Keywords: نوسان میانگین مربع ریشه; CVDs; cardiovascular diseases; sEH; soluble epoxide hydrolase; MD; molecular dynamics; EETs; epoxyeicosatrienoic acids; DHETs; dihydroxy-eicosatrienoic acids; MM/PBSA; molecular mechanics poisson-boltzmann surface area; ROF; rule of five; NVT; number of p
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Keywords: نوسان میانگین مربع ریشه; aFAK; active FAK; AL; activation loop; CL; catalytic loop; CMD; classical molecular dynamics; FAK; focal adhesion kinase; FAT; focal adhesion targeting domain; FERM; 4.1 ezrin radixin moesin; GL; glycine rich loop; H; helix; hFAK; hyperactive FAK; iFAK; i
Keywords: نوسان میانگین مربع ریشه; DTNB; 5,5â²-dithiobis(2-nitrobenzoate); DTPA; diethylenetriaminepentaacetic acid; FTIR; Fourier transform infrared spectroscopy; HB; hydrogen bond/bonding; HSA; human serum albumin; HSA-SH; thiol of human serum albumin; HSA-Sâ; thiolate of human se
Keywords: نوسان میانگین مربع ریشه; ADA; Adenosine Deaminase; MD; molecular dynamics; DEG; Database of Essential Genes; ROF; Lipinski's rule of five; MW; molecular weight; clogP; Octanol-water partition co-efficient; HBD; hydrogen bond donor; HBA; hydrogen bond acceptor; NVT; Number of part
Keywords: نوسان میانگین مربع ریشه; PPL-Cl; procine pancreatic lipase in closed conformation; PPL-O; lipase in closed conformation; PPL+Â colip; lipase-colipase complex; PPL-colip; only lipase chain of lipase-colipase complex; RMSD; root mean square deviation; RMSF; root mean square flu
Keywords: نوسان میانگین مربع ریشه; PPL-Cl; procine pancreatic lipase in closed conformation; PPL-O; lipase in closed conformation; PPL+Â colip; lipase-colipase complex; PPL-colip; only lipase chain of lipase-colipase complex; PPLmut-Cl; lipase with point mutations D250V and E254 in closed
Keywords: نوسان میانگین مربع ریشه; Molecular dynamics; Disease; Diagnostic use; Protein stability; AGAL; lysosomal alpha-galactosidase; DGJ; 1-deoxy-galactonojirimycin; RMSD; Root mean square deviation; RMSF; root mean square fluctuation;
Keywords: نوسان میانگین مربع ریشه; PMSF; Phenylmethanesulfonyl fluoride; VPR; A subtilisin-like serine proteinase from a psychrotrophic Vibrio species; AQUI; Aqualysin I; Suc-AAPF-NH-Np; Succinyl-AlaAlaProPhe-p-nitroanilide; MD; Molecular dynamics; rmsf; Root mean square fluctuation; Subtl
A Computational workflow for the identification of the potent inhibitor of type II secretion system traffic ATPase of Pseudomonas aeruginosa
Keywords: نوسان میانگین مربع ریشه; kj/mol; kilojoule per mol; MD; molecular dynamics; MM; molecular mechanics; MM-GBSA; molecular mechanics - generalized born and surface area; OPLS; optimized potential for liquid simulations; GBSA; generalized-born surface area; PME; particle mesh ewa
Network and structure based inference of functional single nucleotide polymorphisms associated with the TGFβ1 gene and its role in colorectal cancer (CRC)
Keywords: نوسان میانگین مربع ریشه; CRC; colorectal cancer; TGFβ1; transforming growth factor-β1; MAPK; mitogen-activated protein kinases; PKC; protein kinase C; SNPs; single nucleotide polymorphisms; TFs; transcription factors; NCBI; National Center for Biotechnology Information; ns-SNPs
Pore formation and the key factors in antibacterial activity of aurein 1.2 and LLAA inside lipid bilayers, a molecular dynamics study
Keywords: نوسان میانگین مربع ریشه; AMPs; antimicrobial peptides; DPPC; dipalmitoyl phosphatidylcholine; RMSD; Root Mean Square Deviation; RMSF; Root Mean Square Fluctuation; MD; molecular dynamics; SAS; solvent accessible surface; DSSP; define secondary structure of proteins; 5PM; 5-peptid
αCGRP, another amyloidogenic member of the CGRP family
Keywords: نوسان میانگین مربع ریشه; CGRP; Calcitonin Gene Related Peptide; CT; calcitonin; IAPP; islet amyloid polypeptide; GPCR; G-Protein Coupled Receptor; RAMP; Receptor Activity Modifying Protein; T2D; Type 2 Diabetes; MTC; Medullary Thyroid Carcinoma; MD; Molecular Dynamics; CD; Circul
Domain communication in Thermotoga maritima Arginine Binding Protein unraveled through protein dissection
Keywords: نوسان میانگین مربع ریشه; TmArgBP; wild-type Arginine Binding Protein isolated from Thermotoga maritima; TmArgBP20-233; residues 20-233 of TmArgBP; D1; domain 1 of TmArgBP; D2; domain 2 of TmArgBP; SBP; substrate binding protein; RMSD; root mean square deviation; RMSF; root me
Lipid metabolism potential and mechanism of CPe-III from chickpea (Cicer arietinum L.)
