Keywords: RMSD، میانگین میانگین انحراف مربع; X-ray crystallography; Asymmetry; Conformational change; Zinc coordination; Hydride transferADH, alcohol dehydrogenase; TFE, 2,2,2-trifluoroethanol (“ETF” in the PDB file, with the methylene carbon labeled as “C2”); rmsd, root mean square deviation
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Keywords: RMSD، میانگین میانگین انحراف مربع; MD, molecular dynamics; SASA, Solvent Accessible Surface Area; RMSD, Root Mean Square Deviation; STI, Soybean Trypsin Inhibitor; KTI, Kunitz-type Trypsin Inhibitor; NMR, Nuclear Magnetic Resonance Imaging; VMD, Visual Molecular Dynamics; FTIR, Fourier Tra
Keywords: RMSD، میانگین میانگین انحراف مربع; VS, virtual screening; HTS, high throughput screening; RC, reference compound; NA, neuraminidase; HA, haemagglutinin; ADME/T, Absorption, Distribution, Metabolism, Excretion, and Toxicity; RMSD, root mean square deviation; APOD, abbreviated profile of dru
Keywords: RMSD، میانگین میانگین انحراف مربع; DAP, days after planting; DOY, day of year; DTE, days to emergence; DTM, days to maturity; GDD, growing degree days; ME, model efficiency; MSE, mean squared error; RMSD, root mean square deviation; SHAW model, Simultaneous Heat and Water modelMicroclimate
NQO1 rs1800566 polymorph is more prone to NOx induced lung injury: Endorsing deleterious functionality through informatics approach
Keywords: RMSD، میانگین میانگین انحراف مربع; WT, Wild type; NQO1, NAD(P)H:quinone oxidoreductase 1; RMSD, Root mean square deviation; CUPSAT, Cologne University Protein Stability Analysis Tool; ΔΔG, unfolding energy; PDB, Protein data bank; MOE, Molecular Operating Environment; NPA, Nosé-Poincaré-An
Pharmacophore modeling, 3D-QSAR and docking study of 2-phenylpyrimidine analogues as selective PDE4B inhibitors
Keywords: RMSD، میانگین میانگین انحراف مربع; 3D-QSAR, 3 dimensional quantitative structure-activity relationship; PLS, partial least square; RMSD, root mean square deviation; RMSE, root mean square error; SD, standard deviation; R2, correlation coefficient; Q2, correlation coefficient for test set;
Molecular principles behind pyrazinamide resistance due to mutations in panD gene in Mycobacterium tuberculosis
Keywords: RMSD، میانگین میانگین انحراف مربع; MD, molecular dynamics; DM, double mutant; RMSD, root mean square deviation; RMSF, root mean square fluctuationDocking; Simulation; Pyrazinamide; RMSD; RMSF
Molecular characterization of RNA binding motif protein 3 (RBM3) gene from Pashmina goat
Keywords: RMSD، میانگین میانگین انحراف مربع; RBM3, RNA binding motif protein 3; RBP, RNA binding protein; CIRBP, cold induced RNA binding protein; qRT-PCR, quantitative real-time PCR; ORF, open reading frame; RNP, ribonucleoprotein; cDNA, complementary DNA; RMSD, root mean square deviation; CDD, Con
Effect of thermal and electric field treatment on the conformation of Ara h 6 peanut protein allergen
Keywords: RMSD، میانگین میانگین انحراف مربع; IgE, Immunoglobulin E; SASA, Solvent Accessible Surface Area; RMSD, Root Mean Square Deviation; SR, Systemic Allergic Reaction; OAS, Oral Allergy Syndrome; NMR, Nuclear Magnetic Resonance Imaging; MD, Molecular Dynamics; FTIR, Fourier Transformation Infra
MutT from the fish pathogen Aliivibrio salmonicida is a cold-active nucleotide-pool sanitization enzyme with unexpectedly high thermostability
