Designing a recombinant coat protein to reduce tobacco mosaic virus infection in plants.

The Tobacco Mosaic Virus (TMV) is a critical plant virus that can cause a significant drop in crop yield. To understand how recombinant coat-protein impacts the affinity and assembly of TMV's subunits, research is being conducted to assess the effect of recombinant protein on virus resistance. To develop a recombinant coat-protein that can lower TMV infection rates in plants, a design strategy was employed that involves creating defective viral subunits leading to incorrect assembly.

Screening of BindingDB database ligands against EGFR, HER2, Estrogen, Progesterone and NF-κB receptors based on machine learning and molecular docking.

Breast cancer, the second most prevalent cancer among women worldwide, necessitates the exploration of novel therapeutic approaches. To target the four subgroups of breast cancer "hormone receptor-positive and HER2-negative, hormone receptor-positive and HER2-positive, hormone receptor-negative and HER2-positive, and hormone receptor-negative and HER2-negative" it is crucial to inhibit specific targets such as EGFR, HER2, ER, NF-κB, and PR. In this study, we evaluated various methods for binary and multiclass classification.

DFT study on capture using boron, nitrogen, and phosphorus-doped in the presence of an electric field.

Burning fossil fuels emits a significant amount of , causing climate change concerns. Capture and Storage (CCS) aims to reduce emissions, with fullerenes showing promise as adsorbents. Recent research focuses on modifying fullerenes using an electric field.

Anti-angiogenic biomolecules in neovascular age-related macular degeneration; therapeutics and drug delivery systems.

Blindness in the elderly is often caused by age-related macular degeneration (AMD). The advanced type of AMD known as neovascular AMD (nAMD) has been linked to being the predominant cause of visual impairment in these people. Multiple neovascular structures including choroidal neovascular (CNV) membranes, fluid exudation, hemorrhages, and subretinal fibrosis, are diagnostic of nAMD.

In silico design of potential Mcl-1 peptide-based inhibitors.

Context: BIM (Bcl-2 interacting mediator of apoptosis)-derived peptides that specifically target over-expressed Mcl-1 (myeloid cell leukemia-1) protein and induce apoptosis are potentially anti-cancer agents. Since the helicity of BIM-derived peptides has a crucial role in their functionality, a range of strategies have been used to increase the helicity including the introduction of unnatural residues and stapling methods that have some drawbacks such as the accumulation in the liver. To avoid these drawbacks, this study aimed to design a more helical peptide by utilizing bioinformatics algorithms and molecular dynamics simulations without exploiting unnatural residues and stapling methods.

Molecular dynamics simulation as a promising approach for computational study of liquid crystal-based aptasensors.

As a potent computational methodology, molecular dynamics (MD) simulation provides advantageous knowledge about biological compounds from the molecular viewpoint. In particular, MD simulation gives exact information about aptamer strands, such as the short synthetic oligomers, their orientation, binding sites, folding-unfolding state, and conformational re-arrangement. Also, the effect of the different chemicals and biochemicals as the components of aptamer-based sensors (aptasensors) on the aptamer-target interaction can be investigated by MD simulation.

approaches to investigate enzyme immobilization: a comprehensive systematic review.

Enzymes are popular catalysts with many applications, especially in industry. Biocatalyst usage on a large scale is facing some limitations, such as low operational stability, low recyclability, and high enzyme cost. Enzyme immobilization is a beneficial strategy to solve these problems.

Construction of an Exudative Age-Related Macular Degeneration Diagnostic and Therapeutic Molecular Network Using Multi-Layer Network Analysis, a Fuzzy Logic Model, and Deep Learning Techniques: Are Retinal and Brain Neurodegenerative Disorders Related?

Neovascular age-related macular degeneration (nAMD) is a leading cause of irreversible visual impairment in the elderly. The current management of nAMD is limited and involves regular intravitreal administration of anti-vascular endothelial growth factor (anti-VEGF). However, the effectiveness of these treatments is limited by overlapping and compensatory pathways leading to unresponsiveness to anti-VEGF treatments in a significant portion of nAMD patients.

Computational designing of the ligands of Protein L affinity chromatography based on molecular docking and molecular dynamics simulations.

