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Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn2+, Cu2+, and VO2+: a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models
Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn2+, Cu2+, and VO2+: a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models
We present a computational strategy based on thermodynamic cycles to predict and describe the chemical equilibrium between...
Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations
Study of SQ109 analogs binding to mycobacterium MmpL3 transporter using MD simulations and alchemical relative binding free energy calculations
N-geranyl-N΄-(2-adamantyl)ethane-1,2-diamine (SQ109) is a tuberculosis drug that has high potency against Mycobacteri...
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa
TargIDe: a machine-learning workflow for target identification of molecules with antibiofilm activity against Pseudomonas aeruginosa
Bacterial biofilms are a source of infectious human diseases and are heavily linked to antibiotic resistance. Pseudomonas ...
Computational insights into ligand–induced G protein and β-arrestin signaling of the dopamine D1 receptor
Computational insights into ligand–induced G protein and β-arrestin signaling of the dopamine D1 receptor
The dopamine D1 receptor (D1R), is a class A G protein coupled-receptor (GPCR) which has been a promising drug target for ...
Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score
Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score
Membrane proteins are attractive targets for drug discovery due to their crucial roles in various biological processes. St...
Improvement of multi-task learning by data enrichment: application for drug discovery
Improvement of multi-task learning by data enrichment: application for drug discovery
Multi-task learning in deep neural networks has become a topic of growing importance in many research fields, inc...
MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Zn
MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Zn
Carbonic anhydrase is an attractive drug target for the treatment of many diseases. This paper examines the ability of end...
Structural mechanism of Fab domain dissociation as a measure of interface stability
Structural mechanism of Fab domain dissociation as a measure of interface stability
Therapeutic antibodies should not only recognize antigens specifically, but also need to be free from developability issue...
Inhibition mechanism of MRTX1133 on KRASG12D: a molecular dynamics simulation and Markov state model study
Inhibition mechanism of MRTX1133 on KRASG12D: a molecular dynamics simulation and Markov state model study
The mutant KRAS was considered as an “undruggable” target for decades, especially KRASG12D. It is a great chal...
GPCRLigNet: rapid screening for GPCR active ligands using machine learning
GPCRLigNet: rapid screening for GPCR active ligands using machine learning
Molecules with bioactivity towards G protein-coupled receptors represent a subset of the vast space of small drug-like mol...
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants
pH-dependent solubility prediction for optimized drug absorption and compound uptake by plants
Aqueous solubility is the most important physicochemical property for agrochemical and drug candidates and a prerequisite ...
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments
Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments
Tuberculosis (TB) is one of the main causes of death from a single pathological agent, Mycobacterium tuberculosis (Mtb). I...
A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity
A combined ligand and target-based virtual screening strategy to repurpose drugs as putrescine uptake inhibitors with trypanocidal activity
Chagas disease, also known as American trypanosomiasis, is a neglected tropical disease caused by the protozoa Trypanosoma...
The slow but steady rise of binding free energy calculations in drug discovery
The slow but steady rise of binding free energy calculations in drug discovery
Binding free energy calculations are increasingly used in drug discovery research to predict protein-ligand binding affini...
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds
DeepCubist: Molecular Generator for Designing Peptidomimetics based on Complex three-dimensional scaffolds
Mimicking bioactive conformations of peptide segments involved in the formation of protein-protein interfaces with small m...
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin
Computational investigation of functional water molecules in GPCRs bound to G protein or arrestin
G protein-coupled receptors (GPCRs) are membrane proteins constituting the largest family of drug targets. The activated G...
Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations
Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations
The Hepatitis C Virus (HCV) NS3/4A is an attractive target for the treatment of Hepatitis C infection. Herein, we present ...
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling
Molecular and thermodynamic insights into interfacial interactions between collagen and cellulose investigated by molecular dynamics simulation and umbrella sampling
Cellulose/collagen composites have been widely used in biomedicine and tissue engineering. Interfacial interactions are cr...
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores
Fragment spaces are an efficient way to model large chemical spaces using a handful of small fragments and a few connectio...
Examining unsupervised ensemble learning using spectroscopy data of organic compounds
Examining unsupervised ensemble learning using spectroscopy data of organic compounds
One solution to the challenge of choosing an appropriate clustering algorithm is to combine different clusterings into a s...
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant
Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host–guest binding: II. regression and dielectric constant
End-point free energy calculations as a powerful tool have been widely applied in protein–ligand and protein–p...
From oncoproteins to spike proteins: the evaluation of intramolecular stability using hydropathic force field
From oncoproteins to spike proteins: the evaluation of intramolecular stability using hydropathic force field
Evaluation of the intramolecular stability of proteins plays a key role in the comprehension of their biological behavior ...
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study
The FMO2 analysis of the ligand-receptor binding energy: the Biscarbene-Gold(I)/DNA G-Quadruplex case study
In this work, the ab initio fragment molecular orbital (FMO) method was applied to calculate and analyze the binding energ...
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation
Reliable gas-phase tautomer equilibria of drug-like molecule scaffolds and the issue of continuum solvation
Accurate calculation of relative tautomer energies in different environments is a prerequisite to many parameters of relev...
Physicochemical QSAR analysis of hERG inhibition revisited: towards a quantitative potency prediction
Physicochemical QSAR analysis of hERG inhibition revisited: towards a quantitative potency prediction
In an earlier study (Didziapetris R & Lanevskij K (2016). J Comput Aided Mol Des. 30:1175–1188) we collected...
Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides
Improved prediction and characterization of blood-brain barrier penetrating peptides using estimated propensity scores of dipeptides
The blood-brain barrier (BBB) is the primary barrier with a highly selective semipermeable border between blood vascular e...
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning
Enabling data-limited chemical bioactivity predictions through deep neural network transfer learning
The main limitation in developing deep neural network (DNN) models to predict bioactivity properties of chemicals is the l...
Protocol for iterative optimization of modified peptides bound to protein targets
Protocol for iterative optimization of modified peptides bound to protein targets
Peptides are commonly used as therapeutic agents. However, they suffer from easy degradation and instability. Rep...
An overview of the SAMPL8 host–guest binding challenge
An overview of the SAMPL8 host–guest binding challenge
The SAMPL series of challenges aim to focus the community on specific modeling challenges, while testing and hopefully dri...
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo
Enhancing sampling of water rehydration upon ligand binding using variants of grand canonical Monte Carlo
Water plays an important role in mediating protein-ligand interactions. Water rearrangement upon a ligand binding or modif...
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