Ligand for Target Protein

Jul 02, 2021

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Ligand for Target Protein

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Ligand

Ligand. Receptor. Receptor/Ligand Binds to promoter elements in DNA and regulates transcription. Cortisol Receptor is located in the cytosol. Retinoid Receptors are in the nucleus. Nucleus:. Target gene in the nucleus. Promoter. Regulation of Transcription. Primary and Secondary Responses.

733 views • 35 slides

Monitoring Protein Phosphorylation for the Ligand Screens

Monitoring Protein Phosphorylation for the Ligand Screens. Goal: sample diversity of cellular response to inputs Current Approach: Multiplex Western blotting with mixtures of phosphospecific antibodies Quantify ligand-induced changes in site-specific protein phosphorylation .

374 views • 12 slides

Ligand configurational entropy and protein binding

Ligand configurational entropy and protein binding. Chia-en A. Chang, Wei Chen, and Michael K. Gilson – PNAS(2007) Presented by Christopher Williams. Remember K*?. Uses conformational entropy of side chains to better predict redesign mutations. What about ligands?. Entropy is lost on binding

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Protein-Ligand Docking

Protein-Ligand Docking. Dr. Noel O’Boyle University College Cork n.oboyle@ucc.ie Sep 2010 EMBO Practical Course Computational aspects of protein structure determination and analysis: from data to structure to function. Outline. Introduction to protein-ligand docking Practical aspects

1.2k views • 39 slides

Ligand

EXTRINSIC PATHWAY. INTRINSIC PATHWAY. Ligand. UV, radiation, chemo, hypoxia. ER Stress (misfolded proteins). Death receptor. Plasma Membrane. Adapter. Procaspase-12. Initiator Caspase-8. Mitochondria. Initiator Caspase-12. Bcl-2/ Bcl-x L. Bid. Ca ++. TRAF2. IP3R. Ca ++. Cyto c.

217 views • 1 slides

Using DOCK to characterize protein ligand interactions

Using DOCK to characterize protein ligand interactions. Sudipto Mukherjee. Robert C. Rizzo Lab. Acknowledgements. The Rizzo Lab Dr. Robert C. Rizzo Brian McGillick Rashi Goyal Yulin Huang. IBM Rochester Carlos P. Sosa Amanda Peters. Support

301 views • 13 slides

Protein-Ligand Interaction Prediction: An Improved Chemogenomics Approach

Protein-Ligand Interaction Prediction: An Improved Chemogenomics Approach. Laurent Jacob Jean-Philippe Vert. Introduction. Predicting interactions between small molecules and proteins Vital to the drug discovery process Key to understanding biological processes. 3 classes of drug targets

531 views • 30 slides

Protein Function in the Context of Protein Ligand Interactions

Protein Function in the Context of Protein Ligand Interactions. Chapter 5 (Page 157-170). 1. Protein Function. Proteins are dynamic molecules. Their functions largely depend on interactions with other molecules and conformational changes associated with these interactions.

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Protein-ligand geometry

Protein-ligand geometry. Schaefer EPSP synthase-inhibitor Rotatonal echo double resonance (REDOR). Secondary Structure. ( 13 C  ), ( 13 C  )  local backbone conformation Internuclear distances  backbone dihedral angles Relative tensor orientations  backbone dihedral angles

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Biosensors to detect enzyme-ligand and Protein-protein interactions

Biosensors to detect enzyme-ligand and Protein-protein interactions . -Physical parameters in binding studies-principles, techniques and instrumentation -Methods to probe non-covalent macromolecular interaction (stopped-flow, BIAcore, and Microcalorimetry)

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HTP Target protein TR8

HTP Target protein TR8. TR8. 133 a.a. + 22 a.a. in His-tag Correlation time is 10.3 ± 0.3 ns Sample concentration <1 mM Monomer (2D H-C planes of HNCO and TROSY-HNCO have equal sensitivity).

311 views • 11 slides

Predicting ligand binding sites on protein surface

Predicting ligand binding sites on protein surface. Zengming Zhang 2010-5-12. What is the binding site?. (Concave, cleft, hole) – shaped region on protein surface A key into a lock! Key-ligand Lock-protein Lock hole-binding sites. Why do we need to find binding sites?.

724 views • 43 slides

Approaches to signal transduction: - pathway - ligand/receptor - protein/protein interactions

Approaches to signal transduction: - pathway - ligand/receptor - protein/protein interactions - second messengers - protein phosphorylation - cellular responses Shutting down a signaling pathway. (second messengers). Approaches for identifying a pathway:

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The Importance of Protein Flexibility in Protein-Ligand Docking

The Importance of Protein Flexibility in Protein-Ligand Docking. Jennifer Metzger October 15th, 2008. Introduction Methods Results Discussion. Talk Outline. Introduction Motivation My Task Methods Preparation of molecules

804 views • 45 slides

Chapter 5.1: Protein Function - Reversible Binding of Protein to a Ligand

Chapter 5.1: Protein Function - Reversible Binding of Protein to a Ligand. CHEM 7784 Biochemistry Professor Bensley. CHAPTER 5.1 Reversible Binding of Protein to a Ligand. Reversible binding of ligands Structure of myoglobin and hemoglobin Origin of cooperativity in hemoglobin.

948 views • 26 slides

ligand

A RECEPTOR KERESZTKÖTÉSE JELÁTVITELI MECHANIZMUSOKAT INDÍT BE. ligand. k ináz aktiváció. foszforiláció. adaptorok toborzása. Transzkripciós faktorok aktiválása. Gén átírás. JEL. a. a. antig e n binding. V. V. V. V. L. L. mIg molecule. Kin ases. H. H. Signal transduction. b.

664 views • 49 slides

Computational Modeling of Protein-Ligand Interactions

Computational Modeling of Protein-Ligand Interactions. Steven R. Gwaltney Department of Chemistry Mississippi State University Mississippi State, MS 39762. Auguste Comte, 1830.

573 views • 43 slides

Protein-protein and Protein-ligand Docking

Protein-protein and Protein-ligand Docking. The geometric filtering. Shape Complementarity. Geometric Docking Algorithms. Based on the assumption of shape complementarity between the participating molecules.

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Week 5 MD simulations of protein-ligand interactions

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Ligand

#. *. *. *. *. GW9662. -. +. -. +. -. +. -. +. -. +. -. +. -. +. Ligand. -. -. TGZ (10 m M). TGZ (100 m M). CGZ (40 m M). RGZ (10 m M). 15dPGJ2 (1 m M). 15dPGJ2 (10 m M).

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Molecular docking for protein-ligand

https://protac.bocsci.com/services/molecular-docking-for-protein-ligand.html

134 views • 5 slides

Protein-Ligand Docking

https://www.profacgen.com/protein-ligand-docking.htm The interaction between proteins and their cognate ligands plays an important role in many essential biological processes and metabolic pathways, including signal transduction, transport, cell regulation, gene expression control, and enzyme inhibition. Many experimental techniques are now available for the detection and measurement of these binding interactions, but it remains difficult and expensive to obtain complex structures by experimental methods, such as X-ray crystallography or NMR. Thus, computational docking is considered an important approach for study of protein-ligand interactions and for drug discovery and development.

101 views • 5 slides

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