Keywords: AZ; antizyme; AZBE; antizyme-binding element; AZIN; antizyme inhibitor; ERGIC; endoplasmic reticulum-Golgi intermediate compartment; ODC; ornithine decarboxylase; GDT_TS; global distance test total score; HA; hemagglutinin; HEK; human embryonic kidney; PA
مقالات ISI (ترجمه نشده)
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Keywords: AF-2; activation function 2; AP; alternative pocket; AR; androgen receptor; BF-3; binding function 3; DBD; DNA-binding domain; ER; estrogen receptor; GP; genomic pocket; GR; glucocorticoid receptor; H12; helix 12; HDX; hydrogen/deuterium exchange; LBD; li
Keywords: Higher heating value; Isoperibol bomb calorimetry; Visible near-infrared diffuse reflectance spectroscopy; Distillers grains; Manure; db; dry basis; DM; dietary dry matter; HHV; higher heating value; HHVdaf; dry, ash-free higher heating value; PLS; partia
Keywords: TNFα; tumour necrosis factor-α; IL-1β; interleukin-1 β; IL-1F; interleukin-1 family; M-I; Mekler-Idlis; MRT; molecular recognition theory; DMSO; dimethylsulphoxide; COSY; correlation spectroscopy; NOE; nuclear Overhauser effect; NOESY; nuclear Ove
Keywords: SPs; synthetic progestins; MPA; medroxyprogesterone acetate; MGA; megestrol acetate; CLA; chlormadinone acetate; NET; norethisterone; NED; norethynodrel; LNG; levonorgestrel; PR; progesterone receptor; mA; monomer A; mB; monomer B; EB; estradiol benzoate;
Keywords: MLP; major latex protein; PDB; Protein Data Bank; PR-10; pathogenesis-related proteins family 10; RMSD; root mean square deviation; RRP; ripening related protein; Act d 11; Kirola; Allergen; Food allergy; Kiwifruit; Bet v 1;
Keywords: 3D; Three-Dimensional; AFM; Atomic Force Microscopy; CCS; Collision Cross Section; EM; Electron Microscopy; EPR; Electron Paramagnetic Resonance; FRET; Förster resonance energy transfer; IM; Ion Mobility; RMSD; Root Mean Square Deviation; MD; Molecular D
Keywords: RNase A superfamily; Microbial RNases; Nucleotide binding proteins; Structure complexes; Substrate subsites; ECP; eosinophil cationic protein; EDN; eosinophil derived neurotoxin; pn, Rn and Bn; protein binding sites for nucleotide phosphate, ribose and ba
Keywords: TGFBIp; transforming growth factor beta induced protein; TGFBI; transforming growth factor beta induced gene; EMI; EMILIN-1 domain; LCD; lattice corneal dystrophy; GCD; granular corneal dystrophy; TBCD; Thiel-Behnke corneal dystrophy; WT; wild-type; FAS
Keywords: PDB; protein data bank; CI2; chymotrypsin inhibitor 2; FKPB; FK506 binding protein; rmsd; root mean square deviation; NOE; nuclear Overhauser enhancement; PB; Poisson-Boltzmann; Hydrogen exchange; NMR; Continuum dielectric; Protein electrostatics; Struc
Keywords: BLAST; alignment search tool; KP; known proteins; MD; molecular dynamics; RMSD; root mean square deviation; UP; unknown proteins; PDB; Protein Data Bank; Schistosoma mansoni; Vaccine; Bioinformatics; Molecular modeling;
Characterization of an RNase with two catalytic centers. Human RNase6 catalytic and phosphate-binding site arrangement favors the endonuclease cleavage of polymeric substrates
Keywords: 3â²-CMP; cytidine 3â²-monophosphate; Câ¯>â¯p; Cytidine 2â²,3â²-cyclic phosphate; ECP; Eosinophil Cationic Protein; poly(C); Polycytidylic acid; RMSD; Root mean square deviation; Endoribonuclease; RNaseA; RNase6; Substrate binding site; Protein cryst
