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Molecular Memory
Приєднався 16 лют 2017
Welcome! I'm KP, and I'm an organic chemist that loves making videos and sharing free chemistry and biochemistry resources. I hope you enjoy and learn something!
PyMOL 101, Lesson 7: Secondary structure H-bonding, measurement wizard, & names panel grouping
In this lesson, KP takes you on a deeper analysis of secondary structure. Building on the measurement techniques from Lesson 6, we’ll model an alpha helix, an antiparallel beta sheet, and a parallel beta sheet. We’ll analyze all three secondary structures to find out about the hydrogen bonding patterns that characterize each.
00:00 Intro
00:24 Setting up your workspace
00:52 Alpha helix modeling
01:34 The i+4 rule for alpha helices
03:32 Alpha helix backbone interactions with the measurement wizard
04:00 Grouping measurements
04:39 Measurement wizard - merge measurements
05:36 Antiparallel vs. parallel beta sheets
06:24 Modeling the antiparallel beta sheet
07:24 Modeling the parallel beta sheet
08:15 Parallel and antiparallel beta sheet structure comparison
REFERENCES:
• PDB ID: 1a0o
• Welch, M., Chinardet, N., Mourey, L. et al. Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY. Nat Struct Mol Biol 5, 25-29 (1998). doi.org/10.1038/nsb0198-25
00:00 Intro
00:24 Setting up your workspace
00:52 Alpha helix modeling
01:34 The i+4 rule for alpha helices
03:32 Alpha helix backbone interactions with the measurement wizard
04:00 Grouping measurements
04:39 Measurement wizard - merge measurements
05:36 Antiparallel vs. parallel beta sheets
06:24 Modeling the antiparallel beta sheet
07:24 Modeling the parallel beta sheet
08:15 Parallel and antiparallel beta sheet structure comparison
REFERENCES:
• PDB ID: 1a0o
• Welch, M., Chinardet, N., Mourey, L. et al. Structure of the CheY-binding domain of histidine kinase CheA in complex with CheY. Nat Struct Mol Biol 5, 25-29 (1998). doi.org/10.1038/nsb0198-25
Переглядів: 2 077
Відео
PyMOL 101, Lesson 6: Introduction to the measurement wizard & polar contacts, the N- & C-terminus
Переглядів 1,8 тис.9 місяців тому
In this lesson, we’ll learn a PyMOL preset to display protein interfaces. Then, we’ll introduce the measurement wizard, and explore different types of molecular interactions. 00:00 Introduction and typical interaction distances 00:22 Interface preset 01:08 Peptide bond formation & the N- and C-terminus 02:10 Grayed out amino acids in the sequence display 02:30 Find polar contacts at the protein...
PyMOL 101, Lesson 5: Select by Distance, the Mouse Control Menu, and Labeling
Переглядів 2,4 тис.9 місяців тому
In this lesson, KP will show you how to generate a binding site quickly, by creating a selection sphere within a certain number of angstroms from a bound ligand. This lesson focuses on the mouse control menu, and how to use edit mode to reposition labels. 00:00 Intro 00:26 Setting up your workspace 01:57 The mouse control menu 02:34 Selected by distance from a ligand 03:41 Adjusting water spher...
PyMOL 101, Lesson 4: Color, Transparency, and Alternate Renderings
Переглядів 3 тис.10 місяців тому
In this installment of PyMOL 101, KP talks about CPK coloring and color settings in PyMOL. We’ll learn to change renderings, color them, and apply transparency. 00:00 Intro AND CPK coloring 00:40 Phosphofructokinase background 01:24 Setting up your workspace 02:06 Color by chain 03:23 Color by secondary structure 03:52 Surface transparency 04:51 Color by element 06:05 Terminology break 06:28 Re...
PyMOL 101, Lesson 3: File Types and Saving - Publication Quality Figures & Scenes
Переглядів 2,4 тис.10 місяців тому
In this lesson, KP takes you through the input and output PyMOL files, how to save your session, how to export a high-quality PNG image. Finally, we’ll learn to save scenes, preserving the different renderings and views as you work through this tutorial. 00:00 Intro 00:21 PDB and CIF files 01:41 Publication quality image guidelines and saving 04:41 Saving scenes in a PyMOL session REFERENCES • ...
PyMOL 101 Lesson 2: Basic Selection, Show, Hide, and Actions Menus (Carbonic Anhydrase Active Site)
Переглядів 2,6 тис.11 місяців тому
In this lesson, KP demonstrates how to display the active site of carbonic anhydrase using the active site amino acid information from a manuscript. We’ll learn how to save and change the renderings of selections in the names panel. Then, we’ll use our selections to identify water molecules that are hydrogen bonding to the active site. Don’t forget to save your work at the end of this lesson-we...
