Keywords: در حال حاضر; 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: در حال حاضر; AFM; atomic force microscopy; ATR; Attenuated total reflectance (IR system); CCC; covalently closed circular DNA; CD; circular dichroism; CT DNA; calf thymus DNA; DEPT; distortionless enhancement by polarization transfer; DMF; Dimethylformamide; DMSO; Dim
Keywords: در حال حاضر; CSP; chemical shift perturbation; PTP; protein tyrosine phosphatase; PTP1B; protein tyrosine phosphatase 1B; VHR; Vaccinia H1-related phosphatase; BB30; benzofuran-based small molecule; pNPP; p-nitrophenylphosphate; SASA; solvent-accessible surface areas;
Keywords: در حال حاضر; Naphthalene diimides; Drug design; DNA; G-quadruplex; Telomeric DNA; Topoisomerase; Antiproliferative; BASASA; Boltzmann Accessible Solvent Accessible Surface Area; BCL-2; B-cell lymphoma 2; dsDNA; double-stranded DNA; hTel; human telomeric; HSP90; heat s
Keywords: در حال حاضر; DC; dendritic cell; PD-L2; programmed cell death ligand 2; SASA; solvent-accessible surface area; FGFR2; fibroblast growth factor receptor 2; LPS; lipopolysaccharide; GST; glutathione S-transferase; PEG; polyethylene glycol; X-ray crystallography; V-set I
Keywords: در حال حاضر; 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: در حال حاضر; 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: در حال حاضر; CaV; Voltage-gated calcium channel; GMs; Gating modifier, gating-modifying peptide; Hd1a; μ-TRTX-Hd1a; KV; Voltage-gated potassium channel; LUV; Large unilamellar vesicle; NaV; Voltage-gated sodium channel; PBs; Pore blocker, pore blocking peptide; POPC;
Keywords: در حال حاضر; 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: در حال حاضر; 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: در حال حاضر; FF; diphenylalanine; MD; molecular dynamics; RMSD; root mean square deviation; dEE; end-to-end distance; SASA; solvent accessible surface area; Diphenylalanine peptide; Piezoelectric peptide; Atomistic molecular dynamics; External electric field; Peptideâ
Keywords: در حال حاضر; PAN; polymerase acidic protein N-terminal domain; MD; molecular dynamics; MM/GBSA; molecular mechanics/generalized Born surface area; H5N1; hemagglutinin type 5 and neuraminidase type; M2 protein; matrix protein 2; HIV; human immunodeficiency virus; SBDD;
Keywords: در حال حاضر; Dp; Dystrophin; DMD; Duchenne Muscular Dystrophy; DAPC; Dystrophin Associated Protein Complex; DG; Dystroglycan; MDDGC9; Muscular Dystrophy, Dystroglycanopathy, Type C9; OMIM; Online Mendelian Inheritance in Man; ABD; Actin Binding Domain; SpR; Spectrin R
Keywords: در حال حاضر; AA; amino acid; UAA; unnatural amino acid; ADC; antibody-drug conjugate; DOPA; l-3,4-dihydroxyphenylalanine; flp; 4-(R)-fluoroproline; GnRH; gonadotropin-releasing hormone; hyp; hydroxyproline; LAR; long acting release; MOF; metal-organic framework; 4-D
Keywords: در حال حاضر; ANOVA; analysis of variance; BCA; bicinchoninic acid; DA; dopamine; DAT; dopamine transporter; FEP; free energy perturbation; GABA; gamma-amino butyric acid; GAT; GABA transporter; HRP; horseradish peroxidase; IL3; intracellular loop 3; MD; molecular dyna
Keywords: در حال حاضر; BIOME-BGC; Carbon budget; Carbon compensation point; Clear-cutting; Forest disturbance; Sasa
Keywords: در حال حاضر; Alanine scanning mutagenesis; Hot-spot; Aromatic residue; Aromatic cluster; Cooperativity; SASA;
Network and structure based inference of functional single nucleotide polymorphisms associated with the TGFβ1 gene and its role in colorectal cancer (CRC)
