Keywords: ASA، سطح دسترسی قابل دسترس; Disorder; Mutation; Stability; Machine learning; Neighboring residueSVM, support vector machine; ASA, accessible surface area
مقالات ISI ASA، سطح دسترسی قابل دسترس (ترجمه نشده)
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Structure-based approach to the identification of a novel group of selective glucosamine analogue inhibitors of Trypanosoma cruzi glucokinase
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, accessible surface area; BENZ-GlcN (Benzoyl glucosamine), 2-benzamido-2-deoxy-d-glucopyranose; CBZ-GlcN (Carboxybenzyl glucosamine), 2-N-carboxybenzyl-2-deoxy-d-glucosamine; DBT-GlcN (Dioxobenzylthiophenyl glucosamine), 2-[[1,1-dioxobenzo[b]thiophen-
A conformation-based phage-display panning to screen neutralizing anti-VEGF VHHs with VEGFR2 mimicry behavior
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, accessible surface area; BSA, bovine serum albumin; BLAST, basic local alignment search; CD, circular dichroism; cDNA, complementary DNA; CDR, complementarity-determining regions; CH, constant heavy domain; DLS, dynamic light-scattering; DMEM, Dulbec
Dynamic and Thermodynamic Response of the Ras Protein Cdc42Hs upon Association with the Effector Domain of PAK3
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, accessible surface area; CRIB, Cdc42/Rac interactive binding; CSA, chemical shift anisotropy; GAP, GTPase-activating protein; GDI, guanine nucleotide dissociation inhibitor; GDP, guanosine diphosphate; GEF, guanine nucleotide exchange factor; GTP, gu
Investigations on the role of π–π interactions and π–π networks in eNOS and nNOS proteins
Keywords: ASA، سطح دسترسی قابل دسترس; eNOS, endothelial Nitric Oxide Synthase; nNOS, neuronal Nitric Oxide Synthase; ASA, Accessible surface area; NCI, Non-canonical interactions; PDB, Protein Data Bank; SC, stabilization centerπ–π Interactions; eNOS; nNOS; Stability; Networks
Mutational analysis of TYR gene and its structural consequences in OCA1A
Keywords: ASA، سطح دسترسی قابل دسترس; nsSNPs, non-synonymous single nucleotide polymorphism; TYR, tyrosinase; OCA1A, oculocutaneous albinism type1A; ASA, accessible surface area; SFE, solvation free energyDeleterious mutation; Flexibility; OCA1A; Salt bridges; Hydrogen bonding
Deletion of extra C-terminal segment and its effect on the function and structure of artemin
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, accessible surface area; CA, carbonic anhydrase; GdmCl, guanidinium chloride; IPTG, isopropyl β-d-thiogalactopyranoside; LB, Luria–Bertani; MD, Molecular Dynamic; Ni–NTA, nickel–nitrilotriacetic acid; PCR, polymerase chain reaction; pNPAc, p-nitrophe
On nucleotide solvent accessibility in RNA structure
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, Accessible surface area; PDB, Protein Data Bank; SS, Single stranded; DS, Double stranded; MAE, Mean Absolute ErrorSolvent accessibility; RNA structure; Prediction; Surface propensity; Codon usage
A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, accessible surface area; rASA, relative accessible surface areaprotein; interaction; promiscuity; interface; evolution
Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein–protein interaction network
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, Accessible Surface Area; CAI, Codon Adaptation Index; COG, Clusters of Orthologous Groups; dN, nonsynonymous substitution rate; dS, synonymous substitution rate; ORF, Open Reading Frame; PDB, Protein Data Bank; RVP-NET, Real Values of Solvent Accessi
A machine-learning approach for predicting B-cell epitopes
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, accessible surface area; AUC, area under the curve; CDR, complementarity determining region; CEP, Conformational Epitope Prediction; PDB, protein data bank; ROC, receiver operating characteristic; 3D, 3-dimensionalAntigen; Antibody; Epitope; Immunoge
