Update Readme Files

.github/CONTRIBUTING.md

@@ -11,7 +11,7 @@ Even better, you can submit a Pull Request with a patch.
 ## Feature requests
 
 We highly appreciate your contributions, and would like to help you crafting the changes and making contributions to the community.
-If you would like to implement a new feature, please **submit a feature requesting issue with a proposal for your work first**. 
+If you would like to implement a new feature, please **submit a feature requesting issue with a proposal for your work first**.
 This help fitting your ideas and work with the development road map well, coordinating our efforts, and avoiding duplication of work.
 
 ## Submitting a Pull Request
@@ -35,7 +35,7 @@ This help fitting your ideas and work with the development road map well, coordi
     ```
 
 5. On GitHub, create a pull request (PR) from your bug-fix branch targeting `dptech-corp/Uni-Dock`.
- 
+
 6. After your pull request is merged, you can safely delete your branch and sync the changes from the main (upstream) repository:
 
 - Delete the remote branch on GitHub either [through the GitHub web UI](https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/managing-branches-in-your-repository/deleting-and-restoring-branches-in-a-pull-request#deleting-a-branch-used-for-a-pull-request) or your local shell as follows:

README.md

@@ -3,6 +3,7 @@
 <picture><source media="(prefers-color-scheme: dark)" srcset="./unidock/assets/logo-dark.svg"><source media="(prefers-color-scheme: light)" srcset="./unidock/assets/logo.svg"><img alt="Uni-Dock logo" src="./unidock/assets/logo.svg"></picture>
 
 [![DeepModeling](https://img.shields.io/badge/DeepModeling-Incubating_Project-blue)](https://github.com/deepmodeling)
+
 ## Introduction
 
 **Uni-Dock** is a GPU-accelerated molecular docking program developed by DP Technology.
@@ -14,6 +15,7 @@ The [paper](https://pubs.acs.org/doi/10.1021/acs.jctc.2c01145) has been accepted
 Check this [subfolder](./unidock/) for instructions on installing Uni-Dock.
 
 **Uni-Dock** joins the DeepModeling community, a community devoted of AI for science, as an incubating level project. To learn more about the DeepModeling community, see the [introduction of community](https://github.com/deepmodeling/community).
+
 ## UniDockTools
 
 **UniDockTools** is a python package developed to handle the inputs and outputs of Uni-Dock.

unidock/README.md

@@ -9,7 +9,13 @@ The [paper](https://pubs.acs.org/doi/10.1021/acs.jctc.2c01145) has been accepted
 
 ## Changelog
 
-- 2023-08-14: Add `unidock_tools` to support SDF format input for vina and vinardo scoring functions.
+Major changes are documented. For the detailed changes, please refer to the commit history.
+
+### v1.1
+
+- Optimize 1:1 ligand docking.
+- Optimize Monte-Carlo simulation speed.
+- Generate compute kernels for various ligands sizes.
 
 ## License
 
@@ -57,7 +63,7 @@ The performance is not guaranteed on legacy GPU models. To build Uni-Dock with a
                            # Otherwise, prepend the building directory to your `PATH` environment variable.
      ```
 
-code foramt
+To format codes if changes are made:
 
 ```shell
 cd ./build/
@@ -195,9 +201,13 @@ python run_dock.py
 
 If you want to use search mode presets, specify the parameter `search_mode` in `config.json` and delete `nt` and `ns` in `config.json`.
 
-## Bug Report
+## Contributing
+
+We warmly welcome contributions from the open-source community. Your bug reports, feature requests, and pull requests helps Uni-Dock improve.
+
+Please submit bug reports and feature requests to the Github [issue tracker](https://github.com/dptech-corp/Uni-Dock/issues/new/choose).
 
-Please report bugs to [Issues](https://github.com/dptech-corp/Uni-Dock/issues) page.
+If you would like to improve the codes, please refer to the [contributing guide](../.github/CONTRIBUTING.md) for details.
 
 ## Ackowledgement
 

unidock_tools/README.md

@@ -50,7 +50,7 @@ By installing UniDockTools, you have obtained an executable file called **Unidoc
 
 ## Use ligands structure as bias
 
-`Unidock --receptor receptor.pdbqt --gpu_batch ligand1.sdf ligand2.sdf --reference ref1.sdf ref2.sdf --scoring gnina --center_x 9 --center_y -5  --center_z -5 --size_x 20  --size_y 20 --size_z 20 --search_mode balance  --dir . `
+`Unidock --receptor receptor.pdbqt --gpu_batch ligand1.sdf ligand2.sdf --reference ref1.sdf ref2.sdf --scoring gnina --center_x 9 --center_y -5  --center_z -5 --size_x 20  --size_y 20 --size_z 20 --search_mode balance  --dir .`
 
 ## Other usage