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Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
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Coarse-grained simulations of conformational dynamics of proteins: Application to apomyoglobin
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Development and testing of a general amber force field
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Increasing protein stability: Importance of ΔCp and the denatured state
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What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties
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Structural heterogeneity of the various forms of apomyoglobin; Implications for protein folding
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Comparison of multiple Amber force fields and development of improved protein backbone parameters
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Thermodynamic and kinetic determinants of Thermotoga maritima cold shock protein stability: A structural and dynamic analysis
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Is Apomyoglobin a Molten Globule? Structural Characterization by NMR
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An improved generalized AMBER force field (GAFF) for urea
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Interactive essential dynamics
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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VMD: Visual molecular dynamics
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Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data
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Principal Component Analysis for Protein Folding Dynamics
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Hydration of Apomyoglobin in Native, Molten Globule, and Unfolded States by Using Microwave Dielectric Spectroscopy
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Similarity of Force-Induced Unfolding of Apomyoglobin to Its Chemical-Induced Unfolding: An Atomistic Molecular Dynamics Simulation Approach
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Primary Folding Dynamics of Sperm Whale Apomyoglobin: Core Formation
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Structural Details, Pathways, and Energetics of Unfolding Apomyoglobin
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Three-state analysis of sperm whale apomyoglobin folding
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Probing the stability of a partly folded apomyoglobin intermediate by site-directed mutagenesis
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Characterization of hydrophobic cores in apomyoglobin: a proton NMR spectroscopy study
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How Ala→Gly Mutations in Different Helices Affect the Stability of the Apomyoglobin Molten Globule
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Effect of Solvent Diffusion on the Apomyoglobin−Water Interface
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Hydration of the Folding Transition State Ensemble of a Protein
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Molecular Dynamics of Apo-Adenylate Kinase: A Principal Component Analysis
inferredcites →https://doi.org/10.1021/jp3012365openalex-snapshot
Microsecond Folding Dynamics of Apomyoglobin at Acidic pH
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Cooperativity of folding of the apomyoglobin pH 4 intermediate studied by glycine and proline mutations
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Multisite Fluorescence in Proteins with Multiple Tryptophan Residues
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Optimal design of thermally stable proteins
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Forces contributing to the conformational stability of proteins
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Protein engineering and design
inferredcites →https://doi.org/10.1110/ps.04635304openalex-snapshot
Modulation of the structural integrity of helix F in apomyoglobin by single amino acid replacements
inferredcites →https://doi.org/10.1126/science.2218495openalex-snapshot
Structural Characterization of a Partly Folded Apomyoglobin Intermediate
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Protein Hydrophobic Collapse and Early Folding Steps Observed in a Microfluidic Mixer
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Resolved Fluorescence of the Two Tryptophan Residues in Horse Apomyoglobin
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inferred← citeshttps://doi.org/10.1101/2020.11.23.394015openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/2024.04.18.590047openalex-snapshot
Understanding the characteristic behavior of the wild-type and mutant protein structure of FLT3 protein by computational methods
inferred← citeshttps://doi.org/10.1155/2023/5469258openalex-snapshot
In Silico Identification and Analysis of Potentially Bioactive Antiviral Phytochemicals against SARS‐CoV‐2: A Molecular Docking and Dynamics Simulation Approach
inferred← citeshttps://doi.org/10.1186/s12879-024-09807-xopenalex-snapshot
TgVax452, an epitope-based candidate vaccine targeting Toxoplasma gondii tachyzoite-specific SAG1-related sequence (SRS) proteins: immunoinformatics, structural simulations and experimental evidence-based approaches