Analysis of B-cell epitopes from the allergen Hev b 6.02 revealed by using blocking antibodies
Keywords: ASA، سطح دسترسی قابل دسترس; 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
Binding Thermodynamics of Ferredoxin:NADP+ Reductase: Two Different Protein Substrates and One Energetics
Keywords: ASA، سطح دسترسی قابل دسترس; apoFld, apoflavodoxin; ASA, accessible surface area; EPPS, N-(2-hydroxyethyl)piperazine-N-3-propanesulfonic acid; ET, electron transfer; Fd, ferredoxin; Fld, flavodoxin; FMN, flavin mononucleotide; FNR, ferredoxin-NADP+ reductase; ITC, isothermal titratio
Computational characterization of B-cell epitopes
Keywords: ASA، سطح دسترسی قابل دسترس; APBS, adaptive Poisson–Boltzmann solver; ASA, accessible surface area; CDR, complementarity determining region; CE, combinatorial extension; CGAL, computational geometry algorithms library; CSU, contacts of structural units; DSSP, dictionary of secondary
Thermodynamics, Kinetics, and Salt dependence of Folding of YopM, a Large Leucine-rich Repeat Protein
Keywords: ASA، سطح دسترسی قابل دسترس; ANK, ankyrin; TPR, tetratricopeptide; LRR, leucine-rich repeat; ASA, accessible surface area; SVD, singular value decompositionrepeat-protein; leucine-rich repeat; cooperative folding; electrostatics; folding kinetics
Small-Angle X-ray Scattering of Reduced Ribonuclease A: Effects of Solution Conditions and Comparisons with a Computational Model of Unfolded Proteins
Keywords: ASA، سطح دسترسی قابل دسترس; RNase A, bovine ribonuclease A; SAXS, small-angle x-ray scattering; RCM, reduced and carboxymethylated; RCAM, reduced and carboxyamidomethylated; ASA, accessible surface area; SSRL, Stanford Synchrotron Radiation Laboratoryribonuclease A; unfolded protein
Architectures and Functional Coverage of Protein–Protein Interfaces
Keywords: ASA، سطح دسترسی قابل دسترس; protein interfaces; protein interaction; structure and function; binding; interface databasePQS, protein quaternary structure database; ASA, accessible surface area; CBM, conserved binding mode; HPRD, Human Protein Reference Database; PDB, Protein Data Ba
Molecular modeling of the complex between Torpedo acetylcholine receptor and anti-MIR Fab198
Keywords: ASA، سطح دسترسی قابل دسترس; AChBP, acetylcholine-binding protein; AChR, acetylcholine receptor; ASA, accessible surface area; CDR, complementarity determining region; ECD, extracellular domain; MIR, main immunogenic region; MG, myasthenia gravis; mAb, monoclonal antibodyNicotinic ac
Thermodynamic Properties of BPTI Variants with Highly Simplified Amino Acid Sequences
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, accessible surface area; BPTI, bovine pancreatic trypsin inhibitor; DSC, differential scanning calorimetry; CNBr, cyanogen bromide; ΔCpapp, apparent heat capacity; Tm, midpoint temperature; ΔHvH, van't Hoff enthalpy; ΔHcal, calorimetric enthalpy; ΔHT
Simulation of conformational changes occurring when a protein interacts with its receptor
Keywords: ASA، سطح دسترسی قابل دسترس; 3D, three-dimensional; ASA, accessible surface area; CASP, comparative assessment of structure prediction; FGF, fibroblast growth factor; FGFR, fibroblast growth factor receptor; G-CSF, granulocyte colony stimulating factor; IL-1β, interleukin-1 beta; IL-
Substrate-induced Conformational Changes and Dynamics of UDP-N-Acetylgalactosamine:Polypeptide N-Acetylgalactosaminyltransferase-2
Keywords: ASA، سطح دسترسی قابل دسترس; ppGalNAcT, UDP-N-acetylgalactosamine:polypeptide N-acetyl-α-galactosaminyltransferase; EA2, peptide STTPAPTTK; GT, glycosyltransferase; mT1, murine ppGalNAcT-1; hT2, human ppGalNAcT-2; hT10, human ppGalNAcT-10; ASA, accessible surface area; MD, molecular
Myosin dynamics on the millisecond time scale