Keywords: نوسان میانگین مربع ریشه; HFD; high-fat diet; HDL; high-density lipoprotein; LDL; low-density lipoprotein; VLDL; very low-density lipoprotein; CETP; cholesteryl ester transfer protein; CE; cholesteryl ester; RCT; reverse cholesterol transport; MD; molecular dynamics; TC; total cho
E7 oncoprotein of human papillomavirus: Structural dynamics and inhibitor screening study
Keywords: نوسان میانگین مربع ریشه; HPV; Human papillomavirus; pRB; Phosphorylated Retiboblastoma; 3D; Three dimensional; MoRFs; Molecular recognition features; DNA; Deoxyribo nucleic acid; CRs; Conserved regions; IDPs; Intrinsically disordered proteins; CD-HIT; Cluster database at high ide
Expression of Cry1Ac toxin-binding region in Plutella xyllostella cadherin-like receptor and studying their interaction mode by molecular docking and site-directed mutagenesis
Keywords: نوسان میانگین مربع ریشه; BSA; bovine serum albumin; cDNA; complementary DNA; ELISA; enzyme-linked immunosorbent assay; HRP; horse radish peroxidase; IPTG; isopropyl-beta-d-thiogalactopyranoside; MPBS; PBS containing skim milk; Ni-NTA; nickel-nitrilotriacetic acid; OD; optical den
Modeling, dynamics and phosphoinositide binding of the pleckstrin homology domain of two novel PLCs: η1 and η2
Keywords: نوسان میانگین مربع ریشه; Pleckstrin homology domain; Phosphoinositide binding; Molecular modeling; Docking; MD simulation; PLC; Phospholipase C; PHη1; PH domain of PLCη1; PHη2; PH domain of PHη2; IP3; inositol-(1,4,5)-triphosphate; IP4; Inositol-(1,3,4,5)-tetrakisphosphate; u
A combined biochemical and computational studies of the rho-class glutathione s-transferase sll1545 of Synechocystis PCC 6803
Keywords: نوسان میانگین مربع ریشه; GST; glutathione S-transferase; GSH; reduced glutathione; CuOOH; cumene hydrogen peroxide; Non-Se-GPX; non-selenium dependent glutathione peroxidase; RMSD; root mean square deviation; RMSF; root mean square fluctuation; ED; essential dynamics; PCA; princi
Anaerobic sulfatase maturase AslB from Escherichia coli activates human recombinant iduronate-2-sulfate sulfatase (IDS) and N-acetylgalactosamine-6-sulfate sulfatase (GALNS)
Keywords: نوسان میانگین مربع ریشه; Cys; Cysteine; FGly; Formylglycine; GALNS; N-acetylgalactosamine-6-sulfate sulfatase; GALNSSer; GALNS cDNA containing mutation C79S; IDS; iduronate-2-sulfate sulfatase; MPS; Mucopolysaccharidoses; anSMEs; Anaerobic sulfatase maturating enzymes; SUMF1; Sul
Electron transfer pathways analysis of oxygen tolerant [NiFe]-hydrogenases for hydrogen production: A quantum mechanics/molecular mechanics - statistical coupled analysis
Keywords: نوسان میانگین مربع ریشه; [NiFe]-hydrogenase; QM/MM; Molecular dynamics; Statistical coupled analysis; MBed; Maxwell-Boltzmann energy distribution; MD; Molecular Dynamics; PCA; Principal Component Analysis; QM/MM; Quantum Mechanics/Molecular Mechanics; RMSD; Root Mean Square Devia
Tracking the amyloidogenic core of IAPP amyloid fibrils: Insights from micro-Raman spectroscopy
Keywords: نوسان میانگین مربع ریشه; hIAPP; human IAPP; rIAPP; rat IAPP; APRs; aggregation-prone regions; STEM; scanning-transmission electron microscopy; ssNMR; solid-state Nuclear Magnetic Resonance; RMSF; root mean square fluctuation; ASA; accessible surface area; TERS; Tip-Enhanced Raman
Systematic prioritization of functional hotspot in RIG-1 domains using pattern based conventional molecular dynamic simulation
