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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...
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...
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...
Design, synthesis, characterization, in silico, in vitro and in vivo antidiabetic studies of novel benzothiophene derivatives
Design, synthesis, characterization, in silico, in vitro and in vivo antidiabetic studies of novel benzothiophene derivatives
This study evaluated the antidiabetic efficacy of novel benzothiophenes using in silico, in vitro and in vivo methods. The...
Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn
Targeting neurodegeneration: three machine learning methods for G9a inhibitors discovery using PubChem and scikit-learn
In light of the increasing interest in G9a’s role in neuroscience, three machine learning (ML) models, that are time...
Exploring Oxazolidinone scaffolds for future antibiotics: synthesis and computational insights with DFT, docking, ADME and MD simulation
Exploring Oxazolidinone scaffolds for future antibiotics: synthesis and computational insights with DFT, docking, ADME and MD simulation
The emergence of antibiotic-resistance is a serious concern in maintaining global health in this era, which necessitates c...
Computational exploration and molecular dynamics simulations for investigating the potential inhibitory mechanism of amantadine on the ion channel activity of bovine viral diarrhea virus p7
Computational exploration and molecular dynamics simulations for investigating the potential inhibitory mechanism of amantadine on the ion channel activity of bovine viral diarrhea virus p7
Bovine viral diarrhea virus (BVDV) p7 functions as a viroporin for the ion balance and membrane permeabilization. Blocking...
Anticancer potential of 2,2′-bipyridine hydroxamic acid derivatives in head and neck cancer therapy
Anticancer potential of 2,2′-bipyridine hydroxamic acid derivatives in head and neck cancer therapy
The genesis of head and neck cancer (HNC) is attributed to the combined influence of genetic and epigenetic irregularities...
Ai-driven de novo design of customizable membrane permeable cyclic peptides
Ai-driven de novo design of customizable membrane permeable cyclic peptides
Cyclic peptides, prized for their remarkable bioactivity and stability, hold great promise across various fields. Yet, des...
Computational and experimental repositioning of quinoline analogues as KSP inhibitors: insights from free energy landscape and PCA analysis
Computational and experimental repositioning of quinoline analogues as KSP inhibitors: insights from free energy landscape and PCA analysis
Eg5 is a mitotic kinesin motor protein essential for the formation of bipolar spindles during cell division. Its inhibitio...
Combined experimental and computational investigation of vildagliptin: spectroscopy, electronic structure, MD and Docking to EGFR, VEGFR2, and HER2 anticancer targets
Combined experimental and computational investigation of vildagliptin: spectroscopy, electronic structure, MD and Docking to EGFR, VEGFR2, and HER2 anticancer targets
This study combines experimental and computational approaches to investigate the molecular geometry and physicochemical pr...
Application of directed message-passing neural network to predict human oral bioavailability of pharmaceuticals
Application of directed message-passing neural network to predict human oral bioavailability of pharmaceuticals
High failure rates in drug development are predominantly driven by suboptimal ADMET (absorption, distribution, metabolism,...
Computational QSAR study of novel 2-aminothiazol-4(5H)-one derivatives as 11β‐HSD1 inhibitors
Computational QSAR study of novel 2-aminothiazol-4(5H)-one derivatives as 11β‐HSD1 inhibitors
This research aims to develop a predictive model to support the design of new 11β-hydroxysteroid dehydrogenase type 1...
Exploring the structural and electronic properties of boron nitride nanotube (BNNT) as nanocarrier for drug delivery applications: DFT approach
Exploring the structural and electronic properties of boron nitride nanotube (BNNT) as nanocarrier for drug delivery applications: DFT approach
Boron nitride nanotubes (BNNTs) have garnered significant interest due to their exceptional mechanical strength, chemical ...
Deploying the drug repurposing approach for the identification of selective monoamine oxidase-B inhibitors against neurological disabilities: an in Silico and in vitro approach
Deploying the drug repurposing approach for the identification of selective monoamine oxidase-B inhibitors against neurological disabilities: an in Silico and in vitro approach
Monoamine oxidase-B (MAO-B) plays a regulatory role in controlling the activity of monoamine neurotransmitters, especially...
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...
ConoDL: a deep learning framework for rapid generation and prediction of conotoxins
ConoDL: a deep learning framework for rapid generation and prediction of conotoxins
Conotoxins, being small disulfide-rich and bioactive peptides, manifest notable pharmacological potential and find extensi...
In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes
In silico design of dehydrophenylalanine containing peptide activators of glucokinase using pharmacophore modelling, molecular dynamics and machine learning: implications in type 2 diabetes
Diabetes represents a significant global health challenge associated with substantial healthcare costs and therapeutic com...
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations
The AI-driven Drug Design (AIDD) platform: an interactive multi-parameter optimization system integrating molecular evolution with physiologically based pharmacokinetic simulations
Computer-aided drug design has advanced rapidly in recent years, and multiple instances of in silico designed molecules ad...
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro
Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 Mpro
Here, we introduce the use of ANI-ML potentials as a rescoring function in the host–guest interaction in molecular d...
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