Identification of the key determinant of the transport promiscuity in Na+-translocating rhodopsins
Keywords: Rhodopsin; Sodium transport; Proton transport; Dokdonia sp.; pump-to-pump conversion; CCCP; m-chlorocarbonylcyanide phenylhydrazone; DDM; n-dodecyl β-d-maltoside; Kr2; Na+-transporting rhodopsin from Krokinobacter eikastus NBRC 100814T; NaR; Na+-tran
Structural insights into chemokine CCL17 recognition by antibody M116
Keywords: mAb; monoclonal antibody; DTT; dithiothreitol; PEG; polyethylene glycol; EDTA; ethylenediaminetetraacetic acid; HEPES; 4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid; CDR; complementarity determining region; VH; variable domain of the heavy chain; VL;
Natronomonas pharaonis halorhodopsin Ser81 plays a role in maintaining chloride ions near the Schiff base
Keywords: Chloride pump; Halorhodopsin; Molecular dynamics; Patch clamp; NpHR; Natronomonas pharaonis halorhodopsin; BS1; binding site-1; MD; molecular dynamics; HR; halorhodopsin; sHR; Halobacterium salinarium halorhodopsin; POPC; phosphatidylcholine; RMSD; root-m
Tauroursodeoxycholic acid binds to the G-protein site on light activated rhodopsin
Keywords: Bile acid; Chemical biology; G protein; G proteinâcoupled receptor (GPCR); Molecular docking; Photoreceptor; Phototransduction; Retina; Rhodopsin; Signal transduction; GPCR; G-protein coupled receptor; G-protein; heterotrimeric GTP-binding protein; R; d
Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring
Keywords: TCR; T cel receptors; MHC; Major Histocompatibility Complex; IEDB; immune epitope database; HLA; human leukocyte antigen; CDR; complementarity determining region; RMSD; root mean square deviation; PDB; Protein Data Bank; MCM; Monte Carlo Method; AUC; area
Crystal structures of the disease-causing D444V mutant and the relevant wild type human dihydrolipoamide dehydrogenase
Keywords: h; human; E3; (dihydro)lipoamide dehydrogenase, the common E3 component of the mitochondrial 2-oxo acid dehydrogenase complexes; LADH; (dihydro)lipoamide dehydrogenase; KGDHc; alpha-ketoglutarate (also known as 2-oxoglutarate) dehydrogenase complex; PDHc;
Computational analysis of non-synonymous single nucleotide polymorphism in the bovine cattle kappa-casein (CSN3) gene
Keywords: SNP; single nucleotide polymorphism; SIFT; Sorting Intolerant From Tolerant; PolyPhen; phenotype polymorphism; nsSNP; nonsynonymous single nucleotide polymorphism; MUSTER; MUlti-Sources ThreadER; NCBI; National Centre for Biological Information; PROVEAN;
Absorption-energy calculations of chlorophyll a and b with an explicit solvent model
Keywords: Chl; chlorophyll; LHC; light harvesting complex; FMO; Fenna Matthews-Olson; QM; quantum mechanics; MM; molecular mechanics; DFT; density functional theory; TD-DFT; time-dependent density functional theory; HF; Hartree Fock; GAFF; generalized Amber force f
Substitutions of a buried glutamate residue hinder the conformational change in horse liver alcohol dehydrogenase and yield a surprising complex with endogenous 3â²-Dephosphocoenzyme A
Keywords: Enzyme kinetics; Coenzyme binding; Conformational change; Hydride transfer; X-ray crystallography; Protein structure; ADH; alcohol dehydrogenase; E267H; substitution Glu-267 with histidine residue; E267â¯H/N; substitution with either histidine or asparag
