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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...
On the relevance of query definition in the performance of 3D ligand-based virtual screening
On the relevance of query definition in the performance of 3D ligand-based virtual screening
Ligand-based virtual screening (LBVS) methods are widely used to explore the vast chemical space in the search of novel co...
From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product
From UK-2A to florylpicoxamid: Active learning to identify a mimic of a macrocyclic natural product
Scaffold replacement as part of an optimization process that requires maintenance of potency, desirable biodistribution, m...
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design
Reactivities of acrylamide warheads toward cysteine targets: a QM/ML approach to covalent inhibitor design
Covalent inhibition offers many advantages over non-covalent inhibition, but covalent warhead reactivity must be carefully...
Correlation of protein binding pocket properties with hits’ chemistries used in generation of ultra-large virtual libraries
Correlation of protein binding pocket properties with hits’ chemistries used in generation of ultra-large virtual libraries
Although the size of virtual libraries of synthesizable compounds is growing rapidly, we are still enumerating only tiny f...
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...
Open-ComBind: harnessing unlabeled data for improved binding pose prediction
Open-ComBind: harnessing unlabeled data for improved binding pose prediction
Determination of the bound pose of a ligand is a critical first step in many in silico drug discovery tasks. Molecular doc...
Correction: Exploring DrugCentral: from molecular structures to clinical effects
Correction: Exploring DrugCentral: from molecular structures to clinical effects
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, whi...
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability
Binding of small molecule inhibitors to RNA polymerase-Spt5 complex impacts RNA and DNA stability
Spt5 is an elongation factor that associates with RNA polymerase II (Pol II) during transcription and has important functi...
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information
Artificial intelligence for prediction of biological activities and generation of molecular hits using stereochemical information
In this work, we develop a method for generating targeted hit compounds by applying deep reinforcement learning and attent...
Correction to: Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT3 as case study
Correction to: Computational workflow for discovering small molecular binders for shallow binding sites by integrating molecular dynamics simulation, pharmacophore modeling, and machine learning: STAT3 as case study
Correction to: Journal of Computer-Aided Molecular Design In the original publication of the articl...
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state
Predicting absolute aqueous solubility by applying a machine learning model for an artificially liquid-state as proxy for the solid-state
In this study, we use machine learning algorithms with QM-derived COSMO-RS descriptors, along with Morgan fingerprints, to...
Mur ligase F as a new target for the flavonoids quercitrin, myricetin, and (–)-epicatechin
Mur ligase F as a new target for the flavonoids quercitrin, myricetin, and (–)-epicatechin
MurC, D, E, and F are ATP-dependent ligases involved in the stepwise assembly of the tetrapeptide stem of forming peptidog...
The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases
The in silico identification of novel broad-spectrum antidotes for poisoning by organophosphate anticholinesterases
Owing to their potential to cause serious adverse health effects, significant efforts have been made to develop antidotes ...
MASSA Algorithm: an automated rational sampling of training and test subsets for QSAR modeling
MASSA Algorithm: an automated rational sampling of training and test subsets for QSAR modeling
QSAR models capable of predicting biological, toxicity, and pharmacokinetic properties were widely used to search lead bio...
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection
TeM-DTBA: time-efficient drug target binding affinity prediction using multiple modalities with Lasso feature selection
Drug discovery, especially virtual screening and drug repositioning, can be accelerated through deeper understanding and p...
Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1)
Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1)
Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-vari...
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory
Correction to: Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which...
Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals
Improving the accuracy of the FMO binding affinity prediction of ligand-receptor complexes containing metals
Polarization and charge transfer strongly characterize the ligand-receptor interaction when metal atoms are present, as fo...
Exploring DrugCentral: from molecular structures to clinical effects
Exploring DrugCentral: from molecular structures to clinical effects
DrugCentral, accessible at https://drugcentral.org , is an open-access online drug information repository. It covers over ...
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