MOE Molecular Docking Analysis | Complete guide for Beginners | Lecture 83 | Dr. Muhammad Naveed
11.1 هزار بار بازدید -
2 سال پیش
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MOE Molecular Docking Analysis Download
MOE Molecular Docking Analysis
Download link: https://www.chemcomp.com/Products.htm
COMPUTER-AIDED MOLECULAR DESIGN
CCG is a leading developer and provider of Molecular Modeling, Simulations and Machine Learning software to Pharmaceutical and Biotechnology companies as well as Academic institutions throughout the world. CCG continuously develops new technologies with its team of mathematicians, scientists and software engineers and through scientific collaborations with customers.
This will focus on fragment-based drug design tools in MOE. Combinatorial fragment design and scaffold replacement in the receptor active site will be covered in detail, along with approaches for fragment linking and growing. A method for generating a series of closely related derivatives through medicinal chemistry transformations will also be presented. Finally, the use of pharmacophores and 2D/3D descriptors to guide drug design processes will be discussed.
CCG maintains a permanent team of scientists, mathematicians and software engineers engaged in a continuous program of research and development in Computer-Aided Molecular Design, Informatics and Computational Chemistry and Biology.
This covers MOE applications for interactive structure based design. Examples include active site visualization, protein-ligand contact analysis and ligand modification/optimization in the receptor pocket. Use of the docking module and its application to assess ligand flexibility will be discussed. A protocol for aligning and superposing protein complexes in the context of protein selectivity will be studied.
An automated approach to summarize pocket shapes and binding hot-spots from a collection of protein structures is presented. Pocket shapes are described using pocket volumes derived from Alpha Sites and molecular surfaces. Binding hot-spots are located using pharmacophore features generated by AutoPH4. Collections of pocket volumes and pharmacophores are analyzed using feature densities which map onto a universal grid the fraction of structures that possess a given feature at each point in space. Regions with high pharmacophore feature densities identify the most persistent interaction binding hot-spots over the collection of structures. Pocket volume densities detect and classify binding site regions into core pockets and sub-pocket regions. Fingerprints that represent pocket shape, sub-pocket presence and pharmacophore feature presence are derived and used to cluster and classify multiple protein structures using standard fingerprint clustering tools. Application of the method to fragment-based drug design, minor pocket detection, selectivity mapping, binding-mode classification and custom docking scoring function creation is presented.
About Dr. Muhammad Naveed
(HoD, Biotechnology, University of Central Punjab, Lahore)
With distinction, Dr. Muhammad Naveed obtained a Ph.D. degree in Biotechnology (Genomics & Bioinformatics) from Quaid-e-Azam University, Islamabad. He has won Ph.D. indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research at the University of Ghent, Belgium. HEC awarded him the best Ph.D. (IRSIP) Scholar of the year in 2013 & QAU honored him as a “Distinguished Alumni” in 2017. He is doing research projects in Bioinformatics, Molecular Biotechnology & Vaccine designing, and Drug designing against infectious diseases. He has supervised 70 MSc. and 60 MPhil. & 01 Ph.D. students. He has published 112 Research articles with 604 impact factors, 2000 citations, 01 book, and 03 book chapters. He was awarded the distinguished “Researcher of the Year” in 2016 (UoG) and 2018, 2019 & 2021 (UCP).
#moe #docking #drugdevelopment
Download link: https://www.chemcomp.com/Products.htm
COMPUTER-AIDED MOLECULAR DESIGN
CCG is a leading developer and provider of Molecular Modeling, Simulations and Machine Learning software to Pharmaceutical and Biotechnology companies as well as Academic institutions throughout the world. CCG continuously develops new technologies with its team of mathematicians, scientists and software engineers and through scientific collaborations with customers.
This will focus on fragment-based drug design tools in MOE. Combinatorial fragment design and scaffold replacement in the receptor active site will be covered in detail, along with approaches for fragment linking and growing. A method for generating a series of closely related derivatives through medicinal chemistry transformations will also be presented. Finally, the use of pharmacophores and 2D/3D descriptors to guide drug design processes will be discussed.
CCG maintains a permanent team of scientists, mathematicians and software engineers engaged in a continuous program of research and development in Computer-Aided Molecular Design, Informatics and Computational Chemistry and Biology.
This covers MOE applications for interactive structure based design. Examples include active site visualization, protein-ligand contact analysis and ligand modification/optimization in the receptor pocket. Use of the docking module and its application to assess ligand flexibility will be discussed. A protocol for aligning and superposing protein complexes in the context of protein selectivity will be studied.
An automated approach to summarize pocket shapes and binding hot-spots from a collection of protein structures is presented. Pocket shapes are described using pocket volumes derived from Alpha Sites and molecular surfaces. Binding hot-spots are located using pharmacophore features generated by AutoPH4. Collections of pocket volumes and pharmacophores are analyzed using feature densities which map onto a universal grid the fraction of structures that possess a given feature at each point in space. Regions with high pharmacophore feature densities identify the most persistent interaction binding hot-spots over the collection of structures. Pocket volume densities detect and classify binding site regions into core pockets and sub-pocket regions. Fingerprints that represent pocket shape, sub-pocket presence and pharmacophore feature presence are derived and used to cluster and classify multiple protein structures using standard fingerprint clustering tools. Application of the method to fragment-based drug design, minor pocket detection, selectivity mapping, binding-mode classification and custom docking scoring function creation is presented.
About Dr. Muhammad Naveed
(HoD, Biotechnology, University of Central Punjab, Lahore)
With distinction, Dr. Muhammad Naveed obtained a Ph.D. degree in Biotechnology (Genomics & Bioinformatics) from Quaid-e-Azam University, Islamabad. He has won Ph.D. indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research at the University of Ghent, Belgium. HEC awarded him the best Ph.D. (IRSIP) Scholar of the year in 2013 & QAU honored him as a “Distinguished Alumni” in 2017. He is doing research projects in Bioinformatics, Molecular Biotechnology & Vaccine designing, and Drug designing against infectious diseases. He has supervised 70 MSc. and 60 MPhil. & 01 Ph.D. students. He has published 112 Research articles with 604 impact factors, 2000 citations, 01 book, and 03 book chapters. He was awarded the distinguished “Researcher of the Year” in 2016 (UoG) and 2018, 2019 & 2021 (UCP).
#moe #docking #drugdevelopment
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