Themed collection Molecular modelling
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A new C–C bond formation model based on the quantum chemical topology of electron density
Pseudodiradical structures and GEDT involved in the C–C single bond formation in non-polar, polar and ionic organic reactions.
RSC Adv., 2014,4, 32415-32428
https://doi.org/10.1039/C4RA04280H
Recent developments in the molecular recognition of carbohydrates by artificial receptors
This review covers representative examples of artificial carbohydrate receptors, which use noncovalent interactions for carbohydrate binding, with a focus on developments in receptor systems over the last two years.
RSC Adv., 2012,2, 2630-2642
https://doi.org/10.1039/C2RA01138G
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Binding selectivity of inhibitors toward the first over the second bromodomain of BRD4: theoretical insights from free energy calculations and multiple short molecular dynamics simulations
Hydrogen bonding interactions of waters with BD1/BD2 and inhibitors play significant roles in inhibitor bindings.
RSC Adv., 2021,11, 745-759
https://doi.org/10.1039/D0RA09469B
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Remdesivir-bound and ligand-free simulations reveal the probable mechanism of inhibiting the RNA dependent RNA polymerase of severe acute respiratory syndrome coronavirus 2
Conformational changes in the remdesivir-bound RdRP leading to its inhibition.
RSC Adv., 2020,10, 26792-26803
https://doi.org/10.1039/D0RA04743K
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Antiproliferative activity of new pentacyclic triterpene and a saponin from Gladiolus segetum Ker-Gawl corms supported by molecular docking study
A new triterpenoidal saponin 1, a new oleanane triterpene 2, and 6 known compounds (3–8) have been isolated from Gladiolus segetum Ker-Gawl corms.
RSC Adv., 2020,10, 22730-22741
https://doi.org/10.1039/D0RA02775H
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Design, in silico studies, and synthesis of new 1,8-naphthyridine-3-carboxylic acid analogues and evaluation of their H1R antagonism effects
New 1,8-naphthyridine-3-carboxylic acid derivatives were designed, synthesized and evaluated for their in vivo antihistaminic activity on guinea pig trachea by using chlorpheniramine maleate as the standard drug.
RSC Adv., 2020,10, 13907-13921
https://doi.org/10.1039/D0RA00746C
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3D-QSAR, molecular docking, and molecular dynamics simulation study of thieno[3,2-b]pyrrole-5-carboxamide derivatives as LSD1 inhibitors
Novel LSD1 inhibitors with potential activity are designed using a series of computer-aided drug design methods.
RSC Adv., 2020,10, 6927-6943
https://doi.org/10.1039/C9RA10085G
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Design, eco-friendly synthesis, molecular modeling and anticancer evaluation of thiazol-5(4H)-ones as potential tubulin polymerization inhibitors targeting the colchicine binding site
In recent years, suppressing tubulin polymerization has been developed as a therapeutic approach for cancer treatment.
RSC Adv., 2020,10, 2791-2811
https://doi.org/10.1039/C9RA10094F
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Multiple 3D-QSAR modeling, e-pharmacophore, molecular docking, and in vitro study to explore novel AChE inhibitors
Ligand-based and energy-optimized structure-based approaches were helpful to obtain excellent candidates as non-toxic, PAS site selective, non-competitive AChE inhibitors.
RSC Adv., 2018,8, 39477-39495
https://doi.org/10.1039/C8RA08198K
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Substituted spirooxindole derivatives as potent anticancer agents through inhibition of phosphodiesterase 1
Spirooxindole is a promising chemo therapeutic agent. Possible targets include cancers of the liver, prostate, lung, stomach, colon, and breast.
RSC Adv., 2018,8, 14335-14346
https://doi.org/10.1039/C8RA02358A
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Comprehensive exploration of the anticancer activities of procaine and its binding with calf thymus DNA: a multi spectroscopic and molecular modelling study
DNA demethylating agent procaine binds at the minor groove of ct-DNA and increases the anticancer activity of doxorubicin.
RSC Adv., 2018,8, 9083-9093
https://doi.org/10.1039/C7RA13647A
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Evaluation of the taste-masking effects of (2-hydroxypropyl)-β-cyclodextrin on ranitidine hydrochloride; a combined biosensor, spectroscopic and molecular modelling assessment
A correlation between taste masking, assessed using a taste sensor system, and inclusion complex formation, assessed using NMR and molecular docking studies, has been identified for ranitidine HCl and (2-hydroxypropyl)-β-cyclodextrin.
RSC Adv., 2018,8, 3564-3573
https://doi.org/10.1039/C7RA11015D
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Changing the shape of hair with keratin peptides
Here we propose a solution which will replace harsh reducing agents at alkaline pH by peptide formulations acting at neutral pH to change hair shape through the re-conformation of disulphide bonds.
RSC Adv., 2017,7, 51581-51592
https://doi.org/10.1039/C7RA10461H
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A DFT study on lignin dissolution in imidazolium-based ionic liquids
Co-interaction lead to dissolution of lignin in ILs: H-bonds and π–π stacking.