inferred← citeshttps://doi.org/10.1186/s13036-024-00456-xopenalex-snapshot
Phytoconstituents of Withania somnifera (L.) Dunal (Ashwagandha) unveiled potential cerebroside sulfotransferase inhibitors: insight through virtual screening, molecular dynamics, toxicity, and reverse pharmacophore analysis
inferred← citeshttps://doi.org/10.13005/bpj/3342openalex-snapshot
Harnessing Phytoactive Compounds for Targeting Neuroinflammation and Inflammatory Receptors: A Polypharmacology Approach Integrating Molecular Dynamics Simulations and In Silico Formulation Design
inferred← citeshttps://doi.org/10.1371/journal.pone.0301747openalex-snapshot
In silico exploration of potent flavonoids for dengue therapeutics
inferred← citeshttps://doi.org/10.1371/journal.pone.0307374openalex-snapshot
Screening of phytoconstituents from Bacopa monnieri (L.) Pennell and Mucuna pruriens (L.) DC. to identify potential inhibitors against Cerebroside sulfotransferase
inferred← citeshttps://doi.org/10.1371/journal.pone.0327862openalex-snapshot
Computational insights into flavonoids inhibition of dengue virus envelope protein: ADMET profiling, molecular docking, dynamics, PCA, and end-state free energy calculations
inferred← citeshttps://doi.org/10.1371/journal.pone.0329126openalex-snapshot
Computational prediction of the pathogenic variants of arachidonate 5-lipoxygenase activating protein using Molecular Dynamics simulation
inferred← citeshttps://doi.org/10.1371/journal.pone.0336841openalex-snapshot
Molecular docking and MD simulations predicted quercetin as a potent human interleukin-1 beta (hIL1β) inhibitor for improved endodontic disease management
inferred← citeshttps://doi.org/10.1371/journal.pone.0341938openalex-snapshot
In silico pharmacological analysis of Tinospora cordifolia compounds targeting African swine fever virus B175L
inferred← citeshttps://doi.org/10.1590/0001-3765202320220633openalex-snapshot
Concatenation of molecular docking and dynamics simulation of human papillomavirus type 16 E7 oncoprotein targeted ligands: In quest of cervical cancer’s treatment
inferred← citeshttps://doi.org/10.17776/csj.1599148openalex-snapshot
Investigation of a Stable Interaction of Levothyroxine with AFP Through Molecular Modelling
inferred← citeshttps://doi.org/10.21203/rs.3.rs-10475900/v1openalex-snapshot
Towards anticancer drug design: Allosteric rewiring of the MDM2–MDMX RING interface by K478R and N448C perturbs structural and functional dynamics
inferred← citeshttps://doi.org/10.21203/rs.3.rs-6881765/v1openalex-snapshot
Aqueous-Phase Detection of Explosive Residues: Sulfonyl Chloride-Appended Oxacalix[4]arene for 2,4-DNT Monitoring
inferred← citeshttps://doi.org/10.21608/rpbs.2023.188482.1202openalex-snapshot
Current advances in computer-aided design of electrochemical sensors: An analytical review
inferred← citeshttps://doi.org/10.2174/1570180819666220106110133openalex-snapshot
Repurposing FDA-approved Drugs Targeting SARS-CoV2 3CL pro : A Study by Applying Virtual Screening, Molecular Dynamics, MM-PBSA Calculations and Covalent Docking
inferred← citeshttps://doi.org/10.2174/1573407219666230614163801openalex-snapshot
Early Blockage of Mycobacterium Tuberculosis Cell-wall Synthesis via EchA\6 Inhibition to Overcome Resistance Strain: Insights from Umbrella Sampling Simulations
inferred← citeshttps://doi.org/10.33263/briac162.064openalex-snapshot
Integrated Enzyme and Computational Screening of Plant-Derived Phytoconstituents as Alpha-Amylase Inhibitors
inferred← citeshttps://doi.org/10.33640/2405-609x.3237openalex-snapshot
Molecular Docking and Dynamics Simulation Studies to Predict Multiple Medicinal Plants’ Bioactive Compounds Interaction and Its Behavior on the Surface of DENV-2 E Protein
inferred← citeshttps://doi.org/10.3389/fendo.2022.1022623openalex-snapshot
Investigation of anti-diabetic potential and molecular simulation studies of dihydropyrimidinone derivatives
inferred← citeshttps://doi.org/10.3390/chemistry6060083openalex-snapshot
Design, Synthesis, and Evaluation of EA-Sulfonamides and Indazole-Sulfonamides as Promising Anticancer Agents: Molecular Docking, ADME Prediction, and Molecular Dynamics Simulations
inferred← citeshttps://doi.org/10.3390/ijms22158048openalex-snapshot
Computational Insights into the Deleterious Impacts of Missense Variants on N-Acetyl-d-glucosamine Kinase Structure and Function
inferred← citeshttps://doi.org/10.3390/ijms231911806openalex-snapshot
Rational Design of a Thermostable 2′-Deoxyribosyltransferase for Nelarabine Production by Prediction of Disulfide Bond Engineering Sites
inferred← citeshttps://doi.org/10.3390/ijms24065819openalex-snapshot
Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology
inferred← citeshttps://doi.org/10.3390/metabo12100937openalex-snapshot
Cheminformatics Identification and Validation of Dipeptidyl Peptidase-IV Modulators from Shikimate Pathway-Derived Phenolic Acids towards Interventive Type-2 Diabetes Therapy
inferred← citeshttps://doi.org/10.3390/mol2net-07-11647openalex-snapshot
Virtual screening based on covalent docking and MM-PBSA calculations predict the drugs neratinib, sacubitril, alprostadil, trandolapril, and florbetapir as promising cruzain inhibitors useful against Chagas disease.
