diff --git a/documentation/prankweb.open-api.yaml b/documentation/prankweb.open-api.yaml
index 8c666d8..b4eb66d 100644
--- a/documentation/prankweb.open-api.yaml
+++ b/documentation/prankweb.open-api.yaml
@@ -2,13 +2,13 @@ openapi: 3.0.2
 
 info:
   title: Prankweb API
-  version: 1.0.1
+  version: 1.1.0
 
 servers:
   - url: https://prankweb.cz/api/v2/
 
 paths:
-  /predictions/{database}/{task}/:
+  /prediction/{database}/{prediction_task_id}:
     get:
       parameters:
         - in: path
@@ -17,18 +17,18 @@ paths:
           schema:
             $ref: '#/components/schemas/DatabaseId'
         - in: path
-          name: task
+          name: prediction_task_id
           required: true
           schema:
-            $ref: '#/components/schemas/TaskId'
+            $ref: '#/components/schemas/PredictionTaskId'
       responses:
         '200':
           description: Success
           content:
             application/json:
               schema:
-                $ref: '#/components/schemas/Task'
-  /predictions/{database}/{task}/log:
+                $ref: '#/components/schemas/PredictionTask'
+  /prediction/{database}/{prediction_task_id}/log:
     get:
       parameters:
         - in: path
@@ -37,10 +37,10 @@ paths:
           schema:
             $ref: '#/components/schemas/DatabaseId'
         - in: path
-          name: task
+          name: prediction_task_id
           required: true
           schema:
-            $ref: '#/components/schemas/TaskId'
+            $ref: '#/components/schemas/PredictionTaskId'
       responses:
         '200':
           description: Success
@@ -48,7 +48,7 @@ paths:
             text/plain:
               schema:
                 type: string
-  /predictions/{database}/{task}/public/prediction.json:
+  /prediction/{database}/{prediction_task_id}/public/prediction.json:
     get:
       parameters:
         - in: path
@@ -57,10 +57,10 @@ paths:
           schema:
             $ref: '#/components/schemas/DatabaseId'
         - in: path
-          name: task
+          name: prediction_task_id
           required: true
           schema:
-            $ref: '#/components/schemas/TaskId'
+            $ref: '#/components/schemas/PredictionTaskId'
       responses:
         '200':
           description: Success
@@ -68,7 +68,7 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/Prediction'
-  /docking/{database}/{task}/tasks:
+  /docking/{database}/{prediction_task_id}/tasks:
     get:
       parameters:
         - in: path
@@ -77,10 +77,10 @@ paths:
           schema:
             $ref: '#/components/schemas/DatabaseId'
         - in: path
-          name: task
+          name: prediction_task_id
           required: true
           schema:
-            $ref: '#/components/schemas/TaskId'
+            $ref: '#/components/schemas/PredictionTaskId'
       responses:
         '200':
           description: Success
@@ -88,8 +88,8 @@ paths:
             application/json:
               schema:
                 $ref: '#/components/schemas/DockingTaskList'
-  /docking/{database}/{task}/public/result.json:
-    post:
+  /docking/{database}/{prediction_task_id}/{docking_task_hash}/public/result.json:
+    get:
       parameters:
         - in: path
           name: database
@@ -97,17 +97,15 @@ paths:
           schema:
             $ref: '#/components/schemas/DatabaseId'
         - in: path
-          name: task
+          name: prediction_task_id
           required: true
           schema:
-            $ref: '#/components/schemas/TaskId'
-      requestBody:
-        description: The request needs to contain the hash of the docking task.
-        required: true
-        content:
-          application/json:
-            schema:
-              $ref: '#/components/schemas/DockingRequest'
+            $ref: '#/components/schemas/PredictionTaskId'
+        - in: path
+          name: docking_task_hash
+          required: true
+          schema:
+            type: string
       responses:
         '200':
           description: Success
@@ -120,13 +118,15 @@ components:
   schemas:
     DatabaseId:
       type : string
-    TaskId:
+    PredictionTaskId:
       type : string
-    Task:
+    PredictionTask:
       type: object
       properties:
         id:
           type: string
+        database:
+          type: string
         created:
           type: string
           format: date-time
@@ -136,6 +136,8 @@ components:
         status:
           type: string
           enum: ['queued', 'running', 'failed', 'successful']
+        metadata:
+          type: object
     Prediction:
       type: object
       properties:
@@ -223,11 +225,6 @@ components:
                     type: string
                   pocket:
                     type: string
-    DockingRequest:
-      type: object
-      properties:
-        hash:
-          type: string
     DockingResponse:
       type: array
       items:
diff --git a/executor-docking/run_task.py b/executor-docking/run_task.py
index 67297c1..cd50cb4 100644
--- a/executor-docking/run_task.py
+++ b/executor-docking/run_task.py
@@ -142,7 +142,7 @@ def execute_directory_task(docking_directory: str, taskId: int):
         return
 
