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Design and evaluation of novel thiazolidinedione-oxadiazole derivatives as potent α-amylase inhibitors for antidiabetic therapy
Design and evaluation of novel thiazolidinedione-oxadiazole derivatives as potent α-amylase inhibitors for antidiabetic therapy
Diabetes mellitus is a chronic metabolic disorder characterized by persistent hyperglycemia. Targeting α-amylase, a k...
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones
Biological engineering aims to enhance biological systems by designing proteins with improved catalytic properties or liga...
Quantum algorithm for protein-ligand docking sites identification in the interaction space
Quantum algorithm for protein-ligand docking sites identification in the interaction space
Over the past two decades, the development of novel drugs evolved into a high-demanding computational field. There is a co...
3CL of SARS-CoV-2 as a new target for bufadienolides: in silico and in vitro study
3CL of SARS-CoV-2 as a new target for bufadienolides: in silico and in vitro study
The rapid spread of SARS-CoV-2 and its widespread public health implications have highlighted the urgent need for effectiv...
Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation
Unveiling a novel ellagic acid derivative as a potent lipoxygenase (LOX) inhibitor: integration of computational modeling and experimental validation
Cornus macrophylla has been traditionally recognized for its medicinal properties, particularly in managing inflammatory c...
A computational study of cardiac glycosides from as PI3K inhibitors for targeting HER2 positive breast cancer
A computational study of cardiac glycosides from as PI3K inhibitors for targeting HER2 positive breast cancer
The PI3K/Akt pathway plays a crucial role in regulating a broad network of proteins involved in the proliferation of HER2-...
Machine learning-based QSAR and structure-based virtual screening guided discovery of novel mIDH1 inhibitors from natural products
Machine learning-based QSAR and structure-based virtual screening guided discovery of novel mIDH1 inhibitors from natural products
Mutations in isocitrate dehydrogenase 1 (IDH1) have been widely observed in various tumors, such as gliomas and acute myel...
Disrupting tuberculosis pathogenesis by targeting DprE1 in cell wall biosynthesis: a structural dynamics perspective
Disrupting tuberculosis pathogenesis by targeting DprE1 in cell wall biosynthesis: a structural dynamics perspective
Mycobacterium tuberculosis (Mtb), the causative agent of TB, remains a major global health challenge due to the emergence ...
New alkyl triphenylphosphonium dipterocarpol derivatives with cytotoxicity against the MCF-7 breast cancer cell line
New alkyl triphenylphosphonium dipterocarpol derivatives with cytotoxicity against the MCF-7 breast cancer cell line
Dipterocarpol exhibited cytotoxic properties; however, its hydrophobic nature resulted in decreased bioavailability. This ...
Anti-inflammatory potential of isoquinoline alkaloids from : in vitro, in vivo, and in silico evaluation
Anti-inflammatory potential of isoquinoline alkaloids from : in vitro, in vivo, and in silico evaluation
The objective of this study is to identify the alkaloids of Fumaria officinalis and to evaluate their anti-inflammatory ac...
CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches
CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches
Identifying orthosteric binding sites and predicting small molecule affinities remains a key challenge in virtual screenin...
Therapeutic potency of a developed optimized polyherbal formulation in ameliorating obesity induced inflammation and oxidative stress in Swiss albino mice by targeting PPARγ, insulin receptor and AMPK signalling pathway
Therapeutic potency of a developed optimized polyherbal formulation in ameliorating obesity induced inflammation and oxidative stress in Swiss albino mice by targeting PPARγ, insulin receptor and AMPK signalling pathway
High fat diet (HFD) induced obesity plays a key role in onset of inflammation, a chronic response of the body to elevated ...
“Heptadecanol” a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation
“Heptadecanol” a phytochemical multi-target inhibitor of SMYD3 & GFPT2 proteins in non-small cell lung cancer: an in-silico & in-vitro investigation
Understanding the mechanism of action of anticancer agent plays a key role in effective clinical application of natural pr...