Keywords: در حال حاضر; 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
In silico analysis of Pax6 protein glycosylation in vertebrates
Keywords: در حال حاضر; PD; paired domain; HD; homeodomain; PST; Proline/Serine/Threonine; Pro; proline; Ser; serine; Thr; threonine; Asn; asparagine; GlcNAc; N-acetylglucosamine; GalNAc; N-acetylgalactosamine; 3D; three dimensional; 2D; secondary structure; EVP; enhancement val
Competitive homo- and hetero- self-assembly of amyloid-β 1-42 and 1-40 in the early stage of fibrillation
Keywords: در حال حاضر; AD; Alzheimer's disease; Aβ; amyloid-β peptide; Aβ40; amyloid-β peptide (1-40); Aβ42; amyloid β peptide (1-42); APP; amyloid precursor protein; Ala; alanine; ATD; arrival time distribution; CCS; collision cross section; DTIMS; drift tube ion m
Molecular genetics âcharacterization and homology modeling of the CHM gene mutation: A study on its association with choroideremia
Keywords: در حال حاضر; CHM; choroideremia; RPE; retinal pigment epithelium; REP-1; Rab escort protein-1; VA; visual acuity; OCT; optical coherence tomography; GGTase; geranylgeranyltransferase; ONL; outer nuclear layer; INL; inner nuclear layer; LCHADD; long-chain 3-hydroxyacyl
Modeling, dynamics and phosphoinositide binding of the pleckstrin homology domain of two novel PLCs: η1 and η2
Keywords: در حال حاضر; 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
Inhibition of TRAF6-Ubc13 interaction in NFkB inflammatory pathway by analyzing the hotspot amino acid residues and protein-protein interactions using molecular docking simulations
Keywords: در حال حاضر; PPI; protein-protein interaction; PDTC; Pyrrolidine dithiocarbamate; NFkB; Nuclear Factor kappa B; IkB; Inhibitor of kappa; RING; Really Interesting New Gene; TRAF6; TNF receptor associated factor 6; IL1; Interleukin 1; Ubc13; Ubiquitin conjugating prot
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: در حال حاضر; 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
Classification and structural analyses of mutational landscapes in hemochromatosis factor E protein: A protein defective in the hereditary hemochromatosis
Keywords: در حال حاضر; HH; hereditary hemochromatosis; HFE; Hereditary Hemochromatosis Factor E; MHC; major histocompatibility complex; RMSD; Root Mean Square Deviations; Rg; Radius of Gyration; RMSF; Root Mean Square Fluctuations; SASA; Solvent Accessible Surface Area; SVM; Su
Molecular dynamics simulation and free energy landscape methods in probing L215H, L217R and L225M βI-tubulin mutations causing paclitaxel resistance in cancer cells
Keywords: در حال حاضر; 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
Smyd3 open & closed lock mechanism for substrate recruitment: The hinge motion of C-terminal domain inferred from μ-second molecular dynamics simulations
Keywords: در حال حاضر; SET; Suppressor of variegation, Enhancer of Zeste, Trithorax; MYND; Myeloid-Nervy-DEAF1; siRNA; small interfering RNA; VEGFR1; vascular endothelial growth factor receptor-1; MD; molecular dynamics; HKMT; histone lysine methyltranferase; RMSD; root-mean sq
Computer-aided design of aptamers for cytochrome p450
Keywords: در حال حاضر; VEGF; vascular endothelial growth factor; SELEX; Systematic Evolution of Ligands by EXponential enrichment; CYP51; cytochrome p450 51A1, lanosterol 14α-demethylase; MD; molecular dynamics; PME; particle mesh Ewald; MM-PBSA; Molecular Mechanics Poissonâ