     #parse the prediction file and do some calculations - in this case just counting the number of residues per pocket
-    #API is /docking/<database_name>/<prediction_name>/public/<file_name>
+    #API is /docking/<database_name>/<prediction_name>/<hash>/public/<file_name>
     #split docking_directory to get database_name and prediction_name
     result = []
     database_name = docking_directory.split("/")[4]
@@ -151,7 +151,7 @@ def execute_directory_task(docking_directory: str, taskId: int):
     else:
         prediction_name = docking_directory.split("/")[6]
 
-    result_url = "./api/v2/docking/" + database_name + "/" + prediction_name + "/public/results.zip"
+    result_url = "./api/v2/docking/" + database_name + "/" + prediction_name + "/" + status["tasks"][taskId]["initialData"]["hash"] + "/public/results.zip"
     result.append({
         "url": result_url
     })
diff --git a/frontend/client/index/index.html b/frontend/client/index/index.html
index b5045dc..2bc13ad 100644
--- a/frontend/client/index/index.html
+++ b/frontend/client/index/index.html
@@ -40,7 +40,7 @@ <h1 class="text-center">
                             <input class="form-check-input" type="radio" id="input-uniprot" value="input-uniprot"
                                 name="input-type">
                             <label class="form-check-label" for="input-uniprot">
-                                Predicted structure
+                                AlphaFold structure
                             </label>
                         </div>
                     </div>
@@ -58,6 +58,15 @@ <h1 class="text-center">
                                 Use original structure
                             </label>
                         </div>
+                        <div class="form-check">
+                            <input class="form-check-input" type="checkbox" id="conservation-pdb"
+                                title="If checked, a model that exploits conservation will be used to classify protein binding sites."
+                                checked="checked">
+                            <label class="form-check-label" for="conservation-pdb">
+                                Use
+                                <a href="./help#conservation" target="_blank">conservation</a>
+                            </label>
+                        </div>
                         <div id="pdb-chains" style="display: none">
                             <input id="pdb-chains-store" style="display: none">
                             <div id="pdb-chains-label">
@@ -80,6 +89,27 @@ <h1 class="text-center">
                             <input type="text" class="form-control" id="user-file-chains" name="userFileChains"
                                 placeholder="A,B" title="Optional. Comma separated list of chains to analyze.">
                         </div>
+                        <div>
+                            <input type="radio" name="user-input-model" id="user-input-model-1" value="default"
+                                title="If selected, a default prediction model will be used.">
+                            <label for="user-input-model-1" class="form-label">Default prediction model</label><br>
+
+                            <input type="radio" name="user-input-model" id="user-input-model-2" value="conservation_hmm"
+                                checked="checked"
+                                title="If selected, a default prediction model with conservation will be used.">
+                            <label for="user-input-model-2" class="form-label">Default model with
+                                <a href="./help#conservation" target="_blank">conservation</a></label><br>
+
+                            <input type="radio" name="user-input-model" id="user-input-model-3" value="alphafold"
+                                title="If selected, an AlphaFold prediction model will be used.">
+                            <label for="user-input-model-3" class="form-label">AlphaFold model</label><br>
+
+                            <input type="radio" name="user-input-model" id="user-input-model-4"
+                                value="alphafold_conservation_hmm"
+                                title="If selected, an AlphaFold prediction model with conservation will be used.">
+                            <label for="user-input-model-4" class="form-label">AlphaFold model with
+                                <a href="./help#conservation" target="_blank">conservation</a></label><br>
+                        </div>
                     </div>
                     <div id="input-uniprot-block" style="display: none">
                         <div class="mb-3">
@@ -87,32 +117,21 @@ <h1 class="text-center">
                             <input type="text" class="form-control" id="uniprot-code" name="uniprotCode"
                                 placeholder="Q5VSL9" title="PrankWeb will use AlphaFold predicted structure.">
                         </div>
-                    </div>
-                </div>
-                <div class="card-footer" id="message" style="display: none">
-                    <!-- Messages are here. -->
-                </div>
-            </div>
-
-            <div class="card" id="conservation-block">
-                <div class="card-header">
-                    Conservation
-                </div>
-                <div class="card-body">
-                    <div>
-                        <div class="form-check-inline">
-                            <input class="form-check-input" type="checkbox" id="conservation"
+                        <div class="form-check">
+                            <input class="form-check-input" type="checkbox" id="conservation-uniprot"
                                 title="If checked, a model that exploits conservation will be used to classify protein binding sites."
                                 checked="checked">
-                            <label class="form-check-label" for="conservation">
+                            <label class="form-check-label" for="conservation-uniprot">
                                 Use
                                 <a href="./help#conservation" target="_blank">conservation</a>
                             </label>
                         </div>
                     </div>
                 </div>
+                <div class="card-footer" id="message" style="display: none">
+                    <!-- Messages are here. -->
+                </div>
             </div>
-
             <div>
                 <button type="submit" class="btn btn-primary float-md-end" id="submit-button">
                     Submit
diff --git a/frontend/client/index/index.js b/frontend/client/index/index.js
index c805587..c67d609 100644
--- a/frontend/client/index/index.js
+++ b/frontend/client/index/index.js
@@ -29,7 +29,8 @@ class View {
     this.uniprotSection = document.getElementById("input-uniprot-block");
     this.uniprotCode = document.getElementById("uniprot-code");
     this.message = document.getElementById("message");
-    this.conservation = document.getElementById("conservation");
+    this.conservationPdb = document.getElementById("conservation-pdb");
+    this.conservationUniprot = document.getElementById("conservation-uniprot");
     this.submit = document.getElementById("submit-button");
     //
     this.controller = null;
@@ -40,13 +41,13 @@ class View {
     //
     this.pdbInput.addEventListener(
       "change",
-      () => controller.onInputChange(View.PDB_VIEW))
+      () => controller.onInputChange(View.PDB_VIEW));
     this.userInput.addEventListener(
       "change",
-      () => controller.onInputChange(View.USER_VIEW))
+      () => controller.onInputChange(View.USER_VIEW));
     this.uniprotInput.addEventListener(
       "change",
-      () => controller.onInputChange(View.UNIPROT_VIEW))
+      () => controller.onInputChange(View.UNIPROT_VIEW));
     this.pdbSealStructure.addEventListener(
       "change",
       (event) => controller.onPdbSealedChange(event.target.checked));
@@ -209,7 +210,7 @@ class View {
     const label = document.createElement("label");
     label.appendChild(input);
     label.appendChild(document.createTextNode(
-      `\u00A0${chain}\u00A0\u00A0`))
+      `\u00A0${chain}\u00A0\u00A0`));
     label.className = "form-check-label";
     return label;
   }
@@ -262,9 +263,22 @@ class View {
   }
 
