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Toxigraphnet: a graph neural network framework for precise toxicity prediction of drug molecules
Toxigraphnet: a graph neural network framework for precise toxicity prediction of drug molecules
Accurate prediction of a drug molecule’s toxicity is a critical step in pharmaceutical research, offering the potent...
OR-ligand: target-aware view-based hybrid feature selection for μ-opioid receptor ligand functional classification
OR-ligand: target-aware view-based hybrid feature selection for μ-opioid receptor ligand functional classification
Understanding active functional class (agonist vs antagonist) at the human μ-opioid receptor (μOR) is critical f...
Pyrimidin-4-bromobenzenesulfonamide/-4-nitrobenzenesulfonamide hybrids as potential BRAF inhibitors: experimental, computational and biological evaluations
Pyrimidin-4-bromobenzenesulfonamide/-4-nitrobenzenesulfonamide hybrids as potential BRAF inhibitors: experimental, computational and biological evaluations
BRAF mutations were first discovered by Davies et al. in 2002. BRAFV600E mutation is the most prevalent, accounting for ap...
GADRC: a graph-based approach for drug repositioning with deep residual networks and computational feature-guided undersampling
GADRC: a graph-based approach for drug repositioning with deep residual networks and computational feature-guided undersampling
Drug repositioning (DR) is a highly promising research strategy aimed at discovering new therapeutic indications for exist...
In silico development of RNA aptamer candidates against thyroid receptor
In silico development of RNA aptamer candidates against thyroid receptor
Aptamers are short oligonucleotides capable of binding to various molecular targets with high affinity and specificity. Th...
Discovery and validation of pyrrolopyrimidine-based VEGFR2 inhibitors targeting tumor angiogenesis via structure-based virtual screening, quantum chemical analysis, and in vitro assays
Discovery and validation of pyrrolopyrimidine-based VEGFR2 inhibitors targeting tumor angiogenesis via structure-based virtual screening, quantum chemical analysis, and in vitro assays
Tumor angiogenesis, largely driven by VEGFR2 signalling, is a critical hallmark of cancer progression. In this study, we e...
Conformational landscape of β-cyclodextrin: a computational resource for host–guest modeling in supramolecular systems
Conformational landscape of β-cyclodextrin: a computational resource for host–guest modeling in supramolecular systems
β-Cyclodextrin (β-CD) is a widely used host molecule in supramolecular chemistry, pharmaceutical formulations, a...
Cytotoxic and gene expression effects of deltamethrin and acetamiprid on MDA-MB-231 breast cancer cells: a molecular and functional study
Cytotoxic and gene expression effects of deltamethrin and acetamiprid on MDA-MB-231 breast cancer cells: a molecular and functional study
The widespread use of pesticides such as deltamethrin (a pyrethroid) and acetamiprid (a neonicotinoid) has sparked concern...
Deep learning-guided rational engineering of synergistic PD-1 and LAG-3 blockade for enhanced tumor immunomodulation
Deep learning-guided rational engineering of synergistic PD-1 and LAG-3 blockade for enhanced tumor immunomodulation
Evolution has optimized proteins over time by the incorporation of precise and context-specific amino acid substitutions a...
FAS-II pathway targeted integrative deep learning based identification of potential anti-tubercular agents
FAS-II pathway targeted integrative deep learning based identification of potential anti-tubercular agents
Mycobacterium tuberculosis (Mtb) continues to be one of the major contributors to the global burden of infectious diseases...
Elucidating ligand recognition of reductive dehalogenases: the role of hydrophobic active site in organohalogen binding
Elucidating ligand recognition of reductive dehalogenases: the role of hydrophobic active site in organohalogen binding
Organohalide-respiring bacteria encoding reductive dehalogenases have shown substantial potential for bioremediation of or...
Design, synthesis, deep learning-guided prediction, and biological evaluation of novel pyridine-thiophene-based imine-benzalacetophenone hybrids as promising antimicrobial agent
Design, synthesis, deep learning-guided prediction, and biological evaluation of novel pyridine-thiophene-based imine-benzalacetophenone hybrids as promising antimicrobial agent
Antimicrobial resistance (AMR) remains a global health crisis, necessitating the development of novel therapeutics against...
Exploring the toxicity of fluoxastrobin: a combined computational and experimental approach
Exploring the toxicity of fluoxastrobin: a combined computational and experimental approach
Fluoxastrobin (FLUO) is a fungicide from strobilurin family used widely worldwide. The use of FLUO pesticide is on the ris...
Synergistic approach utilizing bioinformatics, machine learning, and traditional screening for the identification of novel CSK inhibitors targeting hepatocellular carcinoma
Synergistic approach utilizing bioinformatics, machine learning, and traditional screening for the identification of novel CSK inhibitors targeting hepatocellular carcinoma
The overexpression or activation of C-terminal Src kinase (CSK) has been recognized as a pivotal factor in the progression...
HCV genotyping and rational computational designing of an immunogenic multiepitope vaccine against genotype 3a
HCV genotyping and rational computational designing of an immunogenic multiepitope vaccine against genotype 3a
Pakistan currently holds the second-highest prevalence rate of Hepatitis C virus (HCV) globally. It makes it crucial to co...
Structure-based identification and experimental evaluation of Oroxin A as a FYN kinase inhibitor
Structure-based identification and experimental evaluation of Oroxin A as a FYN kinase inhibitor
FYN, a member of the Src family kinases (SFKs) and a non-receptor tyrosine kinase, plays a critical role in signal transdu...
Integrated computational and experimental evaluation of grossamide as a natural product scaffold for dual carbohydrase inhibition in diabetes
Integrated computational and experimental evaluation of grossamide as a natural product scaffold for dual carbohydrase inhibition in diabetes
Despite the widespread use of Grossamide-containing plants in traditional medicine and its documented anti-inflammatory an...
Multi-stage variational autoencoders for hierarchical molecular generation and activity optimization
Multi-stage variational autoencoders for hierarchical molecular generation and activity optimization
Deep generative models may detect novel compounds with favourable features, exhibiting chemical design potential. Traditio...
Evaluation of Protein-Ligand binding interactions of alkaline phosphatase inhibitors by Quantum-Mechanical methods
Evaluation of Protein-Ligand binding interactions of alkaline phosphatase inhibitors by Quantum-Mechanical methods
Quantum-mechanical (QM) methods were applied to compute the relative binding energies of a set of structurally similar alk...
LiteBoost: a lightweight and explainable boosting model for predicting polymer density from SMILES data
LiteBoost: a lightweight and explainable boosting model for predicting polymer density from SMILES data
Accurately predicting polymer density from SMILES strings remains challenging due to the small size, high noise, and chemi...
Computational design and experimental confirmation of a disulfide-stapled YAP helix-trap derived from TEAD4 helical hairpin to selectively capture YAP α1-helix with potent antitumor activity
Computational design and experimental confirmation of a disulfide-stapled YAP helix-trap derived from TEAD4 helical hairpin to selectively capture YAP α1-helix with potent antitumor activity
Human Hippo signaling pathway is an evolutionarily conserved regulator network that controls organ development and has bee...
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space
De novo drug design through gradient-based regularized search in information-theoretically controlled latent space
Over the last decade, automatic chemical design frameworks for discovering molecules with drug-like properties have signif...
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...
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...
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...
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 stress response sigma factors σ and σ deciphered using computer modeling and point mutagenesis
Promoter recognition specificity of stress response sigma factors σ and σ 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 ...
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