diff --git a/README.md b/README.md index d383416016a119630be736fb56919e7380d3b2f2..b520e1b7ea74f8f8ca6b5eafdc9c404b924ca294 100644 --- a/README.md +++ b/README.md @@ -8,14 +8,19 @@ released by DeepMind in July 2021. After DeepMind released AlphaFold-Multimer [v ## Updates and Features -#### Version 1.2 (2022-02-19) +#### Version 1.2.2 (2022-03-10) -- Added support to AF-Multimer neural network models in both paired and unpaired MSAs modes +- Minor bug fix +- Support AF-Multimer v2 neural network models (AF v2.2.0) + +#### Version 1.2.0 (2022-02-19) + +- Added support to AF-Multimer neural network models (AF v2.1.0) in both paired and unpaired MSAs modes - Domain cropping pre-generated full monomer features (in unpaired MSAs mode only) - Checkpoint option for model inference - Refactored code -#### Version 1.0 (2021-11-09) +#### Version 1.0.0 (2021-11-09) - Predicting structural models of a protein complex - Paired MSAs not required for complex modeling diff --git a/example/README.md b/example/README.md index 060d6b19e35ae5ca4cd2d7f33443dbf029e09fc5..907332d6c6f0fb32f1486c2ae42b602bdac4380d 100644 --- a/example/README.md +++ b/example/README.md @@ -4,7 +4,7 @@ The main script for the example is the shell script `run_af2comp.sh`. First, use a text editor to open this script, and modify it to provide the correct python environment of AlphaFold, if not already loaded. Then, provide the correct path to the parameter files of AlphaFold neural network -models. In AF's releases, these models are named as `model_x_ptm.npz` or `model_x_multimer.npz`. Note that AlphaFold-Multimer's models (version 2.1.1) are not required if you only wish to run the original monomer DL models. +models. In AF's releases, these models are named as `params_model_x_ptm.npz` (AF version 2.0.x), `params_model_x_multimer.npz` (AF version 2.1.x), `params_model_x_multimer_v2.npz` (AF version 2.2.x). Note that AlphaFold-Multimer's models are not required if you only wish to run the original monomer DL models. Run the script with the command, ```sh diff --git a/example/run_af2comp.sh b/example/run_af2comp.sh index e228caa6c1ce2d702be91b2b4a81b5c5ac17f5c5..ccda7653602291000c4e8d9868b0c475ce5c6b09 100755 --- a/example/run_af2comp.sh +++ b/example/run_af2comp.sh @@ -16,10 +16,12 @@ out_dir=af2c_mod # model output directory, $out_dir/$target ### This preset defined the number of recycles, ensembles, MSA cluster sizes (for monomer_ptm models) preset=super # up to 20 recycles, 1 ensemble. -### Choose neural network model(s) from ['model_1/2/3/4/5_multimer' and 'model_1/2/3/4/5_ptm'] +### Choose neural network model(s) from ['model_1/2/3/4/5_multimer', 'model_1/2/3/4/5_multimer_v2', or 'model_1/2/3/4/5_ptm'] # Using AF2 multimer model released in version 2.1.1 #model=model_1_multimer,model_2_multime,rmodel_3_multimer,model_4_multimer,model_5_multimer -model=model_1_multimer,model_2_multimer +# Using AF2 multimer model released in version 2.2.0 +#model=model_1_multimer_v2,model_2_multime_v2,rmodel_3_multimer_v2,model_4_multimer_v2,model_5_multimer_v2 +model=model_1_multimer_v2,model_2_multimer_v2 # Using AF2 monomer_ptm model released in version 2.0.1 #model=model_1_ptm,model_2_ptm,model_3_ptm,model_4_ptm,model_5_ptm