Keywords: RMSD، میانگین میانگین انحراف مربع; 8-oxoG, 8-oxo-Guanine; Nudix, nucleoside diphosphates linked to some other moiety X; RMSD, root mean square deviation; MTH1, MutT homologue 1 from human; A:T to C:G, adenine:thymine to cytosine:guanine; NMR, nuclear magnetic resonance; DSC, differential s
Prediction of dual agents as an activator of mutant p53 and inhibitor of Hsp90 by docking, molecular dynamic simulation and virtual screening
Keywords: RMSD، میانگین میانگین انحراف مربع; Hsp90, heat shock protein90; MDs, molecular dynamic simulations; Rg, radius of gyration; RMSD, root mean square deviation; RMSF, root mean square fluctuation; VS, virtual screeningDocking; Dual agent; Hsp90 inhibitors; Molecular dynamic simulations; P53;
Laboratory and field assessment of the capacitance sensors Decagon 10HS and 5TE for estimating the water content of irrigated soils
Keywords: RMSD، میانگین میانگین انحراف مربع; DDL, diffuse double layer; FDR, frequency domain reflectometry; RMSD, root mean square deviation; TDR, time domain reflectometry; ɛb, apparent soil dielectric permittivity; θ, soil volumetric water content; σb, apparent soil electrical conductivityIrrigat
D2N: Distance to the native
Keywords: RMSD، میانگین میانگین انحراف مربع; D2N, Distance to native; PCC, Pearson correlation coefficient; RMSD, Root mean square deviation; GDT, Global distance test; TM, Topology modelingProtein folding; Native; Decoy; Quality assessment
Molecular recognition of Cullin3 by KCTDs: Insights from experimental and computational investigations
Keywords: RMSD، میانگین میانگین انحراف مربع; MD, molecular dynamics; RMSF, root mean square fluctuation; RMSD, root mean square deviation; RMSIP, root mean square inner product; ITC, isothermal titration calorimetry; PDB, Protein Data Bank; INC, insomniac protein; Cul3, Cullin3; CRL, Cullin RING lig
Structure-guided engineering of Anticalins with improved binding behavior and biochemical characteristics for application in radio-immuno imaging and/or therapy
Keywords: RMSD، میانگین میانگین انحراف مربع; DOTA, 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid; DTPA, diethylene triamine pentaacetic acid; PRIT, pretargeted RIT; RID, radio-immuno diagnostics; RIT, radio-immuno therapy; RMSD, root mean square deviation; SPR, surface plasmon resonance;
3D shape-based analysis of cell line-specific compound response in cancers
Keywords: RMSD، میانگین میانگین انحراف مربع; SAR, structure–activity relationship; NCI, National Cancer Institute; MDDR, MDL Drug Data Report; RMSD, root mean square deviation; PCC, Pearson's correlation coefficient; MOA, mechanism of actionCancer drug sensitivity; NCI60 compounds; Structure–activit
ViewMotions Rainbow: A new method to illustrate molecular motions in proteins
Keywords: RMSD، میانگین میانگین انحراف مربع; RMSD, root mean square deviation; Database of Macromolecular Movements (Morph Server), http://molmovdb.org; ViewMotions Server, http://viewmotions.bc.eduDatabase of Macromolecular Movements; Sieve-fit; Structural alignment; Domain motions; Visualization
The structure of the CD3 ζζ transmembrane dimer in POPC and raft-like lipid bilayer: A molecular dynamics study
Keywords: RMSD، میانگین میانگین انحراف مربع; CHOL, cholesterol; MD, molecular dynamics; POPC, palmitoyl-oleoyl-phosphatidylcholine; RMSD, root mean square deviation; RDF, radial distribution function; SM, sphingomyelin; TCRT, cell receptor; TM, transmembraneCD3 ζζ; Membrane protein; Molecular dynami
Exploring the effect of PARP-1 flexibility in docking studies
