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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 ...
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics
MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics
Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand–protein conformational dynamics and ...
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study
Structural impacts of two disease-linked ADAR1 mutants: a molecular dynamics study
Adenosine deaminases acting on RNA (ADARs) are pivotal RNA-editing enzymes responsible for converting adenosine to inosine...
From mundane to surprising nonadditivity: drivers and impact on ML models
From mundane to surprising nonadditivity: drivers and impact on ML models
Nonadditivity (NA) in Structure-Activity and Structure-Property Relationship (SAR) data is a rare but very information ric...
Development of QSARs for cysteine-containing di- and tripeptides with antioxidant activity:influence of the cysteine position
Development of QSARs for cysteine-containing di- and tripeptides with antioxidant activity:influence of the cysteine position
Antioxidants agents play an essential role in the food industry for improving the oxidative stability of food products. In...
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay
Development of human lactate dehydrogenase a inhibitors: high-throughput screening, molecular dynamics simulation and enzyme activity assay
Lactate dehydrogenase A (LDHA) is highly expressed in many tumor cells and promotes the conversion of pyruvate to lactic a...
FitScore: a fast machine learning-based score for 3D virtual screening enrichment
FitScore: a fast machine learning-based score for 3D virtual screening enrichment
Enhancing virtual screening enrichment has become an urgent problem in computational chemistry, driven by increasingly lar...
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors
Holistic in silico developability assessment of novel classes of small proteins using publicly available sequence-based predictors
The development of novel therapeutic proteins is a lengthy and costly process, with an average attrition rate of 91% (Thom...
Computational design and experimental confirmation of a disulfide-stapled YAP helixα1-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 helixα1-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...
QM assisted ML for 19F NMR chemical shift prediction
QM assisted ML for 19F NMR chemical shift prediction
Ligand-observed 19F NMR detection is an efficient method for screening libraries of fluorinated molecules in fragment-base...
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison
Molecular dynamics study on micelle-small molecule interactions: developing a strategy for an extensive comparison
Theoretical predictions of the solubilizing capacity of micelles and vesicles present in intestinal fluid are important fo...
Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface
Identification of a druggable site on GRP78 at the GRP78-SARS-CoV-2 interface and virtual screening of compounds to disrupt that interface
SARS-CoV-2, the virus that causes COVID-19, led to a global health emergency that claimed the lives of millions. Despite t...
A deep neural network: mechanistic hybrid model to predict pharmacokinetics in rat
A deep neural network: mechanistic hybrid model to predict pharmacokinetics in rat
An important aspect in the development of small molecules as drugs or agrochemicals is their systemic availability after i...
Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey
Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: a dynamic odyssey
The Janus kinases (JAK) are crucial targets in drug development for several diseases. However, accounting for the impact o...
Rethinking the applicability domain analysis in QSAR models
Rethinking the applicability domain analysis in QSAR models
Notwithstanding the wide adoption of the OECD principles (or best practices) for QSAR modeling, disparities between in sil...
Molecule auto-correction to facilitate molecular design
Molecule auto-correction to facilitate molecular design
Ensuring that computationally designed molecules are chemically reasonable is at best cumbersome. We present a molecule co...
Molecular dynamics simulations as a guide for modulating small molecule aggregation
Molecular dynamics simulations as a guide for modulating small molecule aggregation
Small colloidally aggregating molecules (SCAMs) can be problematic for biological assays in drug discovery campaigns. Howe...
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design
Correction: Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, whic...
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces
The growing size of make-on-demand chemical libraries is posing new challenges to cheminformatics. These ultra-large chemi...
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...
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