Uni Dock Versions Save

Uni-Dock: a GPU-accelerated molecular docking program

1.1.2

1 month ago

What's Changed

docs: remove unidock_ad4 in README by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/98
fix: ligandprep skip failed cases by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/99
Update version number in CMakeLists.txt by @ysyecust in https://github.com/dptech-corp/Uni-Dock/pull/101
Docs: add conda-forge install instructions by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/103
Docs: fix typo in conda-forge instructions by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/104
Docs: add introduction to uni-dock benchmarks by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/105
Fix path error in README.md by @ysyecust in https://github.com/dptech-corp/Uni-Dock/pull/108
build: add unidock_tools dependency in toml by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/110
fix:unidock pipeline one ligand failed case by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/116
[feature] unidock tools add required dependencies by @Hong-Rui in https://github.com/dptech-corp/Uni-Dock/pull/119
fix: env readd mgltools and remove tests using ad4 temporary by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/121
test: readd ad4 tests by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/122
fix: unidock pipeline ligand index list too long err by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/127
build: change docker build runner from github to self by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/128
feat: update ligand group method by @ysyecust in https://github.com/dptech-corp/Uni-Dock/pull/125

Full Changelog: https://github.com/dptech-corp/Uni-Dock/compare/1.1.1...1.1.2

1.1.1

3 months ago

What's Changed

fix: mcdock write same conf in confgen stage by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/79
Format code and remove unused code by @ysyecust in https://github.com/dptech-corp/Uni-Dock/pull/81
Test: use public image for testing unidock_tools by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/83
Refactor CMakeLists.txt by @wzf03 in https://github.com/dptech-corp/Uni-Dock/pull/80
Fix: array index out of range by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/86
fix:mcdock rigid docking; test:remove mcdock rmsd assert by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/87
Build: update conda build script for CUDA 12 and uni-dock subfolder by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/90
feat: unidock_pipeline add support for score_only and local_only; doc: update unidock perf png by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/91
doc: update unidock perf images by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/92
Build: disable sm_90 arch for forward compatibility on CUDA 11.2 by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/95
fix: unidock_pipeline read only one ligand for big sdf by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/96
Docs: add cuda toolkit requirement by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/97

New Contributors

@wzf03 made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/80

Full Changelog: https://github.com/dptech-corp/Uni-Dock/compare/1.1.0...1.1.1

1.1.0

4 months ago

What's Changed

Features

v1.1 by @ysyecust @dp-yuanyn @zhengh96 @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/77
- Templatize compute kernels
- Update docs, CI/CD pipeline, and Dockerfiles
unidock_tools support PDB-format protein file, support ligand file without hydrogen and 3D conf by @YNYuan in https://github.com/dptech-corp/Uni-Dock/pull/19
Hypnopump/rough edges by @hypnopump in https://github.com/dptech-corp/Uni-Dock/pull/22
sync torsion tree update from nashtools by @Hong-Rui in https://github.com/dptech-corp/Uni-Dock/pull/43
Warp parallel by @lucifer1004 in https://github.com/dptech-corp/Uni-Dock/pull/56
CUDA stream optimisation by @envidian in https://github.com/dptech-corp/Uni-Dock/pull/63
Feature/hbond by @ysyecust in https://github.com/dptech-corp/Uni-Dock/pull/64
[GPU setting] device id by @envidian in https://github.com/dptech-corp/Uni-Dock/pull/71
[paired_batch_size] Write score by @envidian in https://github.com/dptech-corp/Uni-Dock/pull/72
Update MAX_NUM_OF_RIGID_ values in SmallConfig, MediumConfig, and Lar… by @ysyecust in https://github.com/dptech-corp/Uni-Dock/pull/78

Bug Fixes

Fix warning by @ysyecust in https://github.com/dptech-corp/Uni-Dock/pull/17
remove obsolete debug info by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/16
Fix typo in logging by @lucifer1004 in https://github.com/dptech-corp/Uni-Dock/pull/36
Style/formatcode by @ysyecust in https://github.com/dptech-corp/Uni-Dock/pull/46
fix ligand_index option bug by @UR-Free in https://github.com/dptech-corp/Uni-Dock/pull/48
Minor fix for logical AND by @prabindh in https://github.com/dptech-corp/Uni-Dock/pull/49

Docs

Update docs for boost version requirement by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/18
Update FAQ in README.md for uni-dock by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/38
docs: update installing instructions by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/47
Update README.md by @baixiaokuang in https://github.com/dptech-corp/Uni-Dock/pull/52
Docs: Add Uni-Dock logo by @caic99 in https://github.com/dptech-corp/Uni-Dock/pull/68

CI/CD

cicd trigger in main by @YNYuan in https://github.com/dptech-corp/Uni-Dock/pull/26
unidock_tools ci by @YNYuan in https://github.com/dptech-corp/Uni-Dock/pull/24
fix ut by @dp-yuanyn in https://github.com/dptech-corp/Uni-Dock/pull/66

New Contributors

@ysyecust made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/17
@caic99 made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/16
@YNYuan made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/19
@UR-Free made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/20
@hypnopump made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/22
@lucifer1004 made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/36
@prabindh made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/49
@baixiaokuang made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/52
@envidian made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/63
@dp-yuanyn made their first contribution in https://github.com/dptech-corp/Uni-Dock/pull/66

Full Changelog: https://github.com/dptech-corp/Uni-Dock/commits/1.1.0

1.0.0

1 year ago

The executable of Uni-Dock using vina & vinardo scoring function unidock and ad4 scoring function unidock_ad4 is provided below. Use conda to install Uni-Dock: conda install -c https://conda.mlops.dp.tech/caic -c conda-forge unidock. An offline conda package is provided in the attachment: run conda install -c conda-forge unidock-1.0.0-5_5.tar.bz2 after downloading the file.