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, Accessible surface area; Block peptides: Conv; converter (AA721-772); L50k; Lower 50kDa actin-binding domain (AA362-462); Lever; lever arm (AA773-812); Loop2; Loop 2 containing peptide (AA526-695); Nterm; N-terminus (AA1-144); U50k; Upper 5
The Stability Effects of Protein Mutations Appear to be Universally Distributed
Keywords: ASA، سطح دسترسی قابل دسترس; PCA, principal component analysis; ASA, accessible surface area; PDB, Protein Data Bankprotein stability; mutational robustness; computational biophysics; ΔΔG distributions; protein models
Design of Disulfide-linked Thioredoxin Dimers and Multimers Through Analysis of Crystal Contacts
Keywords: ASA، سطح دسترسی قابل دسترس; MODIP, modeling of disulfide bridges in proteins; PDB, Protein Data Bank; ASA, accessible surface area; DSC, differential scanning calorimetry; GdmCl, guanidinium chloride; CGH-10, 10 mM citrate, 10 mM glycine and 10 mM Hepes; ESI-MS, electrospray ionizat
Structural and thermodynamic consequences of b heme binding for monomeric apoglobins and other apoproteins
Keywords: ASA، سطح دسترسی قابل دسترس; apoMb, apomyoglobin; ASA, accessible surface area; bj, Bradyrhizobium japonicum; CCP, cytochrome c peroxidase; CD, circular dichroism; cyt b5, cytochrome b5; cyt b562, cytochrome b562; ΔG°U, apparent standard free energy of unfolding; Dos, direct oxygen s
Evaluation of carboxylic acid-induced conformational transitions of β-lactoglobulin: Comparison of the alcohol effects on β-lactoglobulin
Keywords: ASA، سطح دسترسی قابل دسترس; ASA, accessible surface area; PFPA, pentafluoropropionic acid; Trp, tryptophan; Cm, midpoint concentration; β-LG, β-lactoglobulin; ΔG, Gibbs free energyβ-Lactoglobulin; Unfolding; Carboxylic acid; Alcohol; Accessible surface area; Cluster formation
Shape of the Free Energy Barriers for Protein Folding Probed by Multiple Perturbation Analysis
Keywords: ASA، سطح دسترسی قابل دسترس; protein folding; Hammond behavior; rate-equilibrium free energy relationships; transition state movementREFER, rate-equilibrium free energy relationship; ASA, accessible surface area; GdmCl, guanidinium chloride
Structure Basis for Antitumor Effect of Aplyronine A
Keywords: ASA، سطح دسترسی قابل دسترس; F-actin depolymerizing agent; antitumor substance; X-ray crystallography; marine macrolide; cytotoxicityAA complex, actin–aplyronine A complex; ASA, accessible surface area
The Crystal Structure of a Plant 3-Ketoacyl-CoA Thiolase Reveals the Potential for Redox Control of Peroxisomal Fatty Acid β-Oxidation
Keywords: ASA، سطح دسترسی قابل دسترس; Arabidopsis thaliana; β-oxidation; 3-ketoacyl-CoA thiolase; redox regulation; Saccharomyces cerevisiaeamp, ampicillin; ASA, accessible surface area; CCP4, Collaborative Computational Project Number 4; CoA, coenzyme A; DPI, diffraction-component precision
Tuning amyloidogenic conformations through cosolvents and hydrostatic pressure: When the soft matter becomes even softer
Keywords: ASA، سطح دسترسی قابل دسترس; AFM, Atomic Force Microscopy; ASA, Accessible Surface Area; CD, Circular Dichroism; DAC, Diamond Anvil Cell; DSC, Differential Scanning Calorimetry; EtOH, Ethanol; FT-IR, Fourier Transform Infrared Spectroscopy; Ig-LC, Immunoglobulin Light Chain; NMR, Nuc
Genetic Selection for Critical Residues in Ribonucleases
Keywords: ASA، سطح دسترسی قابل دسترس; ALS, amyotrophic lateral sclerosis; ANG, human angiogenin; ASA, accessible surface area; B, cytosine, guanine, or thymine; CFIS, chain-folding initiation site; D, adenine, guanine, or thymine; H, adenine, cytosine, or thymine; PBS, phosphate-buffered sali
Insights into Protein–Protein Interfaces using a Bayesian Network Prediction Method
Keywords: ASA، سطح دسترسی قابل دسترس; SVM, support vector machine; ASA, accessible surface area; ROC, receiver operating characteristic; AUC, area under a ROC curve; MCC, Matthews correlation coefficient; MSA, multiple sequence alignmentBayesian network; protein–protein binding sites; interac