to explore and identify potential herbal inhibitors for the p21-activated kinase 1 (PAK1). C-I, NA, PAK1, SPN
21  2020 A computational strategy to understand structure-activity relationship of 1,3-disubstituted imidazole [1,5-alpha] pyrazine derivatives described as ATP competitive inhibitors of the IGF-1 receptor related to Ewing sarcoma. 1,5-alpha, LIE
22  2020 A computational study of effects on membrane recruitment of the polar linkers in Vitamin E derivatives. VE
23  2020 A dynamic simulation study of FDA drug from zinc database against COVID-19 main protease receptor. Mpro
24  2020 A hybrid theoretical method for predicting electrokinetic energy conversion in nanochannels. CDFT, EKEC, NS, PB
25  2020 A Method for Obtaining Liquid-Solid Adsorption Rates from Molecular Dynamics Simulations: Applied to Methanol on Pt(111) in H2O. ---
26  2020 A molecular dynamics approach on the Y393C variant of protein disulfide isomerase A1. PDIA1
27  2020 A Molecular Dynamics Investigation of the Temperature Effect on the Mechanical Properties of Selected Thin Films for Hydrogen Separation. ---
28  2020 A molecular dynamics study on magnetic imidazolium-based ionic liquids: the effect of an external magnetic field. MIL, RDF, SDF
29  2020 A molecular dynamics study on the buckling behavior of single-walled carbon nanotubes filled with gold nanowires. GNWs, SWCNTs
30  2020 A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2. MLR, PCA, QSAR, Rg, RMSD, RMSF, SASA
31  2020 A new approach to separate hydrogen from carbon dioxide using graphdiyne-like membrane. DFT, GDY-H, GPU
32  2020 A New Class of Ionically Conducting Fluorinated Ether Electrolytes with High Electrochemical Stability. HFEs, NMR
33  2020 A new functional JAZ degron sequence in strawberry JAZ1 revealed by structural and interaction studies on the COI1-JA-Ile/COR-JAZs complexes. JA-Ile
34  2020 A novel approach to calculate protein adsorption isotherms by molecular dynamics simulations. SMA
35  2020 A novel cathepsin L inhibitor prevents the progression of idiopathic pulmonary fibrosis. SAR
36  2020 A novel diterpene agent isolated from Microbispora hainanensis strain CSR-4 and its in vitro and in silico inhibition effects on acetylcholine esterase enzyme. ANI, CAS, DDH, PAS, rhAChE
37  2020 A novel hotspot and rare somatic mutation p.A138V, at TP53 is associated with poor survival of pancreatic ductal and periampullary adenocarcinoma patients. PAC, PDAC
38  2020 A novel hybrid technique to fabricate silicon-based micro-implants with near defect-free quality for neuroprosthetics application. ---
39  2020 A novel multiscale scheme to accelerate atomistic simulations of bio-macromolecules by adaptively driving coarse-grained coordinates. ADMS, CG
40  2020 A Remarkable Difference That One Fluorine Atom Confers on the Mechanisms of Inactivation of Human Ornithine Aminotransferase by Two Cyclohexene Analogues of gamma-Aminobutyric Acid. ESP, HCC, hOAT
41  2020 A Role of Newly Found Auxiliary Site in Phospholipase A1 from Thai Banded Tiger Wasp (Vespa affinis) in Its Enzymatic Enhancement: In Silico Homology Modeling and Molecular Dynamics Insights. DMPC
42  2020 A second shell residue modulates a conserved ATP-binding site with radically different affinities for ATP. ---
43  2020 A single amino acid substitution alters ClpS2 binding specificity. ---
44  2020 A singularity-free torsion angle potential for coarse-grained molecular dynamics simulations. CG
45  2020 A solvent-solute cooperative mechanism for symmetry-breaking charge transfer. BA, SBCT, TF
46  2020 A spectroscopic and computational intervention of interaction of lysozyme with 6-mercaptopurine. 6-MP, CD, FCS, HEW, LYZ
47  2020 A Structural Model for Bax∆2-Mediated Activation of Caspase 8-Dependent Apoptosis. ---
48  2020 A study of starch-urea-water mixtures with a combination of molecular dynamics simulation and traditional characterization methods. ---
49  2020 A Supervised Molecular Dynamics Approach to Unbiased Ligand-Protein Unbinding. SuMD
50  2020 A survey of algorithms for transforming molecular dynamics data into metadata for in situ analytics based on machine learning methods. ---
51  2020 A Switch between Two Intrinsically Disordered Conformational Ensembles Modulates the Active Site of a Basic-Helix-Loop-Helix Transcription Factor. bHLH, EPR, MAX, NMR
52  2020 A systematic strategy for the investigation of vaccines and drugs targeting bacteria. ---
53  2020 A Two-Ended Data-Driven Accelerated Sampling Method for Exploring the Transition Pathways between Two Known States of Protein. ADK
54  2020 A Unified De Novo Approach for Predicting the Structures of Ordered and Disordered Proteins. IDPs, MC
55  2020 A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories. IFPs, RAMD
56  2020 Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms. FFT, GPU
57  2020 Accelerated Protein Folding Using Greedy-Proximal A. ---
58  2020 Acceleration of Liquid-Crystalline Phase Transition Simulations Using Selectively Scaled and Returned Molecular Dynamics. LC, ssrMD
59  2020 Accessing slow diffusion in solids by employing metadynamics simulation. CI-NEB, MTD
60  2020 Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion. FF
61  2020 Accurate Vapor Pressure Prediction for Large Organic Molecules: Application to Materials Utilized in Organic Light-Emitting Diodes. OLEDs