Protein L is a multidomain protein from with binding affinity to kappa light chain of human immunoglobulin (Ig) which is used for the purification of antibody fragments by affinity chromatography. The advances in protein engineering and computational biology approaches lead to the development of engineered affinity ligands with improved properties including binding affinity. In this study, molecular dynamics simulations (MDs) and Osprey software were used to design single B domains of the Protein L with higher affinity to antibody fragments.

EasyModel: a user-friendly web-based interface based on MODELLER.

Three-dimensional protein structures are invaluable sources of information for the functional annotation of protein molecules. Describing the function of a protein sequence is one of the most common problems in biology. Generally, this problem can be facilitated by studying the tertiary structure of proteins.

Rational peptide design for targeting cancer cell invasion.

Cell invasion is an important process in cancer progression and recurrence. Invasion and implantation of cancer cells from their original place to other tissues, by disabling vital organs, challenges the treatment of cancer patients. Given the importance of the matter, many molecular treatments have been developed to inhibit cancer cell invasion.

Reducing the assemblies of amyloid-beta multimers by sodium dodecyl sulfate surfactant at concentrations lower than critical micelle concentration: molecular dynamics simulation exploration.

Amyloid-β peptide, the predominant proteinaceous component of senile plaques, is responsible for the incidence of Alzheimer's disease (AD), an age-associated neurodegenerative disorder. Specifically, the amyloid-β(1-42) (Aβ1-42) isoform, known for its high toxicity, is the predominant biomarker for the preliminary diagnosis of AD. The aggregation of the Aβ1-42 peptides can be affected by the components of the cellular medium through changing their structures and molecular interactions.

Reconstructing the cell-cell interaction network among mouse immune cells.

Intercellular interactions and cell-cell communication are critical to regulating cell functions, especially in normal immune cells and immunotherapies. Ligand-receptor pairs mediating these cell-cell interactions can be identified using diverse experimental and computational approaches. Here, we reconstructed the intercellular interaction network between Mus musculus immune cells using publicly available receptor-ligand interaction databases and gene expression data from the immunological genome project.

Investigation of thermal stability characteristic in family A DNA polymerase - A theoretical study.

DNA polymerases create complementary DNA strands in living cells and are crucial to genome transmission and maintenance. These enzymes possess similar human right-handed folds which contain thumb, fingers, and palm subdomains and contribute to polymerization activities. These enzymes are classified into seven evolutionary families, A, B, C, D, X, Y, and RT, based on amino acid sequence analysis and biochemical characteristics.

Kallistatin as an inhibitory protein against colorectal cancer cells through binding to LRP6.

Kallistatin (KL) is a member of the serine proteinase inhibitor (serpin) family regulating oxidative stress, vascular relaxation, inflammation, angiogenesis, cell proliferation, and invasion. The heparin-binding site of Kallistatin has an important role in the interaction with LRP6 leading to the blockade of the Wnt signaling pathway. In this study, we aimed to explore the structural basis of the Kallistatin-LRP6E1E4 complex using in silico approaches and evaluating the anti-proliferative, apoptotic, and cell cycle arrest activities of Kallistatin in colon cancer lines.

The coat protein of tobacco mosaic virus as an anti-tobacco mosaic virus: a molecular dynamics simulation.

The Coat Protein (CP) of the Tobacco Mosaic Virus (TMV) executes an important duty in the protection of virus RNA. The interaction between the virus CP and host plant proteins induces infection in the host and creates dark and light green mosaics on crops, which disturb the growth and function of the plant. The interaction between the virus CP and the modified CP, expressed in transgenic plants, causes Coat Protein-Mediated Resistance (CP-MR), which reduces virus infection in transgenic plants.

A Novel SELEX Method to Screen and Identify Aptamers against .

Background: Vibrio cholerae, the causative agent of cholera, has been responsible for global epidemics and many other problems over the centuries. It is one of the main public health issues in less-developed and developing countries and is considered one of the deadliest infectious agents. Therefore, precise and susceptible detection of V.

In Silico Analysis of Neutralizing Antibody Epitopes on The Hepatitis C Virus Surface Glycoproteins.