PyMOL 101, Lesson 1: GUI Basics - loading structures, mouse/trackpad motions, sequence, zoom & clip
Переглядів 3 тис.11 місяців тому
In this first installment of PyMOL 101, KP teaches you the basics of the PyMOL Graphical User Interface (GUI, pronounced “gooey”). In lesson 1, you’ll learn to: • Load the biological unit of structures • Rotate, zoom, and reposition molecules • Interpret the sequence display • Zoom in on a feature of a particular structure • Adjust clipping CHAPTERS 00:00 - Intro 00:38 - Loading Structures 02:3...
Antibody Structure: The Immunoglobulin Fold and Antibody-Antigen Interactions
Переглядів 8 тис.2 роки тому
Dr. KP gives an overview of antibody structure, and takes a look at a human antibody bound to the SARS-CoV-2 spike protein. PDB IDs Available at rcsb.org: 1igt, 7k90 REFERENCES • Akkaya, M., Kwak, K. & Pierce, S.K. B cell memory: building two walls of protection against pathogens. Nat Rev Immunol 20, 229-238 (2020). doi.org/10.1038/s41577-019-0244-2 • Alberts B, Johnson A, Lewis J, et al. Molec...
The Mechanisms of Glycolysis (Part 2)
Переглядів 4,4 тис.2 роки тому
Dr. KP takes you through the arrow pushing for the final 5 steps of glycolysis. These reactions are part of the energy-yielding payoff phase of the pathway! 00:00 Intro 00:24 Glyceraldehyde-3-phosphate dehydrogenase 04:47 Phosphoglycerate kinase 05:46 Phosphoglycerate mutase 07:14 Enolase 08:45 Pyruvate kinase REFERENCES: • Appling, D. R., Anthony-Cahill, S. J., & Mathews, C. K. (2016). Biochem...
The Mechanisms of Glycolysis (Part 1)
Переглядів 9 тис.2 роки тому
Dr. KP takes you through the arrow pushing for the first 5 steps of glycolysis. 00:00 Introduction 00:12 Hexokinase 03:43 Glucose-6-phosphate isomerase 08:10 Phosphofructokinase 10:15 Aldolase 14:50 Triose phosphate isomerase REFERENCES: • Appling, D. R., Anthony-Cahill, S. J., & Mathews, C. K. (2016). Biochemistry: Concepts and connections. Pearson Education. • McMurry, J., Begley, T. P., & Be...
Where's My Dimer? Symmetry Mates in PyMOL
Переглядів 8 тис.3 роки тому
If you've ever modeled a protein in PyMOL and it looks like you're missing a subunit of your dimer, you may need to generate a symmetry mate to visualize the whole structure. This tutorial will help!
Understanding PHI and PSI Angles, Ramachandran Plots, & Newman Projections
Переглядів 103 тис.3 роки тому
This video was created using models, images, and inspiration from the Proteopedia page: The Ramachandran Principle Phi (φ) and Psi (ψ) Angles in Proteins proteopedia.org/wiki/index.php/Tutorial:Ramachandran_principle_and_phi_psi_angles REFERENCES: • Ramachandran, G.N.; Ramakrishnan, C.; Sasisekharan, V. (1963). "Stereochemistry of polypeptide chain configurations". Journal of Molecular Biology....
PyMOL Tutorial: Modeling the SARS-CoV-2 RBD Interactions with ACE (COVID-19 Coronavirus Proteins)
Переглядів 38 тис.4 роки тому
A follow up PyMOL tutorial for my SARS-CoV-2 Structure. How I modeled the polar interactions between the spike protein RBD and ACE before the paper was published (and a follow up interaction now that the paper is published!) PDB ID: 6VW1 Reference: Shang, J., Ye, G., Shi, K., Wan, Y., Luo, C., Aihara, H., ... & Li, F. (2020). Structural basis of receptor recognition by SARS-CoV-2. Nature, 1-8.
SARS-CoV-2 Structure (COVID-19 Coronavirus)
Переглядів 245 тис.4 роки тому
A structural exploration of the proteins produced by SARS-CoV-2. PDB FILES: 6VSB - Spike protein 6VW1 - RBD of the spike protein in complex with ACE2 6SGC - Rabbit ribosome stalled on a poly-A tail 6Y2E - SARS CoV-2 main protease 6Y2F - SARS CoV-2 main protease bound to an inhibitor REFERENCES: • Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C. L., Abiona, O., ... & McLellan, J....
PyMOL: Superimpose (& Amazing NMR Structures!)
Переглядів 36 тис.4 роки тому
How to superimpose proteins to examine structural changes, and a look at how we can explore protein dynamics with NMR solution structures.
