Results 141 to 150 of about 4,190,416 (396)

Consensus virtual screening approaches to predict protein ligands [PDF]

, 2011
In order to exploit the advantages of receptor-based virtual screening, namely time/cost saving and specificity, it is important to rely on algorithms that predict a high number of active ligands at the top ranks of a small molecule database.
Andreas Kukol, Bruning, Chen, Cheng, Darapaneni, Garcia-Sosa, Huang, Huey, Lee, Morris, Nicholls, Park, Plewczynski, Trott, Wang, Yang   +15 more
core   +2 more sources

Synergistic application of molecular docking and machine learning for improved binding pose

National Science Open
Accurate prediction of protein-ligand complex structures is a crucial step in structure-based drug design. Traditional molecular docking methods exhibit limitations in terms of accuracy and sampling space, while relying on machine-learning approaches may
Li Yaqi, Lin Hongrui, Yang He, Yuan Yannan, Zou Rongfeng, Zhou Gengmo, Zheng Linfeng, Zheng Hang   +7 more
doaj   +1 more source

Revealing protein structures: crystallization of protein‐ligand complexes – co‐crystallization and crystal soaking

FEBS Open Bio, Volume 15, Issue 4, Page 542-550, April 2025.
Co‐crystallization crystallizes a protein with its ligand, resulting in protein–ligand complex crystals. In contrast, soaking introduces a ligand into preformed protein crystals, allowing it to bind. Both methods produce crystals for X‐ray diffraction, which generates diffraction patterns that are analyzed to determine the three‐dimensional structure ...
Barbora Kaščáková, Anna Koutská, Michaela Burdová, Petra Havlíčková, Ivana Kutá Smatanová   +4 more
wiley   +1 more source

Uses of Molecular Docking Simulations in Elucidating Synergistic, Additive, and/or Multi-Target (SAM) Effects of Herbal Medicines

Molecules
The philosophy of herbal medicines is that they contain multiple active components that target many aspects of a given disease. This is in line with the recent multiple-target strategy adopted due to shortcomings with the previous “magic bullet”, single ...
Sean P. Rigby
doaj   +1 more source

Enhanced discovery of bacterial laccase‐like multicopper oxidase through computer simulation and metagenomic analysis of industrial wastewater

FEBS Open Bio, EarlyView.
We obtained potential bacterial laccase‐like multicopper oxidase (LMCO) sequences through metagenomic sequencing. All sequences exhibited significant differences from known LMCOs in databases. To select the most promising candidates, we performed structure prediction and molecular docking using alphafold2, metal3d and rosetta.
Ting Cui, Ariel Kushmaro, Hana Barak, Anja Poehlein, Rolf Daniel, Hans‐Jürgen Mägert   +5 more
wiley   +1 more source

Traditional Chinese medicine for the treatment of chronic inflammatory diseases: A review of inhibitors for NLRP3 inflammasome

Advanced Chinese Medicine, Volume 2, Issue 1, Page 1-12, March 2025.
Abstract The NLR family pyrin domain‐containing 3 (NLRP3) inflammasome is a vital part of the innate immune response, whilst its aberrant activation drives the progression of several noncommunicable diseases. It induces caspase‐1 activation and the downstream substrates involved with the processing and secretion of the pro‐inflammatory cytokines IL‐1β ...
Yucen Zou, Pei Ma, Bin Li, Jiushi Liu, Lifeng Yue, Bengang Zhang, Haitao Liu   +6 more
wiley   +1 more source

Herbal Formula Yi‐Fei‐Jie‐Du‐Tang Regulates Epithelial‐Mesenchymal Transition and Vasculogenic Mimicry in Lung Cancer via HIF1A‐Mediated Ferroptosis

Advanced Biology, Volume 9, Issue 3, March 2025.
Yi‐Fei‐Jie‐Du‐Tang (YFJDT), a traditional Chinese medicine, has shown potential in lung cancer treatment by targeting key pathways. This study explores the mechanisms of YFJDT using bioinformatics, xenograft models, and A549 cells, demonstrating that YFJDT downregulates HIF1A, promotes ferroptosis, and inhibits epithelial‐mesenchymal transition (EMT ...
Shanshan Wang, Die Yang, Chengjia Yuan, Yang Wu, Qingying Wang, Yongjian Wu, Xiaochun Zhang   +6 more
wiley   +1 more source

Implicit Ligand Theory: Rigorous Binding Free Energies and Thermodynamic Expectations from Molecular Docking

, 2012
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived.
Minh, David D. L.
core   +1 more source

Nelfinavir was predicted to be a potential inhibitor of 2019-nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation

bioRxiv, 2020
2019-nCov has caused more than 80 deaths as of 27 January 2020 in China, and infection cases have been reported in more than 10 countries. However, there is no approved drug to treat the disease.
Zhijian Xu, Cheng Peng, Yulong Shi, Zhengdan Zhu, Kaijie Mu, Xiaoyu Wang, Weiliang Zhu   +6 more
semanticscholar   +1 more source

Molecular modelling studies of binding of DACD derivatives into G-Quadruplex DNA: comparison of force field and quantum polarized ligand docking methods [PDF]

, 2012
The DNA G-qadruplexes are one of the targets being actively explored for anti-cancer therapy by inhibiting them through small molecules. This computational study was conducted to predict the binding strengths and orientations of a set of novel dimethyl ...
Cardin, Christine J., Subramanian, Arun Kumar   +1 more
core