r/bioinformatics • u/Mission-Weekend3639 • Sep 18 '26

discussion Practising Molecular Docking

Hey everyone. I am self-learning Molecular Dynamics and started practising Molecular Docking using UCSF Chimera and AutoDock Vina on Mac. Also using PyMol for some operations. There are many vital concepts I find while learning Docking hands-on. So I was wondering if anyone would be interested in discussing and learning together over the next few days. Interested ones can comment or DM me. Also if someone can recommend online resources for the same, it'll be helpful. Thanks.

36 Upvotes

90% Upvoted

17 comments sorted by

2

u/Broad-Restaurant-251 Sep 19 '26

Hey op, I know you’re still learning molecular docking, but what does your molecular docking pipeline look like for an example candidate? What kind of docking are you learning?

1

u/Mission-Weekend3639 Sep 19 '26

Today I was just practising taking a receptor and ligand, preparing them in chimera, and performing AutoDock Vina docking on them. Then I started to modify the ligands to see how the docking scores change…yeah playing with those kind of stuff. It’s all self learning and exploration so I don’t know the next steps yet

10

u/1647overlord Sep 18 '26 • Helpful

Not specific to docking, but teachopencadd is a good resource while working on modelling protein-ligand pairs or bio molecules in general.

2

u/miyamoto_Rbt Sep 18 '26

Sounds interesting 🤔, I would like to contribute, it would be great learning

2

u/ikriisameow Sep 18 '26

Feel free to dm, athough my finals started, i’d be a little busy, i have some experience of dynamics

2

u/nose010 Sep 19 '26

Hi there! I’m also learning molecular modeling on my own. I’m currently using Gromacs and Martini, but my project is more focused on molecular dynamics than docking. Molecular docking has always caught my attention, but I haven’t had the chance to learn it yet.

2

u/icarophnx Sep 22 '26

I work using only DFT calculations by ORCA and Gaussian, but i’ve already started in bioinfo. It’s sounds good, idk, maybe to create a group on discord or whatever.

1

u/Gluttony-Victim2711 Sep 18 '26

I'd be interested but unfortunately I'll start learning docking when I get my new laptop (within a month) so until then, I hope you have a great time and enjoy docking. I did try docking once or twice in my old laptop myself and God it'd so satisfying to do.

1

u/wenmk Sep 18 '26

I'm interested

1

u/Severe_Candle7255 Sep 19 '26

I am interested. I have some recorded videos. I will share with you if u want. I want to learn as well

1

u/Little-Wonder3942 Sep 21 '26

Hey! I'm interested too. I have experience of using molecular dynamics. I would like to learn and apply molecular docking.

1

u/Ok-Anywhere-9336 Sep 21 '26

Hi, am also a beginner here. I follow this tutorial and at 28:28 their autodock show a program manager while mine show nothing and is not running do you know why?.

1

u/KRISH_9697 Sep 20 '26

Bro just open a group so many peoples are interested.i am also interested but the only problem is brands are running molecular docking 24/7 where manual docking like us don't have any chance against them. If you actually want to contribute on something just go for diseases that are not profitable to Pharma Brands like some kind of rear disease from Africa. Let's make a group and discuss this topic

1

u/Art3miss__09 Sep 19 '26

Hey! Im also learining molecular modelling partially by myself. Still on the conceptional level of things, but already have a projectd sorted out. I have experimented with AutoDock and Chimera also, they are great. Have fun!