Journal of Molecular Graphics & Modelling

This study delves into the prediction of protein-peptide interactions using advanced machine learning techniques, comparing models such as sequence-based, standard CNNs, and traditional classifiers. Leveraging pre-trained language models and multi-view window scanning CNNs, our approach yields significant improvements, with ProtTrans standing out based on 2.1 billion protein sequences and 393 billion amino acids. The integrated model demonstrates remarkable performance, achieving an AUC of 0.856 and 0.823 on the PepBCL Set_1 and Set_2 datasets, respectively...

Water is an indispensable material for human life. Unfortunately, the development of industrial activities has reduced the quality of water resources in the world. Meantime, heavy metals are an important factor in water pollution due to their toxicity. This study highlights the method for the capture of heavy metal ions from wastewater using the procedure of adsorption. The adsorption of toxic heavy metal ions (Pb2+ , Hg2+ , and Cd2+ ) on Ca2 C as well as Cr2 C carbide-nitride MXene monolayers is investigated using the density functional theory...

In this paper, we have performed an all-atom molecular dynamics simulation to understand the structure and dynamics of Na+ ions in water mixed Ionic liquids (Water in Ionic liquid). Two ionic liquid (IL) systems consist of (1) 1-butyl-3-methylimidazolium [BMIM] tetrafluoroborate [BF4 ] and (2) 1-butyl-3-methylimidazolium [BMIM] hexafluorophosphate [PF6 ] were considered in this work. We understand various inter- molecular structures and dynamic and thermodynamic behaviours of Na+ ions in the water- mixed IL systems...

H2 S is a highly toxic, flammable gas that poses risks to health, the environment, and industrial infrastructure. Zeolites, with their high porosity, offer a promising solution for its removal. This study employs density functional theory (DFT) to investigate the adsorption behavior of H2 S within the Li-ABW zeolite framework, focusing on the synergistic effect of co-adsorbed water molecules. Six distinct systems were modeled: empty Li-ABW zeolite, half and full filled Li-ABW with H2 O or H2 S molecules, and equally filled zeolite with H2 S and H2 O molecules...

Bruton tyrosine kinases (BTKs) play critical roles in various diseases, including chronic lymphatic leukemia (CLL), Waldenström Macroglobulinemia, Marginal Zone Lymphoma, Mantle Cell Lymphoma (MCL), and Graft Versus Host diseases. BTKs are a family of tyrosine kinases involved in B lymphocyte signal transduction, development, and maturation. Their overexpression can lead to cancer as they are essential for the activation of the B Cell Receptor (BCR) signaling pathway. Blocking the activation of BTKs presents a promising approach for treating CLL...

STING (stimulator of interferon genes) is a crucial protein in the innate immune system's response to viral and bacterial infections. In this study, we investigated the mechanistic and energetic mechanism of the conformational transition process of STING activated by cGAMP binding. We found that the STING connector region undergoes an energetically unfavorable rotation during this process, which is compensated by the favorable interaction between cGAMP and the STING ligand binding domain. We further studied several disease-causing mutations and found that the V155 M mutation facilitates a smoother transition in the STING connector region...

The graphene-like monolayer of carbon, boron and nitrogen that maintains the native hexagonal atomic lattice (BCN), is a novel semiconductor with special thermal properties. Herein, with the aid of a non-equilibrium molecular dynamics approach (NEMD), we study phonon thermal rectification in a hybrid system of pure graphene and BCN (G-BCN) in various configurations under a series of positive and negative temperature gradients. We begin by investigating the relation of thermal rectification to sample's mean temperature, T, and the imposed temperature difference, ΔT, between the two heat baths at its ends...

A new iminophosphorane-thiourea superbase was rationally designed and investigated as an organocatalyst for the enantioselective Michael addition reaction of nitromethane to 4-phenylbut-3-en-2-one. Starting from an iminophosphorane-thiourea organocatalyst structure already known, we have used theoretical calculations to determine the structures of transition states involved in the carbon-carbon bond formation step and carried out structural modifications to accelerate the reaction rate and to increase the enantioselectivity...

ADP-glucose pyrophosphorylase plays a pivotal role as an allosteric enzyme, essential for starch biosynthesis in plants. The higher plant AGPase comparises of a pair of large and a pair of small subunits to form a heterotetrameric complex. Growing evidence indicates that each subunit plays a distinct role in regulating the underlying mechanism of starch biosynthesis. In the rice genome, there are four large subunit genes (OsL1-L4) and three small subunit genes (OsS1, OsS2a, and OsS2b). While the structural assembly of cytosolic rice AGPase subunits (OsL2:OsS2b) has been elucidated, there is currently no such documented research available for plastidial rice AGPases (OsL1:OsS1)...

Microsatellite instability (MSI) is a relatively common feature associated with multiple cancers, and Werner syndrome (WRN) ATP-dependent helicase has been recognized as a novel target for treating MSI cancers, such as colorectal cancer. A small-molecule inhibitor targeting WRN would be a promising strategy for treating colorectal cancer with high MSI expression. In this study, we employed a computer-assisted drug discovery strategy to screen over 30,000 natural product molecules. By using a combination of docking, ligand efficiency, Molecular Mechanics/Generalized Born Surface Area (MM/GBSA), and thermodynamic integration (TI) calculations, we identified MOL008980, MOL010740, MOL011832, T4743, TN1166, and TNP-002173 as potential WRN inhibitors...

