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Abbreviation : ED
Long Form : essential dynamics
No. Year Title Co-occurring Abbreviation
2019 Delineating the effect of mutations on the conformational dynamics of N-terminal domain of TDP-43. FEL, MD, NTD, TDP-43, WT
2019 Insight derived from molecular dynamics simulation into dynamics and molecular motions of cuticle-degrading serine protease Ver112. FEL, MD
2019 Insights into the DNA binding induced thermal stabilization of transcription factor FOXP3. MD
2019 Transcript expression profiling in two contrasting cultivars and molecular cloning of a SKP-1 like gene, a component of SCF-ubiquitin proteasome system from mungbean Vigna radiate L. FEL, MD, UPS
2018 Alterations in local stability and dynamics of A4V SOD1 in the presence of trifluoroethanol. ALS, CD, FEL, MD, TFE
2018 Impact of a non-synonymous Q281R polymorphism on structure of human Lipoprotein-Associated Phospholipase A2 (Lp-PLA2 ). LDL, Lp-PLA2, MD, nsSNPs, ProSA, SVM, WT
2018 Impact of tyrosine nitration at positions Tyr307 and Tyr335 on structural dynamics of Lipoprotein-associated phospholipase A2-A therapeutically important cardiovascular biomarker for atherosclerosis. 3-NT, Lp-PLA2, MD, PAF, PTN
2018 Met117 oxidation leads to enhanced flexibility of cardiovascular biomarker- lipoprotein- associated phospholipase A2 and reduced substrate binding affinity with platelet-activating factor. LDL, Lp-PLA2, MD, PAF
2017 Effect of the R119G mutation on human P5CR structure and its interactions with NAD: Insights derived from molecular dynamics simulation and free energy analysis. MD, MM-PBSA, P5CR, WT
10  2017 JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories. DV, PCA
11  2016 Extending the essential dynamics analysis to investigate molecular properties: application to the redox potential of proteins. MD
12  2015 Essential dynamics for the study of microstructures in liquids. MD
13  2015 Systematic methods for defining coarse-grained maps in large biomolecules. CG, ENM, MD, PCA
14  2014 Insight derived from molecular dynamics simulations into molecular motions, thermodynamics and kinetics of HIV-1 gp120. FEL, MD
15  2014 Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms. FEL
16  2013 Molecular simulations study of ligand-release mechanism in an odorant-binding protein from the southern house mosquito. OBP
17  2013 Probing the conformational flexibility of monomeric FtsZ in GTP-bound, GDP-bound, and nucleotide-free states. ---
18  2012 Interaction of wild type, G68R and L125M isoforms of the arylamine-N-acetyltransferase from Mycobacterium tuberculosis with isoniazid: a computational study on a new possible mechanism of resistance. CP, LIE, MD, TB
19  2012 Molecular dynamics simulations of the Bcl-2 protein to predict the structure of its unordered flexible loop domain. BH, FLD, MD, PMDB, TM
20  2011 Understanding the specificity of a docking interaction between JNK1 and the scaffolding protein JIP1. ---
21  2010 Insight derived from molecular dynamics simulation into substrate-induced changes in protein motions of proteinase K. MD
22  2010 Insights derived from molecular dynamics simulation into the molecular motions of serine protease proteinase K. ---
23  2010 Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses. CGNM, ENM, RCNMA
24  2010 Mechanism of influence of phosphorylation on serine 124 on a decrease of catalytic activity of human thymidylate synthase. hTS, MD
25  2010 Releasing of the chromophore from the drug delivery protein C-1027: a molecular dynamics simulations study. Apo, Chr, MD, SMD
26  2009 Complexes of HIV-1 integrase with HAT proteins: multiscale models, dynamics, and hypotheses on allosteric sites of inhibition. CGMD, IN
27  2008 Study on the molecular mechanism of inhibiting HIV-1 integrase by EBR28 peptide via molecular modeling approach. HIV-1, IN, MD
28  2006 Insight into catalytically relevant correlated motions in human purine nucleoside phosphorylase. hPNP, TS
29  2006 Study of the influence of temperature on the dynamics of the catalytic cleft in 1,3-1,4-beta-glucanase by molecular dynamics simulations. ---
30  2006 The natural mutation by deletion of Lys9 in the thrombin A-chain affects the pKa value of catalytic residues, the overall enzyme's stability and conformational transitions linked to Na+ binding. alpha-NAPAP, MD, WT
31  2004 Interactive essential dynamics. MD
32  2004 Solvent interactions and protein dynamics in spin-labeled T4 lysozyme. EPR, MD
33  2003 Molecular dynamics simulation of highly charged proteins: comparison of the particle-particle particle-mesh and reaction field methods for the calculation of electrostatic interactions. ADBp, MD, RF
34  2003 Subtle functional collective motions in pancreatic-like ribonucleases: from ribonuclease A to angiogenin. Ang, MD
35  2000 Computational studies of essential dynamics of Pseudomonas cepacia lipase. MD
36  2000 Theoretical studies of the response of a protein structure to cavity-creating mutations. MD
37  1998 Essential dynamics of DNA containing a cis.syn cyclobutane thymine dimer lesion. MD
38  1996 An extended sampling of the configurational space of HPr from E. coli. MD
39  1996 Bending of the calmodulin central helix: a theoretical study. CaM, MD, NMA