RSC Adv., 2017,7, 12670-12681
https://doi.org/10.1039/C6RA27059J
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Discovery of new acetylcholinesterase and butyrylcholinesterase inhibitors through structure-based virtual screening
Small molecule cholinesterase (ChE) inhibitors represent one of the most effective therapeutic strategies for the treatment of Alzheimer's disease (AD).
RSC Adv., 2017,7, 3429-3438
https://doi.org/10.1039/C6RA25887E
Interaction of an anticancer drug, gefitinib with human serum albumin: insights from fluorescence spectroscopy and computational modeling analysis
Binding orientation of the GEF in the binding site III, located in subdomain IB of HSA.
RSC Adv., 2016,6, 91756-91767
https://doi.org/10.1039/C6RA12019A
Understanding the mechanism of non-enzymatic glycation inhibition by cinnamic acid: an in vitro interaction and molecular modelling study
Under hyperglycaemic conditions non-enzymatic glycation of proteins gives rise to advanced glycation end products (AGEs).
RSC Adv., 2016,6, 65322-65337
https://doi.org/10.1039/C6RA12321J
Facile and expedient access to bis-coumarin–iminothiazole hybrids by molecular hybridization approach: synthesis, molecular modelling and assessment of alkaline phosphatase inhibition, anticancer and antileishmanial potential
A series of new cytotoxic bis-coumarin–iminothiazole hybrids was developed as potential inhibitors of alkaline phosphatase and leishmaniasis.
RSC Adv., 2015,5, 89919-89931
https://doi.org/10.1039/C5RA14900B
Antihypertensive activity of a quinoline appended chalcone derivative and its site specific binding interaction with a relevant target carrier protein
The usefulness of heterocyclic chalcone derivative as a therapeutic target in controlling hypertension and its site specific binding interaction with model transport protein to get a clear picture about its delivery mechanism.
RSC Adv., 2015,5, 65496-65513
https://doi.org/10.1039/C5RA08778C
Molecular docking studies and biological evaluation of chalcone based pyrazolines as tyrosinase inhibitors and potential anticancer agents
A series of synthetic chalcones and pyrazoline derivatives showed antityrosinase, anticancer and considerable tubulin polymerization activity.
RSC Adv., 2015,5, 46330-46338
https://doi.org/10.1039/C5RA02995C
Exploration of a library of triazolothiadiazole and triazolothiadiazine compounds as a highly potent and selective family of cholinesterase and monoamine oxidase inhibitors: design, synthesis, X-ray diffraction analysis and molecular docking studies
There is a high demand for the collection of small organic molecules (especially N-heterocycles) with diversity and complexity in the process of drug discovery.
RSC Adv., 2015,5, 21249-21267
https://doi.org/10.1039/C5RA00906E
Spectroscopic and molecular modeling studies of human serum albumin interaction with propyl gallate
For the first time, PG interaction with HSA using fluorescence quenching method, circular dichroism spectroscopy and molecular modeling was investigated.
RSC Adv., 2014,4, 64559-64564
https://doi.org/10.1039/C4RA11103F
How does PEDOT combine with PSS? Insights from structural studies
PEDOT and PSS mutually combine to form a supramolecular assembly of unique stability in aqueous medium. Formation of this complex is theoretically modeled and its spectroscopic and morphological properties are studied.
RSC Adv., 2014,4, 43912-43920
https://doi.org/10.1039/C4RA08666J
In vitro investigation of domain specific interactions of phenothiazine dye with serum proteins by spectroscopic and molecular docking approaches
In the present study the interaction of the chemotherapeutic agent, Azure A (AZA) with Human Serum Albumin (HSA) and Bovine Serum Albumin (BSA) was investigated by multi spectroscopic and molecular docking methods.
RSC Adv., 2014,4, 36267-36281
https://doi.org/10.1039/C4RA04630G
Microscopic and thermodynamic analysis of PEG–β-lactoglobulin interaction
We report the binding of milk β-lactoglobulin (β-LG) with PEG-3000, PEG-6000 and methoxypoly(ethylene glycol) anthracene (mPEG-anthracene) in aqueous solution at pH 7.4, using multiple spectroscopic methods, thermodynamic analysis, transmission electron microscopy (TEM) and molecular modeling.
RSC Adv., 2014,4, 31084-31093
https://doi.org/10.1039/C4RA03303E
Mechanical stabilities of silicene
Both planar and low-buckled silicene are mechanically stable under various strains.
RSC Adv., 2013,3, 13772-13781
https://doi.org/10.1039/C3RA41347K
About this collection
We are very pleased to present our 10th Anniversary collection on Molecular modelling!Looking back over the last 10 years, we would like to showcase some of the very best articles that have been published in RSC Advances. Many of these papers have been cited hundreds of times, providing valuable advances for further research, and some continue to be among the journal’s most downloaded articles as of today.
We hope you enjoy our 10th Anniversary collection on Molecular modelling!