Teaching Online 5: Content Creation
Переглядів 1,2 тис.4 роки тому
Teaching Online 5: Content Creation
Teaching Online 2: Successful Discussions
Переглядів 7924 роки тому
Teaching Online 2: Successful Discussions
PyMOL: Build Your Own Sequences (for Learners & Instructors)
Переглядів 26 тис.4 роки тому
PyMOL: Build Your Own Sequences (for Learners & Instructors)
How to Sketch Molecular Orbitals for π Systems
Переглядів 3,2 тис.4 роки тому
How to Sketch Molecular Orbitals for π Systems
Acetoacetic & Malonic Esters (& Dianions)
Переглядів 8254 роки тому
Acetoacetic & Malonic Esters (& Dianions)
Aldol Reaction: Mechanism and Retrosynthesis
Переглядів 1,7 тис.4 роки тому
Aldol Reaction: Mechanism and Retrosynthesis
Weinreb Amides and More (Forming Ketones Using Organometallic Reagents)
Переглядів 2,3 тис.4 роки тому
Weinreb Amides and More (Forming Ketones Using Organometallic Reagents)
Allylic and Benzylic Substrates: SN1/SN2/E1 or E2?
Переглядів 7 тис.4 роки тому
Allylic and Benzylic Substrates: SN1/SN2/E1 or E2?
glucose is not neutral, it needs GLUT transporters to go through the cell membrane
Great tutorial..thank you!
please can you do a tutorial on predict putative ligand binding sites based on physicochemical properties, conservation analysis, and structural constraints and also protein refinement and looping of modelled protein
I'm new to PyMol and your videos are extremely helpful! Thank you for sharing!
Pka of 18 is not acidic
Wow Thank you Mam
Hi, after following your instructions, some proteins 3d structure generate output with overlap structure, but some other 3d structure do not have this problem and success to make the dimer symmetry. Could you please give me the suggestion on how to resolve the overlap structure?
Thank you for this tutorial
how to reverse this PNG back to PDB ?
thank you ❤❤❤
Ma'am how you add this cheat sheet into this vedio??
Great video!!!!
extremely helpful, thank you, ma'dam
Many thanks for this series, really useful for a PyMol Novice!
This is the best explanation of how to use PyMOL movie commands I’ve ever seen!
Great 😊😊
thank you so much, this helps me a lot
this video saved my life, thxxxx ❤❤❤❤❤
How to draw dashed lines manually or via command between two atoms in a ligand to show any interaction. Please answer.
Dr G N Ramachandran would have been so delighted to see your video if he was still amidst us. He did an amazing discovery and I have tried reading Lehninger, Voet to truly grasp the concept of phi and psi and no book could have done more justice to his contribution than your animated video. Heartfelt thanks.
Very clear!
Why do we study this
I truly did not understand phi/psi angles and Ramachandran plots until watching this video. It was really helpful, thanks!
where i can download chemdraw? please i need it
Very useful! Thank you so much!!
honestly one of the most thorough video of the mechanism for glycolysis, super helpful
Sorry, but how can i judged active site in sequence? why are you clicked "/B/A/998"?, is it catalytic(=active) site?
This is the best video to understand the molecule, thank you!
This may be one of the best videos I’ve ever watched. I can explain how much difficultly I’ve had trying to work with this
thank you, it was very helpful question: does anybody know how I can rotate a single bond in ChemDraw?
Does NADH elevate 4py?
nice
THANK YOU FOR THE VIDEO MAKER AND THE PROTEOPEDIA FOR PROVING SUCH DETAILED EXPLANATION
Solid organic chemistry explanation for the role of thiamine!
Excellent!
There is -1 carbon atom at ethyl ester?
CCO2Et not CO2Et
I wish she would show molecular docing of COVID (SARS) like HADOCK does
The series with KP only gets better and better, this series is invaluable for students
This was VERY useful! I'll watch this a few times over and over!
Brilliant! Keep going and making more videos!!
Thank you so much.
Thanks for diving into the binding pocket. The other hydroxyls of glucose would be hydrogen bonded through their H atoms to oxygens in the backbone of the peptide or side chain oxygens? Would those hydroxyl oxygens also H bond as donors to hydrogens on backbone amino hydrogens and the hydrogens on polar side chains like the ones on serine and threonine?
Very well done, you can tell you love what you do in chemistry!
i disliked glycolysis so much in gen bio, until i took organic chemistry and now coming back to this topic in biochem. now, it is actually interesting. I just needed more in depth info.
Beautiful, thank you
Great jump start tutorial!
Hey, thank you for your videos, my pymol skills improved 100 %. I have a question. Can I combine this style of movie with a trajectory of molecular dynamics? Im having a difficult time trying to set this up. If you have any hints i will be glad. Thank you again!
Fantastic!!!
03:15
Please make an exclusive video on how to use pymol code.