62  2020 Activation Microswitches in Adenosine Receptor A2A Function as Rheostats in the Cell Membrane. GPCRs
63  2020 Activation of the G-Protein-Coupled Receptor Rhodopsin by Water. ---
64  2020 Adaptive Markov state model estimation using short reseeding trajectories. MSM
65  2020 Addressing free fatty acid receptor 1 (FFAR1) activation using supervised molecular dynamics. ECL2, FFAR1, GPCR, SuMD, T2DM
66  2020 Adiabatic-Molecular Dynamics Generalized Vertical Hessian Approach: A Mixed Quantum Classical Method To Compute Electronic Spectra of Flexible Molecules in the Condensed Phase. ---
67  2020 Adsorption and sequential thermal release of F2 , Cl2 , and Br2 molecules by a porous organic cage material (CC3-R): Molecular dynamics and grand-canonical Monte Carlo simulations. GCMC, RDF
68  2020 Adsorption behavior of beta-cyclodextrin onto gold nanoparticles. AuNP, beta-CD, CDs
69  2020 Adsorption of sulfamethoxazole and sulfadiazine on phosphorus-containing stalk cellulose under different water pH studied by quantitative evaluation. DFT, EDA, FOT, HOMO, SAs, SD, SMZ, vdW
70  2020 Adsorption of three pesticides on polyethylene microplastics in aqueous solutions: Kinetics, isotherms, thermodynamics, and molecular dynamics simulation. GCMC, PE
71  2020 Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems. SBDD
72  2020 Advancing Aptamers as Molecular Probes for Cancer Theranostic Applications-The Role of Molecular Dynamics Simulation. SELEX
73  2020 Aggregated Amphiphilic Antimicrobial Peptides Embedded in Bacterial Membranes. AMPs, MICs, NR, STORM
74  2020 Agonism activities of lyso-phosphatidylcholines (LPC) Ligands binding to peroxisome proliferator-activated receptor gamma (PPARgamma). LBD, LPC, PPAR, PPARgamma
75  2020 Agonist-Specific Conformations of the M2 Muscarinic Acetylcholine Receptor Assessed by Molecular Dynamics. ---
76  2020 All-atom molecular dynamics simulations of weak polyionic brushes: influence of charge density on the properties of polyelectrolyte chains, brush-supported counterions, and water molecules. PAA
77  2020 Allosteric Coupling Between Drug Binding and the Aromatic Cassette in the Pore Domain of the hERG1 Channel: Implications for a State-Dependent Blockade. VSD
78  2020 Allosteric Priming of E.coli CheY by the Flagellar Motor Protein FliM. FliMN
79  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
80  2020 Aluminium nanoparticle modelling coupled with molecular dynamic simulation method to compare the effect of annealing rates on diethyl ether coating and oxidation behaviours. Al
81  2020 AMBER Force Field Parameters for Cobalt-Containing Biological Systems: A Systematic Derivation Study. ---
82  2020 AMBER force field parameters for the Zn (II) ions of the tunneling-fold enzymes GTP cyclohydrolase I and 6-pyruvoyl tetrahydropterin synthase. PTPS, QM
83  2020 An Atomistic Study of the Stress Corrosion Cracking in Graphene. ---
84  2020 An exclusive computational insight toward molecular mechanism of MMV007571, a multitarget inhibitor of Plasmodium falciparum. FMN, NPP, PfDHODH
85  2020 An experimental and steered molecular dynamics simulation approach to histidine assisted liquid-phase exfoliation of graphite into few-layer graphene. His
86  2020 An in silico approach for identification of novel inhibitors as potential therapeutics targeting COVID-19 main protease. ---
87  2020 An in silico mechanistic insight into HDAC8 activation facilitates the discovery of new small-molecule activators. CdLS, FCTM, HDAC8
88  2020 An inelastic neutron scattering, Raman, far-infrared, and molecular dynamics study of the intermolecular dynamics of two ionic liquids. FIR, INS, OKE
89  2020 An insight into the role of riboflavin ligand in the self-assembly of poly(lactic-co-glycolic acid)-based nanoparticles - a molecular simulation and experimental approach. NPs, PEG, PLGA, RF
90  2020 An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors. COVID-19, SARS-CoV-2, SMD, SuMD
91  2020 An Integrated In Silico Approach and In Vitro Study for the Discovery of USP7 Small Molecule Inhibitors as Potential Cancer Therapies. USP7
92  2020 An investigation into the allosteric mechanism of GPCR A2A adenosine receptor with trajectory-based information theory and complex network model. A2AAR, EC, GPCRs, IC, TM, TM5
93  2020 An On-the-Fly Approach to Construct Generalized Energy-Based Fragmentation Machine Learning Force Fields of Complex Systems. GEBF, GP, ML, QM
94  2020 Analysis of beta2AR-Gs and beta2AR-Gi complex formation by NMR spectroscopy. beta2AR, GPCR, ICL2, NMR
95  2020 Analysis of Dynamics Targeting CNT-Based Drug Delivery through Lung Cancer Cells: Design, Simulation, and Computational Approach. CN, CNTs
96  2020 Analysis of membrane permeability due to synergistic effect of controlled shock wave and electric field application. DPPC
97  2020 Analysis of phthalate plasticizer migration from PVDC packaging materials to food simulants using molecular dynamics simulations and artificial neural network. PVDC
98  2020 Analysis of polyphenolic metabolites from in vitro gastrointestinal digested soft fruit extracts identify malvidin-3-glucoside as an inhibitor of PTP1B. IVGD
99  2020 Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition. HLA
100  2020 Analysis of the SARS-CoV-2 spike protein glycan shield: implications for immune recognition. HLA