Keywords: RMSD، میانگین میانگین انحراف مربع; PARP, poly(ADP-ribose) polymerase; REMD, replica exchange molecular dynamics; PCA, principal components analysis; RMSD, root mean square deviation; EF, enrichment factorReplica exchange molecular dynamics; PARP; Molecular docking; Virtual screening
Communication between the active site and the allosteric site in class A beta-lactamases
Keywords: RMSD، میانگین میانگین انحراف مربع; BLIP, beta-lactamase inhibitor protein; MD, molecular dynamics; MSF, mean square fluctuations; RMSD, root mean square deviation; VMD, visual molecular dynamicsBeta-lactamase; Ligand binding; Molecular dynamics simulations; Binding free energy; Allostery
Alternate glucocorticoid receptor ligand binding structures influence outcomes in an in vivo tissue regeneration model
Keywords: RMSD، میانگین میانگین انحراف مربع; dpf, Days post fertilization; dpa, Days post amputation; GR-LBD, GR ligand binding domain; DEX, dexamethasone; BDP, Beclomethasone dipropionate; Beclo, beclomethasone; PDB, Protein data bank; RMSD, Root mean square deviation; HB, hydrogen bondingDocking;
Selected C7-substituted chromone derivatives as monoamine oxidase inhibitors
Keywords: RMSD، میانگین میانگین انحراف مربع; DMSO, dimethyl sulfoxide; FAD, flavin adenine dinucleotide; MAO, monoamine oxidase; PDB, protein data bank; RMSD, root mean square deviation; SAR, structure–activity relationship; SI, selectivity indexMonoamine oxidase; Inhibition; Reversible; Chromone; C
Conformational, receptor interaction and alanine scan studies of glucose-dependent insulinotropic polypeptide
Keywords: RMSD، میانگین میانگین انحراف مربع; Nt-ECD, N-terminal extracellular receptor domain; GIP, glucose-dependent insulinotropic polypeptide; NOE, nuclear Overhauser effect; NOESY, nuclear Overhauser effect spectroscopy; RMSD, root mean square deviation; TOCSY, total correlation spectroscopyGIP;
Hinge-loop mutation can be used to control 3D domain swapping and amyloidogenesis of human cystatin C
Keywords: RMSD، میانگین میانگین انحراف مربع; Cysteine protease inhibitor; 3D domain swapping; Protein aggregation; Amyloid; Crystal structureAS, appending structure; HCCAA-I, hereditary cystatin C amyloid angiopathy Icelandic type; hCC, human cystatin C; rmsd, root mean square deviation
The structure of Aspergillus niger phytase PhyA in complex with a phytate mimetic
Keywords: RMSD، میانگین میانگین انحراف مربع; IHP, myo-inositol hexakis phosphate; IHS, myo-inositol hexakis sulfate; RMSD, root mean square deviation; PNGase F, peptide-N-glycosidase F3-Phytase; Phytate; PhyA; Michaelis complex; Aspergillus niger; Protein structure
The conserved Cys76 plays a crucial role for the conformation of reduced glutathione peroxidase-type tryparedoxin peroxidase
Keywords: RMSD، میانگین میانگین انحراف مربع; CD, circular dichroism; Px, glutathione peroxidase-type tryparedoxin peroxidase; RmsD, root mean square deviation; WT, wildtypeTrypanothione; Tryparedoxin; Glutathione peroxidase; Protein structure; Trypanosoma brucei
Site-directed mutagenesis and structural modeling of Coq10p indicate the presence of a tunnel for coenzyme Q6 binding
Keywords: RMSD، میانگین میانگین انحراف مربع; CoQ, coenzyme Q; NMR, nuclear magnetic resonance; RMSD, root mean square deviation; ΔΔGstat, statistical couplingCoenzyme Q; Mitochondrion; COQ10
An interpretation of positional displacement of the helix12 in nuclear receptors: Preexistent swing-up motion triggered by ligand binding