   getConservation() {
-    return this.conservation.checked;
+    // this does not apply to user uploaded files, those are treated differently as the user
+    // selects the model directly
+    switch (this.getInputSection()) {
+      case View.PDB_VIEW:
+        return this.conservationPdb.checked;
+      case View.UNIPROT_VIEW:
+        return this.conservationUniprot.checked;
+      default:
+        return false;
+    }
   }
 
+  getModelUserUpload() {
+    const selectedModel = document.querySelector('input[name="user-input-model"]:checked');
+    return selectedModel.value;
+  }
 }
 
 class Controller {
@@ -338,7 +352,7 @@ class Controller {
       return true;
     } else {
       if (chains.count > 0) {
-        this.view.setMessage("At least one chain must be selected.")
+        this.view.setMessage("At least one chain must be selected.");
       }
       return false;
     }
@@ -400,7 +414,7 @@ class Controller {
     if (!this.validatePdbCode(code)) {
       return;
     }
-    await this.fetchChainsForPdbCode(code, false)
+    await this.fetchChainsForPdbCode(code, false);
     if (code !== this.view.getPdbCode()) {
       // User changed the code in a meanwhile.
       return;
@@ -454,8 +468,7 @@ class Submit {
   submitUserFile(view) {
     const structure = view.getUserFileObject();
     const chains = view.getUserChains();
-    const conservation = view.getConservation();
-    //
+    const model = view.getModelUserUpload();
     const formData = new FormData();
     formData.append(
       "structure", structure, structure.name);
@@ -464,14 +477,14 @@ class Submit {
       this.asJsonBlob({
         "chains": chains,
         "structure-sealed": chains.length === 0,
-        "compute-conservation": conservation,
+        "prediction-model": model,
       }),
       "configuration.json");
     this.sendPostRequest("./api/v2/prediction/v3-user-upload", formData);
   }
 
   asJsonBlob(content) {
-    return new Blob([JSON.stringify(content)], {"type": "text/json"});
+    return new Blob([JSON.stringify(content)], { "type": "text/json" });
   }
 
