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Desidustat's cardioprotective mechanisms in heart failure: a network pharmacology, molecular docking and dynamics approach. [PDF]

Sci Rep
Sadiqbasha MF, Gunasekaran A, Thirulokachandar JC, Sundararajan S.   +3 more
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Simulation of STAT and HP1 interaction by molecular docking

Cellular Signalling, 2023
Heterochromatin Protein 1 (HP1) is a major component of heterochromatin. Multiple proteins have been shown to interact with HP1 with the HP1-binding motif PxVxL/I, thereby affecting heterochromatin stability. The HP1-interacting proteins include the signal transducer and activator of transcription (STAT) protein, which can be regulated by ...
Kangxin, Xu, Jinghong, Li, Willis X, Li
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Molecular docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors

Journal of Biomolecular Structure and Dynamics, 2021
Pin1 (protein interacting with never-in-mitosis akinase-1) is a member of the PPIase (peptidylprolyl cis-trans isomerase) family. It can interact with a variety of carcinogenic or tumor suppressive phosphorylated proteins. The interaction results in the conformational changes of target proteins, and ultimately regulates the activity of these proteins ...
Jiangheng, Zhao, Min, Liu, Jieying, Zang, Shuangshuang, Yang, Ruiyou, Chen, Xin, Zhao, Lina, Ding   +6 more
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Protein docking algorithms: simulating molecular recognition

Current Opinion in Structural Biology, 1993
Docking algorithms simulate protein-protein association in molecular assemblies such as protease-inhibitor or antigen-antibody complexes by reconstituting the complexes from their component molecules. They not only efficiently retrieve native structures but also select a number of non-native structures with structural and physicochemical features that ...
Jacqueline Cherfils, Joël Janin
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Molecular Docking Simulations with ArgusLab

2019
Molecular docking is the major computational technique employed in the early stages of computer-aided drug discovery. The availability of free software to carry out docking simulations of protein-ligand systems has allowed for an increasing number of studies using this technique. Among the available free docking programs, we discuss the use of ArgusLab
Gabriela, Bitencourt-Ferreira, Walter Filgueira, de Azevedo   +1 more
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Integrating Molecular Docking and Molecular Dynamics Simulations

2019
Computational methods, applied at the early stages of the drug design process, use current technology to provide valuable insights into the understanding of chemical systems in a virtual manner, complementing experimental analysis. Molecular docking is an in silico method employed to foresee binding modes of small compounds or macromolecules in contact
Lucianna H S, Santos, Rafaela S, Ferreira, Ernesto R, Caffarena   +2 more
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Web Services for Molecular Docking Simulations

2019
Docking process is one of the most significant activities for the analysis of protein-protein or protein-ligand complexes. These tools have become of unique importance when allocated in web services, collaborating scientifically with several areas of knowledge in an interdisciplinary way.
Nelson J F, da Silveira, Felipe Siconha S, Pereira, Thiago C, Elias, Tiago, Henrique   +3 more
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Bio-Inspired Algorithms Applied to Molecular Docking Simulations

Current Medicinal Chemistry, 2011
Nature as a source of inspiration has been shown to have a great beneficial impact on the development of new computational methodologies. In this scenario, analyses of the interactions between a protein target and a ligand can be simulated by biologically inspired algorithms (BIAs).
G, Heberlé, W F, de Azevedo
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Distance-constrained molecular docking by simulated annealing

"Protein Engineering, Design and Selection", 1990
An optimized method based on the principle of simulated annealing is presented for determining the relative position and orientation of interacting molecules. The spatial relationships of these molecules are described by intermolecular distance constraints between specific pairs of atoms, such as found in hydrogen bonds or from experimentally ...
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Molecular dynamics simulation of the docking of substrates to proteins

Proteins: Structure, Function, and Bioinformatics, 1994
AbstractA simple method is described to perform docking of subtrates to proteins or probes to receptor molecules by a modification of molecular dynamics simulations. The method consists of a separation of the center‐of‐mass motion of the substrate from its internal and rotational motions, and a separate coupling to different thermal baths for both ...
DINOLA, A, ROCCATANO, D, BERENDSEN, HJC
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