Comments (7)
Convert the mol2 files into sdf files with some external tools (e.g., convert.py in OpenEye), and then load them into the RDkit using "Chem.MolFromMolFile".
from rtmscore.
Thank you for your reply. I have other following questions. First, I saw you uploaded the processed graphs at https://zenodo.org/record/6859325#.Y6KpS3ZBxD-. I found that each data point is stored in a heterogeneous graph object. I guess I should convert it into two separate protein and ligand graphs before feeding it to RTMScore. Alternatively, I can also modify the model to make it possible to process heterogeneous graphs. Am I right? Second, the heterogeneous graph contains three types of distance (cadist, cedist, and mindist). Is mindist equal to the result returned by the function “compute_euclidean_distances_matrix” at model2.py? Do these three types of distance lead to similar performance? Third, do the two auxiliary tasks matter? Do you test the model performance by removing the two auxiliary tasks? To my understanding, the model is just trained to recover the information already included in the input features for the auxiliary tasks. I am looking forward to your reply. Thank you.
from rtmscore.
- Perhaps what you see is the graphs for our previous version. In our published version (Version 2 in the same link), the protein and ligand graphs are seperately stored.
- "mindist" is used as the final indicator to represent the distance for each residue-atom pair in our final version. Yes, it is returned by "compute_euclidean_distances_matrix" function. "mindist" performs significantly better than the other two indicators, so we finally use it.
- These two auxiliary tasks are just for training and useless for predictions. Yes, I think what you guess is true, i.e., they are just used to recover the information already included in the input features. However, it should be noted that the decline of MDN loss may in turn lead to the change of the atom/bond types of the ligand, and the inclusion of these two terms can guarantee the reasonability of the ligand to some extents. Of course we have't tested the performance with the removing of these two tasks, but at least the inclusion of them is harmless. We just inherit these two terms from DeepDock.
from rtmscore.
Thank you for your reply. I might have the following question. To my understanding, RTMScore is trained to predict a Gaussian-like distribution where mu is supposed to be at a position close to the true distance (i.e., y in the source code). However, when I check the prediction of the trained RTMScore I found that the predicted mu is far away from the true distance y. Is that normal, or perhaps I misunderstood the algorithm?
from rtmscore.
sigma and mu are all a group of parameters to determine the distribution of the distance, and the final distribution of a specific residue-atom pair shall be the mixtures of multiple Gaussians. Hence there shall be no relation between a single mu and the correponding y. It should be noticed that mu and y have different dimentions.
Hence I think perhaps you misunderstand the algorithm. To better understand the algorthm, perhaps you can refer to the original paper of DeepDock.
from rtmscore.
Thank you very much for your reply. I tried to apply for a license for OpenEye, but I haven’t received any feedback yet. Could you please upload the processed graphs or converted sdf files for CASF2016 decoys_docking set?
from rtmscore.
The following are the scores of the poses in CASF-2016 docking set predicted by our models, and I think they are enough to show the performance of our methodology.
rtmscore1_casf2016_docking.tar.gz
rtmscore2_casf2016_docking.tar.gz
rtmscore3_casf2016_docking.tar.gz
from rtmscore.
Related Issues (19)
- error of create conda env HOT 3
- Could you provide raw data of pdbbind2020? HOT 1
- integrating w/ docking HOT 1
- sanity checking on new target HOT 40
- data preprocess script for training on new dataset HOT 7
- Some of the ligands in CASF core set cannot be read by RDKit successfully HOT 2
- Additive terms in MDN outputs HOT 2
- How should we preprocess .pdbqt files before using RTMScore? HOT 6
- Graph files on zenodo HOT 2
- Meaning of the distance threshold HOT 2
- casf对接和筛选能力 HOT 10
- Pretrained models - question HOT 2
- 环境问题 HOT 6
- RTMScore的score的打分如何查看?
- 使用新的口袋和配体测试Score为0 HOT 1
- The AUC values presented in Table 6 and Figure 6A seem to be inconsistent. HOT 2
- How to Batch Process RTMScore for Multiple Models in PDB and SDF Files
- Question about csaf2016_docking.py
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from rtmscore.