inferred← citeshttps://doi.org/10.3390/molecules26226956openalex-snapshot
Simulation of pH-Dependent Conformational Transitions in Membrane Proteins: The CLC-ec1 Cl−/H+ Antiporter
inferred← citeshttps://doi.org/10.3390/molecules27206861openalex-snapshot
Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions
inferred← citeshttps://doi.org/10.3390/molecules30193939openalex-snapshot
Theoretical Study of the Influence of K20N Glycosylation on the Dynamic Behavior of Im7 Protein
inferred← citeshttps://doi.org/10.3390/pathogens10091208openalex-snapshot
Evaluation of Inhibitory Activity In Silico of In-House Thiomorpholine Compounds between the ACE2 Receptor and S1 Subunit of SARS-CoV-2 Spike
inferred← citeshttps://doi.org/10.3390/ph16040489openalex-snapshot
Antidiarrheal Potential of Viola canescens: In Vivo and In Silico Approaches
inferred← citeshttps://doi.org/10.3390/v14010001openalex-snapshot
RBD Double Mutations of SARS-CoV-2 Strains Increase Transmissibility through Enhanced Interaction between RBD and ACE2 Receptor
inferred← citeshttps://doi.org/10.4155/fmc-2021-0340openalex-snapshot
Discovery of New Chemotypes of Dual 5-HT 2A /D 2 Receptor Antagonists With a Strategy of Drug Design Methodologies
inferred← citeshttps://doi.org/10.48048/tis.2023.4891openalex-snapshot
Molecular Docking and Molecular Dynamics Simulation-Based Identification of Natural Inhibitors against Druggable Human Papilloma Virus Type 16 Target
inferred← citeshttps://doi.org/10.48550/arxiv.2012.03132openalex-snapshot
Current MD forcefields fail to capture key features of protein structure and fluctuations: A case study of cyclophilin A and T4 lysozyme
inferred← citeshttps://doi.org/10.5101/nbe.v12i1.p90-98openalex-snapshot
Application of Molecular Dynamics in Coating Ag-Conjugated Nanoparticles with Potential Therapeutic Applications
inferred← citeshttps://doi.org/10.5455/javar.2021.h544openalex-snapshot
Active site-specific quantum tunneling of hACE2 receptor to assess its complexing poses with selective bioactive compounds in co-suppressing SARS-CoV-2 influx and subsequent cardiac injury
inferred← citeshttps://doi.org/10.5455/javar.2022.i588openalex-snapshot
Point-specific interactions of isovitexin with the neighboring amino acid residues of the hACE2 receptor as a targeted therapeutic agent in suppressing the SARS-CoV-2 influx mechanism
inferred← citeshttps://doi.org/10.5812/jjm-131974openalex-snapshot
Identification and Characterization of Indolebutyroyl Aspartic Acid: A Promising Inhibitor of VIM-2 Metallo-β-Lactamase Against Carbapenem-Resistant Pseudomonas aeruginosa Strains
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