Investigations on the role of CHâ¦O interactions and its impact on stability and specificity of penicillin binding proteins
Keywords: در حال حاضر; HBAT; Hydrogen Bond Analysis Tool; HMM; high molecular mass penicillin binding proteins; LMM; low molecular mass penicillin binding proteins; PBPs; penicillin binding proteins; PDB; protein data bank; SASA; solvent accessible surface area; Gram positive b
The E. coli thioredoxin folding mechanism: The key role of the C-terminal helix
Keywords: در حال حاضر; CD; circular dichroism; CTH; C-terminal α-helix; DLS; dynamic light scattering; ESI-MS; electrospray ionization mass spectrometry; GdmCl; guanidinium chloride; HB; hydrogen bond; Iâ and Iâ-sim; high energy intermediate state inferred from experiments
A theoretical view of the C3d:CR2 binding controversy
Keywords: در حال حاضر; C3d; complement fragment 3d; CR2; complement receptor 2; SCR; short consensus repeat; PDB; protein data bank; MD; molecular dynamics; SASA; solvent-accessible surface area; SMD; steered molecular dynamics; AESOP; analysis of electrostatic similarities of
Catalytic performance and molecular dynamic simulation of immobilized CC bond hydrolase based on carbon nanotube matrix
Keywords: در حال حاضر; AFM; atomic force microscopy; CD; circular dichroism; CNT; carbon nanotube; DMF; dimethylformamide; EDC; N-ethyl-Nâ²-(3-(dimethyllamino) propyl) carbodiimide hydrochloride; MD; molecular dynamics; MES; 2-(N-morpholino) ethanesulfonic acid; MWCNT; multi w
Structure-activity relationships of the thujaplicins for inhibition of human tyrosinase
Keywords: در حال حاضر; MBTH; 3-methyl-2-benzothiazolinone hydrazone; MM-GB/SA; molecular mechanics-generalized born/surface area; SASA; solvent-accessible surface area; GB; generalized born; AbTYR; Agaricus bisporus mushroom tyrosinase; BmTYR; Bacillus megaterium tyrosinase; Sc
A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity
Keywords: در حال حاضر; 1-NP; 1-naphthol; APBS; adaptive Poisson-Boltzmann solver; DBI; Davies-Bouldin index; DMSO; dimethylsulfoxide; EC; extracellular buffer; GAFF; generalized amber force field; hERG; human ether-á-go-go-related K+ ion channel; IC; intracellular buffer;
Computer-aided identification of novel 3,5-substituted rhodanine derivatives with activity against Staphylococcus aureus DNA gyrase
Keywords: در حال حاضر; PNP; purine nucleoside phosphorylase; MESG; 2-amino-6-mercapto-7-methylpurine ribose; GLIDE XP; grid-based ligand docking with energetics extra-precision; OPLS; optimized potentials for liquid simulations; SPC water; simple point charge water; NPT ensembl
Protein engineering and the use of molecular modeling and simulation: The case of heterodimeric Fc engineering
Keywords: در حال حاضر; RMSD; root mean squared deviation; RMSF; root mean squared fluctuation; RDF; radial distribution function; SASA; solvent exposed surface area; CCSD; close contact surface density (ÎÏtot); KBP; knowledge based potential; LJ; Lennard-Jones contributions;
Carbonylation of mitochondrial aconitase with 4-hydroxy-2-(E)-nonenal: Localization and relative reactivity of addition sites
Keywords: در حال حاضر; ACO2; mitochondrial aconitase; CID; collision-induced dissociation; DTT; dithiothreitol; FDR; false discovery rate; HCD; higher-energy C-trap dissociation; HNE; 4-hydroxy-2-(E)-nonenal; MWCO; molecular weight cut-off; PSM; peptide-spectrum match; SASA; so
Extending the applicability of the O-ring theory to protein–DNA complexes
