The Experts below are selected from a list of 87480 Experts worldwide ranked by ideXlab platform
Adriano D. Andricopulo - One of the best experts on this subject based on the ideXlab platform.
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Practices in Molecular Docking and structure-based virtual screening
Methods in molecular biology (Clifton N.J.), 2018Co-Authors: Ricardo N. Dos Santos, Leonardo L. G. Ferreira, Adriano D. AndricopuloAbstract:Drug discovery has evolved significantly over the past two decades. Progress in key areas such as Molecular and structural biology has contributed to the elucidation of the three-dimensional structure and function of a wide range of biological molecules of therapeutic interest. In this context, the integration of experimental techniques, such as X-ray crystallography, and computational methods, such as Molecular Docking, has promoted the emergence of several areas in drug discovery, such as structure-based drug design (SBDD). SBDD strategies have been broadly used to identify, predict and optimize the activity of small molecules toward a Molecular target and have contributed to major scientific breakthroughs in pharmaceutical R&D. This chapter outlines Molecular Docking and structure-based virtual screening (SBVS) protocols used to predict the interaction of small molecules with the phosphatidylinositol-bisphosphate-kinase PI3Kδ, which is a Molecular target for hematological diseases. A detailed description of the Molecular Docking and SBVS procedures and an evaluation of the results are provided.
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Molecular Docking and structure based drug design strategies
Molecules, 2015Co-Authors: Leonardo L. G. Ferreira, Ricardo Dos N Santos, Glaucius Oliva, Adriano D. AndricopuloAbstract:Pharmaceutical research has successfully incorporated a wealth of Molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, Molecular Docking methods explore the ligand conformations adopted within the binding sites of macroMolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the interMolecular recognition process. Today, as a variety of Docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current Molecular Docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.
Marimuthu Citartan - One of the best experts on this subject based on the ideXlab platform.
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In silico Molecular Docking in DNA aptamer development.
Biochimie, 2020Co-Authors: Tholasi Nadhan Navien, Ramesh Thevendran, Hazrina Yusof Hamdani, Thean-hock Tang, Marimuthu CitartanAbstract:Abstract Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico Molecular Docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico Molecular Docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.
Jack A. Tuszynski - One of the best experts on this subject based on the ideXlab platform.
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Software for Molecular Docking: a review
Biophysical reviews, 2017Co-Authors: Nataraj Sekhar Pagadala, Khajamohiddin Syed, Jack A. TuszynskiAbstract:Molecular Docking methodology explores the behavior of small molecules in the binding site of a target protein. As more protein structures are determined experimentally using X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, Molecular Docking is increasingly used as a tool in drug discovery. Docking against homology-modeled targets also becomes possible for proteins whose structures are not known. With the Docking strategies, the druggability of the compounds and their specificity against a particular target can be calculated for further lead optimization processes. Molecular Docking programs perform a search algorithm in which the conformation of the ligand is evaluated recursively until the convergence to the minimum energy is reached. Finally, an affinity scoring function, ΔG [U total in kcal/mol], is employed to rank the candidate poses as the sum of the electrostatic and van der Waals energies. The driving forces for these specific interactions in biological systems aim toward complementarities between the shape and electrostatics of the binding site surfaces and the ligand or substrate.
Tholasi Nadhan Navien - One of the best experts on this subject based on the ideXlab platform.
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In silico Molecular Docking in DNA aptamer development.
Biochimie, 2020Co-Authors: Tholasi Nadhan Navien, Ramesh Thevendran, Hazrina Yusof Hamdani, Thean-hock Tang, Marimuthu CitartanAbstract:Abstract Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico Molecular Docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico Molecular Docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.
Leonardo L. G. Ferreira - One of the best experts on this subject based on the ideXlab platform.
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Practices in Molecular Docking and structure-based virtual screening
Methods in molecular biology (Clifton N.J.), 2018Co-Authors: Ricardo N. Dos Santos, Leonardo L. G. Ferreira, Adriano D. AndricopuloAbstract:Drug discovery has evolved significantly over the past two decades. Progress in key areas such as Molecular and structural biology has contributed to the elucidation of the three-dimensional structure and function of a wide range of biological molecules of therapeutic interest. In this context, the integration of experimental techniques, such as X-ray crystallography, and computational methods, such as Molecular Docking, has promoted the emergence of several areas in drug discovery, such as structure-based drug design (SBDD). SBDD strategies have been broadly used to identify, predict and optimize the activity of small molecules toward a Molecular target and have contributed to major scientific breakthroughs in pharmaceutical R&D. This chapter outlines Molecular Docking and structure-based virtual screening (SBVS) protocols used to predict the interaction of small molecules with the phosphatidylinositol-bisphosphate-kinase PI3Kδ, which is a Molecular target for hematological diseases. A detailed description of the Molecular Docking and SBVS procedures and an evaluation of the results are provided.
-
Molecular Docking and structure based drug design strategies
Molecules, 2015Co-Authors: Leonardo L. G. Ferreira, Ricardo Dos N Santos, Glaucius Oliva, Adriano D. AndricopuloAbstract:Pharmaceutical research has successfully incorporated a wealth of Molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, Molecular Docking methods explore the ligand conformations adopted within the binding sites of macroMolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the interMolecular recognition process. Today, as a variety of Docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current Molecular Docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.
