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How to select a ligand in VMD?

Representation (mathematics)

Ligand (biochemistry)

Docking (molecular)

Quantitative structure–activity relationship

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Journal Article•DOI Multi-conformational Ligand Representation in 4D-QSAR: Reducing the Bias Associated with Ligand Alignment Angelo Vedani, Daniel R. McMasters, Max Dobler - Show less +2 more 01 Apr 2000-Quantitative Structure-activity Relationships 29 Citations	The results indicate that the use of a multiple-ligand representation is superior to a single-conformer concept and reduces the user bias associated with the ligand alignment.
Journal Article•DOI Modeling of human ghrelin receptor (hGHS-R1a) in its close state and validation by molecular docking. Alessandro Pedretti, Giulio Vistoli - Show less +1 more 15 Apr 2007-Bioorganic & Medicinal Chemistry 12 Citations	may be involved in ligand binding and could find fertile applications in ligand design.
Open access•Journal Article•DOI DINC: A new AutoDock-based protocol for docking large ligands Ankur Dhanik, John S. McMurray, Lydia E. Kavraki - Show less +2 more 08 Nov 2013-BMC Structural Biology 46 Citations	We also show that positional restraints can be applied to the large ligand using DINC: this is useful when computing a docked conformation of the ligand.

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How to do ligand docking in protein?5 answersLigand docking in proteins involves several steps. First, a suitable search strategy and scoring function are needed for efficient and effective docking. One approach is to use AutoDock Vina, which employs an exhaustiveness parameter and a grid box to define the ligand binding site. Another method, FitDock, utilizes a hierarchical multi-feature alignment approach to fit the initial conformation to a given template, resulting in improved docking success rates and faster performance. Additionally, flexible protein-ligand docking can be achieved using a deep learning model based on the prediction of an intermolecular Euclidean distance matrix, which outperforms traditional docking methods. Finally, computational molecular docking can be used to generate a density of binding states, which can be used to calculate binding strengths, conformations, and atomic interactions between the ligand and protein.

What techniques can be used to understand the binding of ligand with the protein?5 answersSeveral techniques can be used to understand the binding of a ligand with a protein. High-resolution structural approaches, such as X-ray crystallography, provide a static view of the protein-ligand complex. Molecular docking simulations, based on force fields like Martini, can accurately predict binding sites and pathways, as well as binding free energies. Big Data analytics techniques, including machine learning and deep learning, can efficiently process a large number of protein-ligand complexes and identify specific protein properties responsible for correct prediction of binding. Differential scanning calorimetry (DSC) can determine the enthalpy change upon protein unfolding and the melting temperature of the protein, providing information on ligand binding. These techniques, along with thermodynamic treatments and experimental designs, can enhance our understanding of protein-ligand interactions.

What is a ligand in biology?5 answersA ligand in biology refers to a molecule that binds to a receptor, enabling communication and interaction between cells and their environment. Ligands can be a wide range of biomolecules, including proteins, carbohydrates, and small molecules. In biological activities, ligands are involved in contact interactions with their complementary partners, such as enzymes and substrates, antigens and immunoglobulins, or neurotransmitters and receptor sites. Ligands can be used in various applications, such as targeting specific cell types or delivering bio-active compounds to cells expressing a particular receptor. Ligand identification methods, such as using oligonucleotides or analogues, can help identify ligands that interact specifically with a target molecule. In the field of chemical genetics, ligands are used to alter protein function and study the consequences of these changes in a cellular or organismal context.

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