Objective: Despite of antiviral drugs and successful treatment, an effective vaccine against hepatitis C virus (HCV) infection is still required. Recently, bioinformatic methods same as prediction algorithms, have greatly contributed to the use of peptides in the design of immunogenic vaccines. Therefore, finding more conserved sites on the surface glycoproteins (E1 and E2) of HCV, as major targets to design an effective vaccine against genetically different viruses in each genotype was the goal of the study.

A comprehensive computer simulation insight into inhibitory mechanisms of EGCG and NQTrp ligands on amyloid-beta assemblies as the Alzheimer's disease insignia.

Amyloid-β peptide with predominant presence in the senile plaques is the most common agent for Alzheimer's disease (AD) incidence. Assembly of the amyloid-β(1-42) (Aβ1-42) isoform is known as the main reason for the AD appearance. Epigallocatechin gallate (EGCG) and 1,4-naphthoquinone-2-yl-L-tryptophan (NQTrp) are two small molecules that inhibit the formation of the Aβ1-42 fibrils.

ApInAPDB: a database of apoptosis-inducing anticancer peptides.

ApInAPDB (Apoptosis-Inducing Anticancer Peptides Database) consists of 818 apoptosis-inducing anticancer peptides which are manually collected from research articles. The database provides scholars with peptide related information such as function, binding target and affinity, IC50 and etc. In addition, GRAVY (grand average of hydropathy), net charge at pH 7, hydrophobicity and other physicochemical properties are calculated and presented.

Effectiveness of Remdesivir in Comparison with Five Approved Antiviral Drugs for Inhibition of RdRp in Combat with SARS-CoV-2.

The treatment of COVID-19 disease has been one of the most critical essential concerns of researchers in recent years. One of the most exciting and potential therapeutic targets for SARS-CoV-2 therapy progression is RNA-dependent RNA polymerase (RdRP), a viral enzyme for viral RNA replication throughout host cells. According to some research, Remdesivir suppresses RdRp.

Design, construction and in vivo functional assessment of a hinge truncated sFLT01.

Gene therapy for the treatment of ocular neovascularization has reached clinical trial phases. The AAV2-sFLT01 construct was already evaluated in a phase 1 open-label trial administered intravitreally to patients with advanced neovascular age-related macular degeneration. SFLT01 protein functions by binding to VEGF and PlGF molecules and inhibiting their activities simultaneously.

Design, synthesis, spectroscopic characterizations, antidiabetic, in silico and kinetic evaluation of novel curcumin-fused aldohexoses.

Curcumin (bis-α,β-unsaturated β-diketone) plays an important role in the prevention of numerous diseases, including diabetes. Curcumin, as an enzyme inhibitor, has ideal structural properties including hydrophobic nature, flexible backbone, and several available hydrogen bond (H-bond) donors and acceptors. In this study, curcumin-fused aldohexose derivatives 3(a-c) were synthesized and used as influential agents in the treatment of diabetes with inhibitory properties against two carbohydrate-hydrolyzing enzymes α-glucosidase (α-Gls) and α-amylase (α-Amy) which are known to be significant therapeutic targets for the reduction of postprandial hyperglycemia.

Solvent-dependent activity of lipase B and its correlation with a regioselective mono aza-Michael addition - experimental and molecular dynamics simulation studies.

With the aim of gaining understanding of the molecular basis of commercially available lipase B (CALB) immobilized on polyacrylic resin catalyzed regioselective mono aza-Michael addition of Benzhydrazide to Diethyl maleate we decided to carry out molecular dynamics (MD) simulation studies in parallel with our experimental study. We found a correlation between the activity of CALB and the choice of solvent. Our study showed that solvent affects the performance of the enzyme due to the binding of solvent molecules to the enzyme active site region, and the solvation energy of substrates in the different solvents.

Protein sequence profile prediction using ProtAlbert transformer.

Profiles are used to model protein families and domains. They are built by multiple sequence alignments obtained by mapping a query sequence against a database to generate a profile based on the substitution scoring matrix. The profile applications are very dependent on the alignment algorithm and scoring system for amino acid substitution.