Keywords: نوسان میانگین مربع ریشه; RIG-1; Retinoic acid inducible gene 1; CARD; Caspase activation and recruitment domain; HEL; Helicase domain; RD; Repressor domain; DO; Distant ortholog; RMSD; Root mean square deviation; RMSF; Root mean square fluctuation; RIG-1; Motif; Distant ortholog;
Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity
Keywords: نوسان میانگین مربع ریشه; Zika virus; Flavivirus; NS3 helicase; Molecular dynamics; FTMap; Drug discovery; ZIKV; Zika virus; NS; non-structural; NS3h; NS3 helicase; PrM; membrane precursor; MD; molecular dynamics; RMSF; root mean square fluctuation; PDB; protein data bank; VMD; Vi
Exploring putative inhibitors of Death Associated Protein Kinase 1 (DAPK1) via targeting Gly-Glu-Leu (GEL) and Pro-Glu-Asn (PEN) substrate recognition motifs
Keywords: نوسان میانگین مربع ریشه; DAPK1; Death Associated Protein Kinase 1; NMDARs; N-methyl-D-aspartate receptors; NMDAR2A or NR2A; N-methyl-D-aspartate receptor subtype 2A; NMDAR2B or NR2B; N-methyl-D-aspartate receptor subtype 2B; NSC; neuronal survival-signaling complex; NDC; neuronal
Effects of interface mutations on the dimerization of alanine glyoxylate aminotransferase and implications in the mistargeting of the pathogenic variants F152I and I244T
Keywords: نوسان میانگین مربع ریشه; Primary hyperoxaluria type I; Human alanine glyoxylate aminotransferase; Interface hot spots; Protein dimerization; Molecular dynamics; Protein mistargeting; AGT-Mi; minor allele of human alanine glyoxylate aminotransferase; PH1; Primary Hyperoxaluria typ
Molecular dynamics simulation and free energy landscape methods in probing L215H, L217R and L225M βI-tubulin mutations causing paclitaxel resistance in cancer cells
Keywords: نوسان میانگین مربع ریشه; Microtubule; βI-tubulin; Paclitaxel; Drug resistance; Molecular dynamics simulation; Free energy landscape; WT; wild type; MT; mutant type; Ptxl; paclitaxel; MD; molecular dynamics; PCA; principle component analysis; FEL; free energy landscape; RMSD; roo
Molecular interaction of δ-conopeptide EVIA with voltage-gated Na+ channels
Keywords: نوسان میانگین مربع ریشه; COSY; correlation spectroscopy; DG; distance geometry; DIEA; N,N-diisopropylethylamine; Fmoc; 9-fluorenylmethoxycarbonyl; GSH; glutathione reduced; GSSG; glutathione oxidized; HBTU; O-(benzotriazol-1-yl)-N,N,Nâ²,Nâ²-tetramethyl-uronium-hexafluorophospha
Inherent conformational flexibility of F1-ATPase α-subunit
Keywords: نوسان میانگین مربع ریشه; Mg(II); free magnesium ion; ATP; adenosine 5â²-triphosphate; ADP; adenosine 5â²-diphosphate; EDTA; ethylenediaminetetraacetic acid; Tris; 2-amino-2-(hydroxymethyl)propane-1,3-diol; MgCl2; magnesium chloride; ATPase; adenosine 5â²-triphosphatase; MF1, T
A multi-subunit based, thermodynamically stable model vaccine using combined immunoinformatics and protein structure based approach
Keywords: نوسان میانگین مربع ریشه; APC; antigen presenting cells; CTL; cytolytic T-lymphocytes; FASTA; FAST-ALL; HBHA; heparin-binding hemagglutinin; HTL; helper T-lymphocytes; IC50; inhibitory concentration; IEDB-AR; immune epitope database analysis resource; JCAT; Java Codon Adaptation T
Research paperMolecular principles behind Boceprevir resistance due to mutations in hepatitis C NS3/4A protease