Keywords: RMSD، میانگین میانگین انحراف مربع; NR, nuclear receptor; H12, helix 12; FMO, fragment molecular orbital; ERα, estrogen receptor α; MD, molecular dynamics; RA, retinoic acid; RAR, retinoic acid receptor; RMSD, root mean square deviation; PC1, first principal component; PC2, second principal
Molecular dynamics simulations of Aβ fibril interactions with β-sheet breaker peptides
Keywords: RMSD، میانگین میانگین انحراف مربع; AD, Alzheimer's disease; Aβ, amyloid-β; MD, molecular dynamics; RMSD, root mean square deviation; REMD, replica exchange molecular dynamicsAlzheimer's disease; Amyloid-β; Molecular dynamics simulation; Replica exchange molecular dynamics; β-Blocker peptid
The C-terminal of CysM from Mycobacterium tuberculosis protects the aminoacrylate intermediate and is involved in sulfur donor selectivity
Keywords: RMSD، میانگین میانگین انحراف مربع; OAS, O-acetyl-l-serine; OPS, O-phospho-l-serine; rmsd, root mean square deviation; PLP, pyridoxal 5′-phosphate; CysO-SH, thiocarboxylated CysO; MtbCysM, CysM from Mycobacterium tuberculosis; EcCysM, CysM from Escherichia coli; MtbCysK1, CysK1 from Mycobac
Analysis of B-cell epitopes from the allergen Hev b 6.02 revealed by using blocking antibodies
Keywords: RMSD، میانگین میانگین انحراف مربع; ASA, accessible surface area; BSA, bovine serum albumin; CDR, complementary determining region; ELISA, enzyme-linked immunosorbent assay; FR, framework region; mAb, monoclonal antibody; NRL, natural rubber latex; RMSD, root mean square deviation; scFv, si
Structure-based drug design: From nucleic acid to membrane protein targets
Keywords: RMSD، میانگین میانگین انحراف مربع; rmsd, root mean square deviation; GPCR, G-protein coupled receptor; ADME, Absorption, Distribution, Metabolism, Excretion, MTT (3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide) cell proliferation assay; EMSA, Electrophoretic Mobility Shift Ass
The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His–Tyr bond
Keywords: RMSD، میانگین میانگین انحراف مربع; pmf, proton motive force; DFT, density functional theory; Em,7, mid-point redox potential at pH 7 relative to NHE; CcO, cytochrome c oxidase; cyt c, cytochrome c; RMSD, root mean square deviation; wt, the model system of the “wild type” structure of the C
Matching Biochemical Reaction Kinetics to the Timescales of Life: Structural Determinants That Influence the Autodephosphorylation Rate of Response Regulator Proteins
Keywords: RMSD، میانگین میانگین انحراف مربع; rmsd, root mean square deviation; ‘59’, the residue in a response regulator that corresponds to position 59 (or whatever number is enclosed by single quotation marks) in Escherichia coli CheYautodephosphorylation; CheY; response regulator; signal transduc
Structure, dynamics, and stability of assemblies of the human prion fragment SNQNNF
Keywords: RMSD، میانگین میانگین انحراف مربع; PrP, prion protein; PrPC, cellular prion protein; PrPSc, scrapie prion protein; RMSD, root mean square deviation; RMSF, root mean square fluctuation; PDB, Protein Data Bank; MD, molecular dynamicsPrion protein; Molecular dynamics; Steric zipper; Prion hyd
Using protein binding site prediction to improve protein docking
Keywords: RMSD، میانگین میانگین انحراف مربع; CAPRI, a critical assessment of predicted interactions; EI, enzyme–inhibitor; FFT, fast Fourier transform; RMSD, root mean square deviation; SVM, support vector machine; ToF, tightness of fit.
