rdk
diff --git a/‎README.md‎
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diff --git a/‎misc/tutorials/aa-mapping.md‎ ‎documentation/aa-mapping.md‎misc/tutorials/aa-mapping.md renamed to documentation/aa-mapping.md b/‎misc/tutorials/aa-mapping.md‎ ‎documentation/aa-mapping.md‎misc/tutorials/aa-mapping.md renamed to documentation/aa-mapping.md
diff --git a/‎…ev/ions/balancing-01-ploop-1_DCA_4_0.png‎ ‎…ev/ions/balancing-01-ploop-1_DCA_4_0.png‎misc/tutorials/dev/ions/balancing-01-ploop-1_DCA_4_0.png renamed to documentation/dev/ions/balancing-01-ploop-1_DCA_4_0.png b/‎…ev/ions/balancing-01-ploop-1_DCA_4_0.png‎ ‎…ev/ions/balancing-01-ploop-1_DCA_4_0.png‎misc/tutorials/dev/ions/balancing-01-ploop-1_DCA_4_0.png renamed to documentation/dev/ions/balancing-01-ploop-1_DCA_4_0.png
diff --git a/‎…ons-prediction-method-development-log.md‎ ‎…ons-prediction-method-development-log.md‎misc/tutorials/dev/ions/ions-prediction-method-development-log.md renamed to documentation/dev/ions/ions-prediction-method-development-log.md b/‎…ons-prediction-method-development-log.md‎ ‎…ons-prediction-method-development-log.md‎misc/tutorials/dev/ions/ions-prediction-method-development-log.md renamed to documentation/dev/ions/ions-prediction-method-development-log.md
diff --git a/‎misc/tutorials/export-points.md‎ ‎documentation/export-points.md‎misc/tutorials/export-points.md renamed to documentation/export-points.md b/‎misc/tutorials/export-points.md‎ ‎documentation/export-points.md‎misc/tutorials/export-points.md renamed to documentation/export-points.md
diff --git a/‎misc/tutorials/feature-setup.md‎ ‎documentation/feature-setup.md‎misc/tutorials/feature-setup.md renamed to documentation/feature-setup.md b/‎misc/tutorials/feature-setup.md‎ ‎documentation/feature-setup.md‎misc/tutorials/feature-setup.md renamed to documentation/feature-setup.md
diff --git a/‎misc/tutorials/hidden-commands.md‎ ‎documentation/hidden-commands.md‎misc/tutorials/hidden-commands.md renamed to documentation/hidden-commands.md b/‎misc/tutorials/hidden-commands.md‎ ‎documentation/hidden-commands.md‎misc/tutorials/hidden-commands.md renamed to documentation/hidden-commands.md
diff --git a/‎…/hyperparameter-optimization-tutorial.md‎ ‎…/hyperparameter-optimization-tutorial.md‎misc/tutorials/hyperparameter-optimization-tutorial.md renamed to documentation/hyperparameter-optimization-tutorial.md b/‎…/hyperparameter-optimization-tutorial.md‎ ‎…/hyperparameter-optimization-tutorial.md‎misc/tutorials/hyperparameter-optimization-tutorial.md renamed to documentation/hyperparameter-optimization-tutorial.md
diff --git a/‎…ls/img/feature-tutorial/DCA_4_0_cons.png‎ ‎…on/img/feature-tutorial/DCA_4_0_cons.png‎misc/tutorials/img/feature-tutorial/DCA_4_0_cons.png renamed to documentation/img/feature-tutorial/DCA_4_0_cons.png b/‎…ls/img/feature-tutorial/DCA_4_0_cons.png‎ ‎…on/img/feature-tutorial/DCA_4_0_cons.png‎misc/tutorials/img/feature-tutorial/DCA_4_0_cons.png renamed to documentation/img/feature-tutorial/DCA_4_0_cons.png
diff --git a/‎…img/feature-tutorial/DCA_4_0_default.png‎ ‎…img/feature-tutorial/DCA_4_0_default.png‎misc/tutorials/img/feature-tutorial/DCA_4_0_default.png renamed to documentation/img/feature-tutorial/DCA_4_0_default.png b/‎…img/feature-tutorial/DCA_4_0_default.png‎ ‎…img/feature-tutorial/DCA_4_0_default.png‎misc/tutorials/img/feature-tutorial/DCA_4_0_default.png renamed to documentation/img/feature-tutorial/DCA_4_0_default.png
@@ -147,15 +147,17 @@ parameters see [Params.groovy](https://github.com/rdk/p2rank/blob/develop/src/ma
 ### Rescoring (PRANK algorithm)
 
 In addition to predicting new ligand binding sites, 
-P2Rank is also able to rescore pockets predicted by other methods 
-(Fpocket, 
-ConCavity, 
-SiteHound, 
-MetaPocket2, 
-LISE, 
+P2Rank is also able to rescore pockets predicted by other methods
+(Fpocket,
+Pocketeer,
+ConCavity,
+SiteHound,
+MetaPocket2,
+LISE,
 DeepSite,
 and PUResNetV2.0
 are supported at the moment).
+See [rescoring documentation](documentation/rescoring.md) for details.
 
 Rescoring output:
 * `{protein_file}_rescored.csv`: list of pockets sorted by the new score
@@ -219,7 +221,7 @@ You can now run the program using:
 distro/prank       # standard mode that is run in production
 ./prank.sh         # development/training mode 
 ``` 
-To use `./prank.sh` (development/training mode) first you need to copy and edit `misc/locval-env.sh` into repo root directory (see [training tutorial](https://github.com/rdk/p2rank/blob/develop/misc/tutorials/training-tutorial.md#preparing-the-environment)).
+To use `./prank.sh` (development/training mode) first you need to copy and edit `misc/local-env.sh` into repo root directory (see [training tutorial](https://github.com/rdk/p2rank/blob/develop/documentation/training-tutorial.md#preparing-the-environment)).
 
 ## ⚖️ Comparison with Fpocket