A Search Service for Abbreviation / Long Form

■ Abbreviation / Long Form : aMD / accelerated molecular dynamics

[Related PubMed/MEDLINE]
Total Number of Papers: 88
[Entries Per Page]
 per page
Page Control
Page: of
Abbreviation:   aMD  (>> Co-occurring Abbreviation)
Long Form:   accelerated molecular dynamics
 Abbreviation Variation
 Long Form Variation
 Pair(Abbreviation/Long Form) Variation
No. Year Title Co-occurring Abbreviation
2022 Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants. ACE2, CoV-2, RBD, SARS
2022 IgG1-b12-HIV-gp120 Interface in Solution: A Computational Study. HIV-1, RBD
2022 In silico method for identifying the key residues in a knotted protein: with MJ0366 as an example. AA, DFF
2022 Mechanisms of isoform-specific residue influence on GTP-bound HRas, KRas, and NRas. ---
2022 Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly Model Long-Timescale Transitions. ---
2022 Ritonavir and xk263 Binding-Unbinding with HIV-1 Protease: Pathways, Energy and Comparison. HIVp
2022 Solution structure ensemble of human obesity-associated protein FTO reveals druggable surface pockets at the interface between the N- and C-terminal domain. m6A, RDCs
2022 Thermostabilizing mechanisms of canonical single amino acid substitutions at a GH1 β-glucosidase probed by multiple MD and computational approaches. eMD, MetaDy, PCA
2021 Accelerated Molecular Dynamics to Explore the Binding of Transition Metals to Amyloid-beta. ---
10  2021 Conformational Changes of Glutamine 5'-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations. cMD, GPATase
11  2021 Conformational dynamics of androgen receptors bound to agonists and antagonists. AR, LBD, PCa, PCA
12  2021 Unravelling the molecular interactions between the SARS-CoV-2 RBD spike protein and various specific monoclonal antibodies. mAbs, RBD
13  2020 A series of molecular modeling techniques to reveal selective mechanisms of inhibitors to beta-Site amyloid precursor protein cleaving enzyme 1 (BACE1) and beta-site amyloid precursor protein cleaving enzyme 2 (BACE2). BACE1, BACE2, CMD
14  2020 Analysis of mutations of defensin protein using accelerated molecular dynamics simulations. RsAFP2
15  2020 Complete Dynamic Reconstruction of C60, C70, and (C59N)2 Encapsulation into an Adaptable Supramolecular Nanocapsule. EMFs, EXSY, MD
16  2020 Conformation Transition of Intracellular Part of Glucagon Receptor in Complex With Agonist Glucagon by Conventional and Accelerated Molecular Dynamics Simulations. ant-GCGR, cMD, GCGR, glu-GCGR, TMH
17  2020 Investigating Conformational Dynamics of Lewis Y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics. CT, LeY, MM/GBSA
18  2020 Molecular Modeling of Chemosensory Protein 3 from Spodoptera litura and Its Binding Property with Plant Defensive Metabolites. CSPs, DIMBOA, MBOA
19  2020 Revealing the selective mechanisms of inhibitors to PARP-1 and PARP-2 via multiple computational methods. MD, PARP-1
20  2020 Simulating Multiple Substrate-Binding Events by γ-Glutamyltransferase Using Accelerated Molecular Dynamics. GGT
21  2020 Substrate-Dependent Mobile Loop Conformational Changes in Alkanesulfonate Monooxygenase from Accelerated Molecular Dynamics. OCS, SsuD
22  2020 Unveiling conformational dynamics changes of H-Ras induced by mutations based on accelerated molecular dynamics. GNP, PC
23  2019 Accelerated Molecular Dynamics Applied to the Peptaibol Folding Problem. ---
24  2019 Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water. MD, RMSD
25  2019 Molecular Mechanism Regarding Allosteric Modulation of Ligand Binding and the Impact of Mutations on Dimerization for CCR5 Homodimer. cMD, PCA, PMF, PSN
26  2018 Conformational Transition of Key Structural Features Involved in Activation of ALK Induced by Two Neuroblastoma Mutations and ATP Binding: Insight from Accelerated Molecular Dynamics Simulations. ALK, RTKs
27  2018 Dynamic Consequences of Mutation of Tryptophan 215 in Thrombin. HDXMS, WT
28  2018 Enhanced Molecular Dynamics Methods Applied to Drug Design Projects. US
29  2018 Integrating Multiple Accelerated Molecular Dynamics To Improve Accuracy of Free Energy Calculations. IaMD, ITS
30  2018 Investigation of selective binding of inhibitors to PTP1B and TCPTP by accelerated molecular dynamics simulations. PTP1B, TCPTP
31  2018 Membrane-embedded substrate recognition by cytochrome P450 3A4. CYP3A4, TST
32  2018 Molecular Mechanism Behind the Resistance of the G1202R-Mutated Anaplastic Lymphoma Kinase to the Approved Drug Ceritinib. ALK, ALKWT, DCCM, NSCLC, PCA, US
33  2018 Prediction of Accurate Binding Modes Using Combination of Classical and Accelerated Molecular Dynamics and Free-Energy Perturbation Calculations: An Application to Toxicity Studies. CMD, PFCAs
34  2018 Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38alpha MAP Kinase Type-I/II/III Inhibitors. DFG, MD, PSIM
35  2018 Using accelerated molecular dynamics simulation to shed light on the mechanism of activation/deactivation upon mutations for CCR5. PMF, PSN, WT
36  2017 Accelerated molecular dynamics simulation analysis of MSI-594 in a lipid bilayer. AMPs