Keywords: در حال حاضر; Protein–DNA interaction; DNA; Alanine-Scanning Mutagenesis; SASA; O-ring
Substrate-induced conformational changes in sarcoplasmic reticulum Ca2+-ATPase probed by surface modification using diethylpyrocarbonate with mass spectrometry
Keywords: در حال حاضر; SERCA; sarcoplasmic/endoplasmic reticulum Ca2+ ATPase; DEPC; diethylpyrocarbonate; SR; sarcoplasmic reticulum; E1P; ADP-sensitive phosphoenzyme; E2P; ADP-insensitive phosphoenzyme; AMPPCP; adenosine 5â²-(βï ,γ-methylene)triphosphate; LC/MS; liquid chr
Computational investigation of pathogenic nsSNPs in CEP63 protein
Keywords: در حال حاضر; CEP63; Centrosomal protein of 63Â kDa; nsSNPs; Non-synonymous single nucleotide polymorphisms; CDK1; Cyclin-dependent kinase 1; MDS; Molecular dynamics simulation; RMSD; Root-mean-square deviation; Rg; Radius of gyration; SASA; Solvent-accessible surface
In silico prediction of a disease-associated STIL mutant and its affect on the recruitment of centromere protein J (CENPJ)
Keywords: در حال حاضر; STIL protein; Docking; Molecular dynamics simulation; CENPJ protein; STIL; SCL/TAL1 interrupting locus; CENPJ; Centromere protein J; MDS; Molecular dynamics simulation; RMSD; Root-mean-square deviation; Rg; Radius of gyration; SASA; Solvent-accessible sur
Computational screening and molecular dynamics simulation of disease associated nsSNPs in CENP-E
Keywords: در حال حاضر; CENP-E; centromere-associated protein-E; nsSNPs; non-synonymous single nucleotide polymorphisms; MDS; molecular dynamics simulation; RMSD; root-mean-square deviation; Rg; radius of gyration; SASA; solvent-accessible surface area; RMSF; root-mean square fl
NMR and conformational studies of linear and cyclic oligo-(1→6)-β-d-glucosamines
Keywords: در حال حاضر; Cyclic oligosaccharides; Glucosamine; Conformation analysis; MM3; SASA; Transglycosidic coupling constants
Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies
Keywords: در حال حاضر; CDR; complementary determining region; HEL; hen egg white lysozyme; SPR; surface plasmon resonance; ITC; isothermal titration calorimetry; FR; framework residues; RU; response unit; IgG; immunoglobin G; SASA; solvent accessible surface area; Enthalpy; Van
Molecular dynamics simulations of a fibrillogenic peptide derived from apolipoprotein C-II
Keywords: در حال حاضر; apo; apolipoprotein; NMR; nuclear magnetic resonance; Aβ; β-amyloid; MD; molecular dynamics; PME; particle mesh Ewald; VMD; visual molecular dynamics; PEPCAT; peptide conformational analysis tool; SASA; solvent accessible surface area; ROGhyd; radius of
Novel composite proton-exchange membrane based on silica-anchored sulfonic acid (SASA)
Keywords: در حال حاضر; PCM; SASA; Fuel cell; Membrane; Methanol oxidation;
Electrostatic calculations and quantitative protein retention models for ion exchange chromatography
Keywords: در حال حاضر; Electrostatic potential; Lactoferrin; Ion exchange chromatography; Protein retention; PLS; PCA; QSPR; SASA; Surface potential; Surface hydrophobicity
Bambusicolous fungi in Japan (5): three species of Tetraploa
Keywords: در حال حاضر; Bamboo; Hyphomycetes; Sasa; Taxonomy; Tetraploa;
Bambusicolous fungi in Japan (4): a new combination, Astrosphaeriella aggregata
Keywords: در حال حاضر; Bamboo; Melanopsamma; Pleosporales; Sasa; Taxonomy;
Bambusicolous fungi in Japan (6): Katumotoa, a new genus of phaeosphaeriaceous ascomycetes
Keywords: در حال حاضر; Bamboo; Phaeosphaeriaceae; Pleosporales; Sasa; Taxonomy;