Mechanistic insights into PROTAC-mediated degradation through an integrated framework of molecular dynamics, free energy landscapes, and quantum mechanics: A case study on kinase degraders
Mechanistic insights into PROTAC-mediated degradation through an integrated framework of molecular dynamics, free energy landscapes, and quantum mechanics: A case study on kinase degraders
Targeted protein degradation by proteolysis-targeting chimeras (PROTAC) is dependent on formation and plasticity of ternar...
Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study
Protein domain movement involved in binding of belinostat and HPOB as inhibitors of histone deacetylase 6 (HDAC6): a hybrid automated-interactive docking study
DockIT is a tool for interactive molecular docking that can model both the local and global conformational response of the...
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer’s disease
Integrated machine learning and deep learning-based virtual screening framework identifies novel natural GSK-3β inhibitors for Alzheimer’s disease
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder lacking effective therapies. Glycogen synthase ...
Design, synthesis, evaluation and molecular modeling of quinazoline derivatives bearing amino acids as small-molecule PD-L1 inhibitors
Design, synthesis, evaluation and molecular modeling of quinazoline derivatives bearing amino acids as small-molecule PD-L1 inhibitors
Herein, we reported a series of quinazoline derivatives bearing amino acids by introducing a rigid pyrimidine structure be...
Comparison study of dominant molecular sequence representation based on diffusion model
Comparison study of dominant molecular sequence representation based on diffusion model
In recent years, the emergence of large language models (LLMs), particularly the advent of ChatGPT, has positioned natural...
Anti-inflammatory potential of from : insights from molecular docking, ADMET, DFT, and studies
Anti-inflammatory potential of from : insights from molecular docking, ADMET, DFT, and studies
Grewia optiva, a medicinal plant native to northern Pakistan, has traditionally been valued for managing pain and inflamma...
Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins
Molecular dynamics simulations reveal mechanistic insights into aptamer-induced structural rearrangements in viral capsid proteins
Macrobrachium rosenbergii nodavirus is a major viral pathogen responsible for white tail disease in giant freshwater prawn...
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands
Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands
So-called “cross-docking” is the prediction of the bound configuration of small-molecule ligands that differ f...
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model
Steered molecular dynamics simulation as a post-process to optimize the iBRAB-designed Fab model
Therapeutic monoclonal antibodies are an effective method of treating acute infectious diseases. However, knowing which of...
Comparative assessment of physics-based in silico methods to calculate relative solubilities
Comparative assessment of physics-based in silico methods to calculate relative solubilities
Relative solubilities, i.e. whether a given molecule is more soluble in one solvent compared to others, is a critical para...
Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ)
Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ)
G-quadruplexes refer to a large group of nucleic acid–based structures. In recent years, they have been attracting a...
Identification of novel inhibitors targeting PI3Kα via ensemble-based virtual screening method, biological evaluation and molecular dynamics simulation
Identification of novel inhibitors targeting PI3Kα via ensemble-based virtual screening method, biological evaluation and molecular dynamics simulation
PIK3CA gene encoding PI3K p110α is one of the most frequently mutated and overexpressed in majority of human cancers....
Understanding the relationship between preferential interactions of peptides in water-acetonitrile mixtures with protein-solvent contact surface area
Understanding the relationship between preferential interactions of peptides in water-acetonitrile mixtures with protein-solvent contact surface area
The influence of polar, water-miscible organic solvents (POS) on protein structure, stability, and functional activity is ...
Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σD and σH deciphered using computer modeling and point mutagenesis
Promoter recognition specificity of Corynebacterium glutamicum stress response sigma factors σD and σH deciphered using computer modeling and point mutagenesis
This study aimed to reveal interactions of the stress response sigma subunits (factors) σD and σH of RNA polymer...
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays
Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays
Although small molecule superposition is a standard technique in drug discovery, a rigorous performance assessment of the ...
MolGraph: a Python package for the implementation of molecular graphs and graph neural networks with TensorFlow and Keras
MolGraph: a Python package for the implementation of molecular graphs and graph neural networks with TensorFlow and Keras
Molecular machine learning (ML) has proven important for tackling various molecular problems, such as predicting molecular...
User-centric design of a 3D search interface for protein-ligand complexes
User-centric design of a 3D search interface for protein-ligand complexes
In this work, we present the frontend of GeoMine and showcase its application, focusing on the new features of its latest ...
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