Boosting the full potential of PyMOL with structural biology plugins

S Rosignoli, A Paiardini - Biomolecules, 2022 - mdpi.com
Over the past few decades, the number of available structural bioinformatics pipelines,
libraries, plugins, web resources and software has increased exponentially and become …

Practical aspects of free-energy calculations: a review

N Hansen, WF Van Gunsteren - Journal of chemical theory and …, 2014 - ACS Publications
Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …

UCSF ChimeraX: Tools for structure building and analysis

EC Meng, TD Goddard, EF Pettersen… - Protein …, 2023 - Wiley Online Library
Advances in computational tools for atomic model building are leading to accurate models of
large molecular assemblies seen in electron microscopy, often at challenging resolutions of …

Single-sequence protein structure prediction using a language model and deep learning

R Chowdhury, N Bouatta, S Biswas, C Floristean… - Nature …, 2022 - nature.com
AlphaFold2 and related computational systems predict protein structure using deep learning
and co-evolutionary relationships encoded in multiple sequence alignments (MSAs) …

Molecular dynamics and multi-spectroscopic of the interaction behavior between bladder cancer cells and calf thymus DNA with rebeccamycin: apoptosis through the …

Z Malek-Esfandiari, A Rezvani-Noghani, T Sohrabi… - Journal of …, 2023 - Springer
The interaction of Rebeccamycin with calf thymus (ctDNA) in the absence and presence of
H1 was investigated by molecular dynamics, multi-spectroscopic, and cellular techniques …

Moltemplate: A tool for coarse-grained modeling of complex biological matter and soft condensed matter physics

AI Jewett, D Stelter, J Lambert, SM Saladi… - Journal of molecular …, 2021 - Elsevier
Coarse-grained models have long been considered indispensable tools in the investigation
of biomolecular dynamics and assembly. However, the process of simulating such models is …

Chemical composition, antioxidant, and anti-diabetic activities of ethyl acetate fraction of Stachys riederi var. japonica (Miq.) in streptozotocin-induced type 2 diabetic …

K Saravanakumar, S Park, AVA Mariadoss… - Food and Chemical …, 2021 - Elsevier
This work analysed the chemical composition, antioxidant, and enzyme inhibitory activities
of solvent extract (SJ-ME) and fractions (SJ-HF, SJ-EAF, and SJ-MF) of the Stachys riederi …

Two-photon nanoprobes based on bioorganic nanoarchitectonics with a photo-oxidation enhanced emission mechanism

S Li, R Chang, L Zhao, R Xing, JCM van Hest… - Nature …, 2023 - nature.com
Two-photon absorption (TPA) fluorescence imaging holds great promise in diagnostics and
biomedicine owing to its unparalleled spatiotemporal resolution. However, the adaptability …

All-temperature batteries enabled by fluorinated electrolytes with non-polar solvents

X Fan, X Ji, L Chen, J Chen, T Deng, F Han, J Yue… - Nature Energy, 2019 - nature.com
Carbonate electrolytes are commonly used in commercial non-aqueous Li-ion batteries.
However, the high affinity between the solvents and the ions and high flammability of the …

Fast identification of possible drug treatment of coronavirus disease-19 (COVID-19) through computational drug repurposing study

J Wang - Journal of chemical information and modeling, 2020 - ACS Publications
The recent outbreak of novel coronavirus disease-19 (COVID-19) calls for and welcomes
possible treatment strategies using drugs on the market. It is very efficient to apply computer …