37  2017 Activation mechanisms of the first sphingosine-1-phosphate receptor. S1PR1, TM
38  2017 Identification of a Different Agonist-Binding Site and Activation Mechanism of the Human P2Y1 Receptor. ADP, cMD, GPCR, P2Y1R
39  2017 Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the beta-solenoid structure formed by a silk-like polypeptide. ---
40  2017 Non-active site mutations disturb the loop dynamics, dimerization, viral budding and egress of VP40 of the Ebola virus. EBOV, NTD, PM, WT
41  2016 Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist-binding position. GPCRs, GPUs, MD, OARs
42  2016 Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor. IFD, mAChR, NAMs, NCI
43  2016 Activation and conformational dynamics of a class B G-protein-coupled glucagon receptor. ELCs, GCGR, glu-GCGR, GPCR, PMF
44  2016 Gaussian Accelerated Molecular Dynamics in NAMD. ACh, cMD, GaMD, GPCR
45  2016 General trends of dihedral conformational transitions in a globular protein. ABF, cMD
46  2016 Molecular Dynamics of "Fuzzy" Transcriptional Activator-Coactivator Interactions. ADs
47  2016 PPARgamma helix 12 exhibits an antagonist conformation. NR, PPARgamma
48  2016 PPARgamma non-covalent antagonists exhibit mutable binding modes with a similar free energy of binding: a case study. ---
49  2016 The Modern Temperature-Accelerated Dynamics Approach. TAD
50  2015 A comment on the reweighting method for accelerated molecular dynamics simulations. ---
51  2015 Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor. ACh, ARC, GPCR, TTP
52  2015 Accelerated molecular dynamics simulations of protein folding. cMD
53  2015 Activation helix orientation of the estrogen receptor is mediated by receptor dimerization: evidence from molecular dynamics simulations. NR
54  2015 Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor. GPCRs
55  2015 Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins. FRET, HTMD, MD, REMD
56  2015 Enhanced molecular dynamics sampling of drug target conformations. MD
57  2015 Functional loop dynamics of the streptavidin-biotin complex. ---
58  2015 Targeting electrostatic interactions in accelerated molecular dynamics with application to protein partial unfolding. DISEI-aMD, T-domain
59  2015 Theoretical Insights Reveal Novel Motions in Csk's SH3 Domain That Control Kinase Activation. Csk, DXMS, SFKs
60  2014 Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units. GPUs, MD
61  2014 Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins. MD
62  2014 Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods. H-REMD, M-REMD
63  2014 Free energy landscape of G-protein coupled receptors, explored by accelerated molecular dynamics. GPCRs
64  2014 Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation. cMD
65  2014 Towards fast, rigorous and efficient conformational sampling of biomolecules: Advances in accelerated molecular dynamics. ---
66  2014 Trypsinogen activation as observed in accelerated molecular dynamics simulations. ---
67  2013 Correlated motions and residual frustration in thrombin. MD
68  2013 Mapping of allosteric druggable sites in activation-associated conformers of the M2 muscarinic receptor. GPCRs
69  2013 Simulations of biased agonists in the beta(2) adrenergic receptor with accelerated molecular dynamics. GPCRs
70  2012 Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions. RaMD
71  2012 Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations. MD
72  2012 Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics. BPTI, GPUs
73  2011 Accelerated molecular dynamics in computational drug design. ---
74  2011 Accelerating chemical reactions: exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics. ---
75  2011 Adaptive Accelerated Molecular Dynamics (Ad-AMD) Revealing the Molecular Plasticity of P450cam. Ad-AMD, Ad-AMD
76  2011 Comparison of SARS and NL63 papain-like protease binding sites and binding site dynamics: inhibitor design implications. SARS-CoV
77  2011 Enhanced Lipid Diffusion and Mixing in Accelerated Molecular Dynamics. cMD
78  2011 Implementation of Accelerated Molecular Dynamics in NAMD. ---
79  2011 Induced fit or conformational selection? The role of the semi-closed state in the maltose binding protein. ABF, CS, IF, MBP, TI
80  2011 Studying functional dynamics in bio-molecules using accelerated molecular dynamics. MD
81  2010 Enhanced conformational space sampling improves the prediction of chemical shifts in proteins. NF-kappaB, RDC
82  2010 Insights into MAPK p38alpha DFG flip mechanism by accelerated molecular dynamics. ---
83  2010 Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations. ---
84  2009 Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics. CMD
85  2009 Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration. REXAMD
86  2008 Essential energy space random walks to accelerate molecular dynamics simulations: convergence improvements via an adaptive-length self-healing strategy. ALSH
87  2007 Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy. ---
88  1994 Synthesis, characterization, and conformational analysis of the D/L-Tic7 stereoisomers of the bradykinin receptor antagonist D-Arg0[Hyp3,Thi5,D-Tic7,Oic8]bradykinin. ---