   sendPostRequest(url, data) {
@@ -493,9 +506,9 @@ class Submit {
     const conservation = view.getConservation();
     let url;
     if (conservation) {
-      url = this.createUrl("v3-alphafold-conservation-hmm", code, [])
+      url = this.createUrl("v3-alphafold-conservation-hmm", code, []);
     } else {
-      url = this.createUrl("v3-alphafold", code, [])
+      url = this.createUrl("v3-alphafold", code, []);
     }
     window.location.href = url;
   }
diff --git a/frontend/client/tasks/server-docking-task.tsx b/frontend/client/tasks/server-docking-task.tsx
index 3b80184..eecb388 100644
--- a/frontend/client/tasks/server-docking-task.tsx
+++ b/frontend/client/tasks/server-docking-task.tsx
@@ -115,19 +115,8 @@ export async function dockingHash(pocket: string, smiles: string, exhaustiveness
  * @returns void
 */
 export async function downloadDockingResult(smiles: string, fileURL: string, pocket: string, exhaustiveness: string) {
-    const hash = await dockingHash(pocket, smiles, exhaustiveness);
-
     // https://stackoverflow.com/questions/50694881/how-to-download-file-in-react-js
-    fetch(fileURL, {
-        method: 'POST',
-        headers: {
-            'Accept': 'application/json',
-            'Content-Type': 'application/json'
-        },
-        body: JSON.stringify({
-            "hash": hash
-        })
-    })
+    fetch(fileURL)
         .then((response) => response.blob())
         .then((blob) => {
             // Create blob link to download
@@ -181,16 +170,8 @@ export async function pollForDockingTask(predictionInfo: PredictionInfo) {
                     //download the computed data
                     if (individualTask.status === "successful") {
                         const hash = await dockingHash(task.pocket.toString(), individualTask.initialData.smiles, individualTask.initialData.exhaustiveness);
-                        const data = await fetch(`./api/v2/docking/${predictionInfo.database}/${predictionInfo.id}/public/result.json`, {
-                            method: 'POST',
-                            headers: {
-                                'Accept': 'application/json',
-                                'Content-Type': 'application/json'
-                            },
-                            body: JSON.stringify({
-                                "hash": hash
-                            })
-                        }).then(res => res.json()).catch(err => console.log(err));
+                        const data = await fetch(`./api/v2/docking/${predictionInfo.database}/${predictionInfo.id}/${hash}/public/result.json`)
+                            .then(res => res.json()).catch(err => console.log(err));
                         tasks[i].responseData = data;
                     }
 
diff --git a/web-server/src/api_v2.py b/web-server/src/api_v2.py
index b47103f..67c4ca2 100644
--- a/web-server/src/api_v2.py
+++ b/web-server/src/api_v2.py
@@ -81,19 +81,13 @@ def route_post_docking_file(database_name: str, prediction_name: str):
     return dt.post_task(prediction_name.upper(), data)
 
 @api_v2.route(
-    "/docking/<database_name>/<prediction_name>/public/<file_name>",
-    methods=["POST"]
+    "/docking/<database_name>/<prediction_name>/<task_hash>/public/<file_name>",
+    methods=["GET"]
 )
-def route_get_docking_file_with_param(database_name: str, prediction_name: str, file_name: str):
-    """Get a docking file from the server.
-    Request body should be a JSON object with the following fields:
-    - hash: str (a hash of the ligand with parameters)"""
-    data = request.get_json(force=True)
-    param = data.get("hash", None)
-    if data is None or param is None:
-        return "", 404
+def route_get_docking_file_with_param(database_name: str, prediction_name: str, task_hash: str, file_name: str):
+    """Get a docking file from the server."""
     dt = DockingTask(database_name=database_name)
-    return dt.get_file_with_post_param(prediction_name.upper(), file_name, param)
+    return dt.get_file_with_post_param(prediction_name.upper(), file_name, task_hash)
 
 @api_v2.route(
     "/docking/<database_name>/<prediction_name>/tasks",
diff --git a/web-server/src/database_v3.py b/web-server/src/database_v3.py
index a5993d1..f8d0bd3 100644
--- a/web-server/src/database_v3.py
+++ b/web-server/src/database_v3.py
@@ -303,14 +303,21 @@ def _configuration_to_prediction(
         chain.upper()
         for chain in user_configuration.get("chains", [])
     })
-    conservation = user_configuration.get("compute-conservation", False)
+
+    allowed_models = ["default", "alphafold", "conservation_hmm", "alphafold_conservation_hmm"]
+    model = user_configuration.get("prediction-model", "default")
+    if model not in allowed_models:
+        model = "default"
+
+    conservation = "conservation" in model
+
     return Prediction(
         directory=os.path.join(root_directory, identifier),
         identifier=identifier,
         database=database,
         chains=chains,
         structure_sealed=user_configuration.get("structure-sealed", False),
-        p2rank_configuration="conservation_hmm" if conservation else "default",
+        p2rank_configuration=model,
         structure_file=structure_file,
         conservation="hmm" if conservation else "none",
         metadata={},