Characterization of metabolic network of oxalic acid biosynthesis through RNA seq data analysis of developing spikes of finger millet (Eleusine coracana): Deciphering the role of key genes involved in oxalate formation in relation to grain calcium accumul
Keywords: SGAT; Serine Glyoxalate Amino-Transferase; GGAT; Glutamate Glyoxylate Amino-Transferase; ICL; Isocitrate Lyase; GLO; Glyoxal Oxidase; MHAR; Mono Dehydro Ascorbate Reductase; APO; Ascorbate Per Oxidase; OXO; Oxalate Oxidase; FPKM; Fragments Per Kilobase of
Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms
Keywords: 6-MP; 6-mercaptopurine; ABC; ATP-binding cassette; ADV; adefovir; AZT; azidothymidine; BLOSUM; blocks substitution matrix; CFTR; cystic fibrosis transmembrane conductance regulator; Chol; cholesterol; cryo-EM; cryo-electronic microscopy; DMAV; dimethylars
Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanYB
Keywords: VRE; vancomycin-resistant Enterococcus; NAM; N-acetylmuramic acid; NAG; N-acetylglucosamine; PEG; polyethylene glycol; SAD; single-wavelength anomalous diffraction; RMSD; root-mean-square deviation; SEC-MALS; size-exclusion chromatography with multi-angle
A Computational workflow for the identification of the potent inhibitor of type II secretion system traffic ATPase of Pseudomonas aeruginosa
Keywords: 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
Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization
Keywords: TmArgBP; arginine binding protein isolated from Thermotoga maritima; TmArgBP20-233; truncated form of TmArgBP; arg-TmArgBP20-233; arginine-bound form of TmArgBP20-233; lf-TmArgBP20-233; ligand-free form of TmArgBP20-233; TmArgBP_C-ter232-246; peptide corr
Assessment of the transmembrane domain structures in GPCR Dock 2013 models
Keywords: GPCR; Homology model; Transmembrane; Ligand docking; RMSD; Classification;
Anthranilate phosphoribosyltransferase: Binding determinants for 5â²-phospho-alpha-d-ribosyl-1â²-pyrophosphate (PRPP) and the implications for inhibitor design
Keywords: AnPRT; anthranilate phosphoribosyltransferase; IC50; absolute IC50, that is the concentration of inhibitor which decreased enzyme activity by 50%; Km; Michaelis-Menten constant; Ki; inhibition constant; Mtb; Mycobacterium tuberculosis; PPi; pyrophosphate;
Quantitative proteomics and biochemical analyses reveal the role of endoplasmin in the regulation of the expression and secretion of A Disintegrin And Metalloproteinase 12
Keywords: ADAM12S; Endoplasmin (GRP94); Label-free quantification; Secretion; Spectral counting; Docking; ADAM12S; the short form of a disintegrin and metalloproteinase 12; CANX; calnexin; CPORT; Consensus Prediction Of interface Residues in Transient complexes; Dl
The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition
Keywords: MD; Molecular Dynamics; RMSD; root mean square deviation; RMSIP; the root mean square inner product; SELEX; Systematic Evolution of Ligands by Exponential Enrichment; APT; Aptamer; PDB; Protein Data Bank; H-bonds; Hydrogen bonds; SELEX; Systematic Evoluti
3D QSAR Pharmacophore Based Virtual Screening for Identification of Potential Inhibitors for CDC25B
Keywords: CDC25B; cell division cycle 25B; CADD; computer aided drug design; HBA; hydrogen bond acceptors; HBD; hydrogen bond doners; HYP; hydrophobe area; RMSD; root mean squared deviation; RMSF; root mean square fluctuations; CDC25B; Hypogen; QSAR; docking;
Prediction of degree of impregnation in thermoplastic unidirectional carbon fiber prepreg by multi-scale computational fluid dynamics