Antitumor studies – Part 2: Structure–activity relationship study for flavin analogs including investigations on their in vitro antitumor assay and docking simulation into protein tyrosine kinase
Keywords: RMSD، میانگین میانگین انحراف مربع; Protein tyrosine kinase; Flavin analog; AutoDock; SAR (structure–activity relationship)PKC, protein kinase C; SAR, structure–activity relationship; Ph, phenyl-; PTK, protein tyrosine kinase; RMSD, root mean square deviation
Two novel uroporphyrinogen decarboxylase (URO-D) mutations causing hepatoerythropoietic porphyria (HEP)
Keywords: RMSD، میانگین میانگین انحراف مربع; copro, coproporphyrinogen III; EBV, Epstein–Barr virus; HEP, hepatoerythropoietic porphyria; HFE, hemochromatosis; HPLC, high-performance liquid chromatography; PCR, polymerase chain reaction; PCT, porphyria cutanea tarda; RMSD, root mean square deviation
An Asymmetric Structure of the Bacillus subtilis Replication Terminator Protein in Complex with DNA
Keywords: RMSD، میانگین میانگین انحراف مربع; RTP, replication terminator protein; RMSD, root mean square deviation; ds, double-stranded; HSQC, heteronuclear single quantum coherencewinged-helix; DNA replication; replication terminator protein; polar fork arrest; cooperative binding
The Structure of a Tandem Pair of Spectrin Repeats of Plectin Reveals a Modular Organization of the Plakin Domain
Keywords: RMSD، میانگین میانگین انحراف مربع; ABD, actin-binding domain; FnIII, fibronectin type III; BPAG1, bullous pemphigoid antigen 1; MACF, microtubule actin crosslinking factor; rmsd, root mean square deviation; SH3, Src-homology 3; SR, spectrin repeat; PDB, Protein Data Bankcytoskeleton; hemid
Hydroxyl Groups in the ββ Sandwich of Metallo-β-lactamases Favor Enzyme Activity: Tyr218 and Ser262 Pull Down the Lid
Keywords: RMSD، میانگین میانگین انحراف مربع; MBL, metallo-β-lactamase; MD, molecular dynamics; NIT, nitrocefin; CEF, cephalothin; CTX, cefotaxime; LOR, cefaloridine; CAZ, ceftazidime; PEN, benzylpenicillin; AMP, ampicillin; IMP, imipenem; RMSD, root mean square deviation; SD, standard deviationmetal
Blind docking of drug-sized compounds to proteins with up to a thousand residues
Keywords: RMSD، میانگین میانگین انحراف مربع; Active site; Binding pocket; Rational design; Pharmacophore; AutoDock; Molecular interactionBD, blind docking; PDB, protein databank; RMSD, root mean square deviation
Insight into the structure of Mesorhizobium loti arylamine N-acetyltransferase 2 (MLNAT2): A biochemical and computational study
Keywords: RMSD، میانگین میانگین انحراف مربع; NAT, arylamine N-acetyltransferase; M. loti, Mesorhizobium loti; RMSD, root mean square deviation; RMSF, root mean square fluctuationRhizobia; Xenobiotic metabolism; Isoform; Circular dichroism; Homology modelling; Stability
Solution conformation of an immunodominant epitope in the hepatitis B virus preS2 surface antigen
Keywords: RMSD، میانگین میانگین انحراف مربع; HBV, hepatitis B virus; mAb, monoclonal antibody; NMR, nuclear magnetic resonance; RMSD, root mean square deviation; COSY, shift correlation spectroscopy; TOCSY, total COSY; NOESY, nuclear Overhauser enhancement spectroscopy; CSI, chemical shift indexHepa
Immunogenic and structural properties of the Asn-Gly-Arg (NGR) tumor neovasculature-homing motif
Keywords: RMSD، میانگین میانگین انحراف مربع; CFA, complete Freund's adjuvant; IFA, incomplete Freund's adjuvant; IFNγ, interferon-γ; KLH, keyhole limpet haemocyanin; OVA, ovalbumin; RMSD, root mean square deviation; TNF, tumor necrosis factor-αTumor necrosis factor; Tumor targeting; Aminopeptidase N
Identification of a buried pocket for potent and selective inhibition of Chk1: Prediction and verification
Keywords: RMSD، میانگین میانگین انحراف مربع; DBH, debromohymenialdisine; PDB, Protein data bank; RMSD, root mean square deviation; SAR, structure–activity relationshipDrug design; Hydrogen bonds; Molecular modelling; Molecular recognition; Oncology; X-ray crystallography
Heterotetrameric Sarcosine Oxidase: Structure of a Diflavin Metalloenzyme at 1.85 Å Resolution
Keywords: RMSD، میانگین میانگین انحراف مربع; TSOX, heterotetrameric sarcosine oxidase; H4folate, tetrahydrofolate; GR, glutathione reductase; RMSD, root mean square deviation; PDB, Protein Data Bank; ICP-MS, inductively coupled plasma mass spectrometry; MSOX, monomeric sarcosine oxidase; EPR, electr
Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1)
Keywords: RMSD، میانگین میانگین انحراف مربع; Thermostable enzyme; Crystal structure; Molecular dynamicsrXynA, recombinant family G/11 β-1,4-xylan xylanohydrolase from Bacillus subtilis strain 1A1; RMSD, root mean square deviation