Keywords: نوسان میانگین مربع ریشه; HCV; hepatitis C virus; MD; molecular dynamics; RMSD; root mean square deviation; RMSF; root mean square fluctuation; Rg; radius of gyration; VMD; visual molecular dynamics; HCV; Molecular dynamics; Simulations; Boceprevir; Resistance; Mutants;
Molecular dynamics simulation study reveals potential substrate entry path into γ-secretase/presenilin-1
Keywords: نوسان میانگین مربع ریشه; PS1; presenilin 1; APP; amyloid precursor protein; AD; Alzheimer's disease; NTF; N-terminal Fragment; CTF; C-terminal Fragment; TM; transmembrane domain; POPC; 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine; POPE; 1-palmitoyl-2-oleoyl-sn-glycero-3-pho
The role of salt bridges on the temperature adaptation of aqualysin I, a thermostable subtilisin-like proteinase
Keywords: نوسان میانگین مربع ریشه; PMSF; phenylmethanesulfonyl fluoride; VPR; a subtilisin-like serine proteinase from a psychrotrophic Vibrio species; AQUI; aqualysin I; Suc-AAPF-NH-Np; succinyl-AlaAlaProPhe-p-nitroanilide; MD; molecular dynamics; rmsf; root mean square fluctuation; Subti
Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics
Keywords: نوسان میانگین مربع ریشه; HNL; hydroxynitrile lyase; S-HNL; S-selective hydroxynitrile lyase; (R)-Man; (R)-mandelonitrile; (S)-Man; (S)-mandelonitrile; rac-Man; racemic mandelonitrile; MD; molecular dynamics; RMSD; root mean square deviation; RMSF; root mean square fluctuation; Me
Selective chaperone effect of aminocyclitol derivatives on G202R and other mutant glucocerebrosidases causing Gaucher disease
Keywords: نوسان میانگین مربع ریشه; BBB; blood-brain barrier; CBE; conduritol β-epoxide; Cer; ceramide; D-MEM; Dulbeco Eagle's minimal essential medium; ERT; enzyme replacement therapy; GBA1; lysosomal glucocerebrosidase; GBA2; non-lysosomal glucocerebrosidase; GlcCer; glucosylceramide;
Molecular modeling and molecular dynamics simulations of GPI 14 in Leishmania major: Insight into the catalytic site for active site directed drug design
Keywords: نوسان میانگین مربع ریشه; CL; cutaneous leishmaniasis; MCL; mucocutaneous leishmaniasis; VL; visceral leishmaniasis; LPG; lipophosphoglycan; GIPLs; glycoinositolphospholipids; GPI; glycosylphosphatidylinositol; iNOS; inducible nitric oxide synthase; NO; nitric oxide; PPG; proteoph
A practical guide to protein dynamics from 15N spin relaxation in solution
Keywords: نوسان میانگین مربع ریشه; Protein dynamics; Spin relaxation; Model-free formalism; ps-ns/μs-ms timescales; Consistency tests; AIC; Akaike information criteria; AICc; small sample size corrected AIC; BIC; Bayesian information criteria; BMRB; Biological Magnetic Resonance Bank
Insights into thermal stability of thermophilic nitrile hydratases by molecular dynamics simulation
Keywords: نوسان میانگین مربع ریشه; Thermal stability; Thermophilic nitrile hydratase; Molecular dynamic simulation; Root mean square fluctuation; Salt-bridge interaction
The conserved glycine/alanine residue of the active-site loop containing the putative acetylCoA-binding motif is essential for the overall structural integrity of Mesorhizobium loti arylamine N-acetyltransferase 1
Keywords: نوسان میانگین مربع ریشه; NAT; arylamine N-acetyltransferase; RMSD; root mean square deviation; RMSF; root mean square fluctuation; MLNAT1; Mesorhizobium loti NAT1; Arylamine N-acetyltransferase; P-loop; Active-site; Steric hindrance; Site-directed mutagenesis;