Keywords: Unidirectional carbon fiber prepreg (UD-CFP); Thermoplastic resin; Resin impregnation die; Degree of impregnation (DoI); Computational fluid dynamics (CFD); Multi-scale simulation; 2D; two-dimensional; 3D; three-dimensional; CF; carbon fiber; CFD; computa
Network and structure based inference of functional single nucleotide polymorphisms associated with the TGFβ1 gene and its role in colorectal cancer (CRC)
Keywords: 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
Structural model, functional modulation by ivermectin and tissue localization of Haemonchus contortus P-glycoprotein-13
Keywords: Nematode; Haemonchus contortus; ABC transporters; P-glycoprotein; Ivermectin; Homology modeling; ABC; ATP-binding cassette; ACD; actinomycin D; AH; anthelmintic; BlastP; protein Basic Local Alignment Search Tool; bp; base pairs; Cel; Caenorhabditis elegan
Calmodulins from Schistosoma mansoni: Biochemical analysis and interaction with IQ-motifs from voltage-gated calcium channels
Keywords: ANS; anilinonaphthalene-8-sulfonate; BS3; bis(sulfosuccinimidyl)suberate; CPZ; chlorpromazine; PZQ; praziquantel; rmsd; root mean square deviation; SmCaM1; one of the two calmodulins from S. mansoni; SmCaM2; one of the two calmodulins from S. mansoni; TFP
Conserved structure and function of chemokine CXCL8 between Chinese tree shrews and humans
Keywords: CXCL8; chemokine (C-X-C) ligand 8; CXCR1; C-X-C motif chemokine receptor 1; CXCR2; C-X-C motif chemokine receptor 2; Ts; tree shrew; 3D; three-dimensional; PBMCs; peripheral blood mononuclear cells; MHC; major histocompatibility complex; IL-2; interleukin
Crystal structure and substrate specificity of ExoY, a unique T3SS mediated secreted nucleotidyl cyclase toxin from Pseudomonas aeruginosa
Keywords: X-ray crystallography; Nucleotidyl cyclase toxins; T3SS; Anthrax toxA family; Non-canonical secondary messengers; One-metal-ion dependent catalysis; ExoY; exogenous toxin Y; T3SS; Type III secretory systems; AA-NC; actin-activated nucleotidyl cyclase; EF;
Insights into the aquaporin 4 of zebrafish (Danio rerio) through evolutionary analysis, molecular modeling and structural dynamics
Keywords: AQPs; Aquaporins; zAQP4; Zebrafish Aquaporin4; NMO; Neuromyelitis optica; PDB; Protein Data Bank; BLAST; Basic Local Alignment Search Tool; RMSD; Root-Mean-Square Deviation; TM score; Template Modeling score; MD; Molecular Dynamics; VMD; Visual Molecular
Computational analysis of deleterious SNPs of SLC45A2 involved in oculocutaneous albinism type 4
Keywords: SNP; Single nucleotide polymorphism; SLC45A2; Solute carrier family 45, member 2; OCA4; Oculocutaneous albinism Type 4; nsSNP; Non-synonymous single nucleotide polymorphism; OA; Ocular albinism; TYR; Tyrosinase; TYRP1; Tyrosinase related protein 1; MATP;
Definition of the R-superfamily of conotoxins: Structural convergence of helix-loop-helix peptidic scaffolds
Keywords: TFA; trifluoroacetic acid; SE; size exclusion; RP; reversed phase; DTT; dithiothreitol; IAM; iodoacetamide; PFG; pulse field gradient; RF; radio frequency; TSP; 3-(trimethylsilyl)-propionic acid-D4, sodium salt; WET; water suppression enhanced through T1
Escherichia coli AlkB and single-stranded DNA binding protein SSB interaction explored by Molecular Dynamics Simulation