The determination of the critical micelle concentration (CMC) is a crucial factor when evaluating surfactants, making it an essential tool in studying the properties of surfactants in various industrial fields. In this present research, we assembled a comprehensive set of 593 different classes of surfactants including, anionic, cationic, nonionic, zwitterionic, and Gemini surfactants to establish a link between their molecular structure and the negative logarithmic value of critical micelle concentration (pCMC) utilizing quantitative structure-property relationship (QSPR) methodologies...

The leishmaniases are NDTs (neglected tropical diseases) that affect people all over the world. They are brought on by protozoans from the genus Leishmania and disseminated by phlebotomine flies that are afflicted with the disease. The best option to manage and lower the incidence of these diseases has been thought by the creation of a safe and effective vaccination. This research used an in silico based mining approach to look for high potential epitopes that might bind to MHC Class I and MHC Class II molecules (mainly; HLA-A*02:01 & HLA-DRB1*03:01) from human population in order to promote vaccine development...

On the basis of the atomic graph-theoretical index - aEAID (atomic Extended Adjacency matrix IDentification) and molecular adjacent topological index - ATID (Adjacent Topological IDentification) suggested by one of the authors (Zhang Q), a highly selective atomic topological index - aATID (atomic Adjacent Topological IDentification) index was suggested to identify the equivalent atoms in this study. The aATID index of an atom was derived from the number of the attached hydrogen atoms of the atom but omitting bond types...

Formaldehyde is a VOC gas that plays a key role in air pollution. To limit emissions into the environment, the utilization of this waste as a raw material is a promising way. In this work, the M06-L functional calculation was used to investigate the structure, electronic properties, and catalytic activity of group IIA metals (Be, Mg, and Ca) partial substitution on Cu-BTC paddlewheels for formaldehyde encapsulation and carbonyl-ene reaction with propylene. Formaldehyde is absorbed by the metal center of the paddlewheel via its oxygen atom...

Through a comprehensive computational analysis utilizing Density Functional Theory (DFT), we clarify the electronic structure and spectroscopic properties of modified iron(II)-terpyridine derivatives, with the aim of enhancing the efficiency of Dye-Sensitized Solar Cells (DSSCs). We optimized a series of nineteen iron(II)-terpyridine derivatives and related compounds in acetonitrile (MeCN) as the solvent using TDDFT, evaluating their potential as dyes for DSSCs. From the conducted computations on the optimized geometries of the nineteen [Fe(Ln )2 ]2+ complexes, containing substituted terpyridine and related ligands L1 -L19 , we determined the wavelengths (λ in nm), transition energy (E in eV), oscillator strength (f), type of transitions, excited state lifetime (τ), light harvesting efficiency (LHE), frontier orbital character and their energies (ELUMO /EHOMO ), natural transition orbitals (NTOs), injection driving force of a dye (ΔGinject ), and regeneration driving force of a dye (ΔGregenerate )...

Density functional theory was used to study the insertion reaction of stannylenoid H2 SnLiF with CH3 X, SiH3 X (X = F, Cl, Br). Comparing the reaction barrier of H2 SnLiF with CH3 X, SiH3 X, it can be found that the order of the difficulty of insertion reaction is F > Cl > Br. The insertion reaction potential barrier of SiH3 X is lower than that of CH3 X, which means that SiH3 X is easier to react. According to the calculation results, the reaction law in THF solvent is consistent with that in vacuum, while in THF solvent, the barrier is lower and therefore more prone to reactions...

Cyclooxygenases 1 and 2 (COX-1/2) are enzymes renowned for inducing inflammatory responses through the production of prostaglandins. Thus, the development of COX inhibitors has been a promising approach for identifying compounds with anti-inflammatory potential. In this study, we designed 27 new compounds (1-27) based on the structure of a previously known COX inhibitor, using the Ligand Designer tool. Our aim was to improve the affinity of the compounds with COX enzymes by inducing interactions with residue Arg120 while retaining the good π-π stacking interactions of the chromene-phenyl scaffold...

Nanolubricant viscosity plays a crucial role in various industries due to its impact on pressure drop, pumping power, and heat transfer. The purpose of this research is to measure the viscosity of a (base oil) C30 H62 -CuO nano-lubricant experimentally using a viscometer and determine its viscosity using the equilibrium molecular dynamics (MD) simulation. In addition, the impacts of nano CuO particle volume fraction and temperature on the viscosity were investigated within different concentrations of nano CuO particles (0%, 0...

In the present work, the electronic structure and stability of acyclic nitronic acids were studied. Depending on the different substituents, the analyzed compounds can be classified as pseudo(mono)radical or zwitterionic nitronic acids. ELF topological analysis of the electron density of nitronic acids containing in their structure EWG substituent (-NO2 (1); -COOCH3 (2); -NO2 , -CH3 (5); -COOCH3 , -OCH3 (6); -NO2 , -H (7); -COOH3 , -H (8)) permits establishing a pseudo(mono)radical electronic structure with a pseudoradical centers at the C1 carbon atom...

With the goal of developing a high-performance organic solar cell, nine molecules of A2 -D-A1 -D-A2 type are originated in the current investigation. The optoelectronic properties of all the proposed compounds are examined by employing the DFT approach and the B3LYP functional with a 6-31G (d, p) basis set. By substituting the terminal moieties of reference molecule with newly proposed acceptor groups, several optoelectronic and photovoltaic characteristics of OSCs have been studied, which are improved to a significant level when compared with reference molecule, i...