Keywords: Alkylation; AlkB; Fe(II)/2-Oxoglutarate-dependent dioxygenase; SSB; DNA repair; 1-methyladenine; 1meA; 3-methlyctosine; 3meC; double-stranded beta-helix; (DSBH); High Ambiguity Driven protein Docking; HADDOCK; molecular dynamics; MD; Root mean square fluc
Extraction of nitrogen compounds from model fuel using 1-ethyl-3-methylimidazolium methanesulfonate
Keywords: COSMO-RS; Conductor-like Screening Model for Real Solvents; BP functional; Becke-Perdew functional; DFT; density functional theory; EDN; extractive denitrogenation; HDN; hydrodenitrogenation; IL; ionic liquid; LLE; liquid-liquid extraction; NRTL; non-rand
Pore formation and the key factors in antibacterial activity of aurein 1.2 and LLAA inside lipid bilayers, a molecular dynamics study
Keywords: 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
X-ray, DFT, FTIR and thermal study of the antimicrobial N-benzenesulfonyl-1H-1,2,3-benzotriazole
Keywords: N-benzenesulfonyl benzotriazole; Trypanosoma cruzi; 3D structure; FTIR; Thermal analysis; NBSBZT; N-benzenesulfonyl-1H-1,2,3-benzotriazole; BZT; Benzotriazole; SCXRD; Single Crystal X-ray Diffraction; XRPD; X-ray Powder Diffraction; DFT; Density Functiona
Conservation and variation of the hepatitis E virus ORF2 capsid protein
Keywords: HEV; hepatitis E virus; ORF; open reading frames; AA; amino acid; ICTV; International Committee on Taxonomy of Virus; PDB; Protein Data Bank; RMSD; root mean square deviation; VLP; virus-like particles; mAb; monoclonal antibody; MW; molecular weight; NCBI
Structural studies of two thermostable laccases from the white-rot fungus Pycnoporus sanguineus
Keywords: ABTS; 2,2â²-azino-bis(3-ethylbenzthiazoline-6-sulfonate); DMP; 2,6-dimethoxyphenol; MAN; mannose; NAG; N-acetyl-glucosamine; PsLac; laccase from Pycnoporus sanguineus; PsLacI; isoform I of laccase from Pycnoporus sanguineus; PsLacII; isoform II of laccas
Unique N-terminal extension domain of human asparaginyl-tRNA synthetase elicits CCR3-mediated chemokine activity
Keywords: NRS; (human) asparaginyl-tRNA synthetase; UNE-N; unique N-terminal extension domain of NRS; CD; canonical domain; BmNRS; Brugia malayi NRS; CCR3; CC chemokine receptor 3; ILD; interstitial lung disease; SAD; single-wavelength anomalous diffraction; RMSD;
Improving the thermostability of Serratia marcescens B4A chitinase via G191V site-directed mutagenesis
Keywords: DNS; 3, 5-dinitrosalicylic acid; PDB; Protein Data Bank; WT; wild type; QCSDM; quick-change site-directed mutagenesis; IPTG; isopropyl-c-D-thiogalactoside; Km; Michaelis constant; Vmax; maximum velocity; RMSD; root-mean-square deviation; β chain; Chitina
Design, synthesis and biological evaluation of novel xanthine oxidase inhibitors bearing a 2-arylbenzo[b]furan scaffold
Keywords: 2-Arylbenzo[b]furan derivatives; Xanthine oxidase inhibitor; Antioxidant; Molecular docking; XO; xanthine oxidase; ROS; reactive oxygen species; SARs; structure-activity relationships; DPPH; 1,1-diphenyl-2-picrylhydrazyl; RMSD; root mean square deviation;
Assessing GPCR homology models constructed from templates of various transmembrane sequence identities: Binding mode prediction and docking enrichment
Keywords: A2AAR; adenosine receptor A2A; AUC; area under curve; β2AR; beta 2 adrenergic receptor; D3R; dopamine receptor D3; δOR; delta-opioid receptor; ECL; extracellular loop; GPCR; G protein-coupled receptor; H1R; histamine receptor H1; ICL; intracellular loop