b2bTools 3.0.7b2__tar.gz → 3.0.8__tar.gz

{b2bTools-3.0.7b2 → b2btools-3.0.8}/PKG-INFO

@@ -1,15 +1,15 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: b2bTools
-Version: 3.0.7b2
+Version: 3.0.8
 Summary: bio2Byte software suite to predict protein biophysical properties from their amino-acid sequences
 Home-page: https://bio2byte.be
 Author: Wim Vranken
 Author-email: Wim.Vranken@vub.be
-Maintainer: Jose Gavalda-Garcia, Adrian Diaz, Wim Vranken
-Maintainer-email: jose.gavalda.garcia@vub.be, adrian.diaz@vub.be, wim.vranken@vub.be
+Maintainer: Adrián Díaz, Sophie-Luise Heidig, Wim Vranken
+Maintainer-email: bio2byte@vub.be
 License: OSI Approved :: GNU General Public License v3 (GPLv3)
 Project-URL: Documentation, https://bio2byte.be/b2btools/package-documentation
-Project-URL: HTML interface, https://bio2byte.be/b2btools
+Project-URL: HTML interface, https://bio2byte.be/online_predictors
 Keywords: bio2byte,b2bTools,biology,bioinformatics,bio-informatics,fasta,proteins,protein-folding
 Classifier: Natural Language :: English
 Classifier: Programming Language :: Python :: 3.7
@@ -29,74 +29,74 @@ Classifier: Intended Audience :: Education
 Classifier: Development Status :: 5 - Production/Stable
 Requires-Python: >=3.7, <3.13
 Description-Content-Type: text/markdown
-Requires-Dist: biopython~=1.81; python_version == "3.7"
-Requires-Dist: Cython~=0.29.37; python_version == "3.7"
-Requires-Dist: matplotlib~=3.5.3; python_version == "3.7"
+Requires-Dist: biopython~=1.79; python_version == "3.7"
+Requires-Dist: matplotlib~=3.5; python_version == "3.7"
 Requires-Dist: numpy~=1.21; python_version == "3.7"
 Requires-Dist: pandas~=1.1; python_version == "3.7"
-Requires-Dist: pomegranate~=0.14; python_version == "3.7"
 Requires-Dist: requests~=2.0; python_version == "3.7"
 Requires-Dist: scikit-learn~=1.0.2; python_version == "3.7"
-Requires-Dist: scipy==1.7.3; python_version == "3.7"
-Requires-Dist: torch==1.13.1; python_version == "3.7"
-Requires-Dist: torchvision==0.14.1; python_version == "3.7"
+Requires-Dist: scipy~=1.7.3; python_version == "3.7"
+Requires-Dist: torch~=1.13.0; python_version == "3.7"
 Requires-Dist: urllib3~=1.26.6; python_version == "3.7"
 Requires-Dist: biopython~=1.81; python_version == "3.8"
-Requires-Dist: Cython~=0.29.37; python_version == "3.8"
-Requires-Dist: matplotlib~=3.5.3; python_version == "3.8"
+Requires-Dist: matplotlib~=3.5; python_version == "3.8"
 Requires-Dist: numpy~=1.24; python_version == "3.8"
-Requires-Dist: pandas~=1.1; python_version == "3.8"
-Requires-Dist: pomegranate~=0.14; python_version == "3.8"
+Requires-Dist: pandas<2,~=1.1; python_version == "3.8"
 Requires-Dist: requests~=2.0; python_version == "3.8"
 Requires-Dist: scikit-learn~=1.0.2; python_version == "3.8"
-Requires-Dist: scipy==1.10.1; python_version == "3.8"
-Requires-Dist: torch==1.13.1; python_version == "3.8"
-Requires-Dist: torchvision==0.14.1; python_version == "3.8"
-Requires-Dist: urllib3~=1.26.6; python_version == "3.8"
+Requires-Dist: scipy~=1.10.1; python_version == "3.8"
+Requires-Dist: torch~=1.13; python_version == "3.8"
+Requires-Dist: urllib3~=1.26; python_version == "3.8"
 Requires-Dist: biopython~=1.81; python_version == "3.9"
-Requires-Dist: Cython~=0.29.37; python_version == "3.9"
-Requires-Dist: matplotlib~=3.5.3; python_version == "3.9"
+Requires-Dist: matplotlib~=3.9.4; python_version == "3.9"
 Requires-Dist: numpy~=1.24; python_version == "3.9"
-Requires-Dist: pandas~=1.1; python_version == "3.9"
-Requires-Dist: pomegranate~=0.14; python_version == "3.9"
+Requires-Dist: pandas<2,~=1.1; python_version == "3.9"
 Requires-Dist: requests~=2.0; python_version == "3.9"
 Requires-Dist: scikit-learn~=1.0.2; python_version == "3.9"
-Requires-Dist: scipy==1.10.1; python_version == "3.9"
-Requires-Dist: torch==1.13.1; python_version == "3.9"
-Requires-Dist: torchvision==0.14.1; python_version == "3.9"
-Requires-Dist: urllib3~=1.26.6; python_version == "3.9"
+Requires-Dist: scipy~=1.10.1; python_version == "3.9"
+Requires-Dist: torch~=1.13; python_version == "3.9"
+Requires-Dist: urllib3~=1.26; python_version == "3.9"
 Requires-Dist: biopython~=1.83; python_version == "3.10"
-Requires-Dist: Cython~=0.29.37; python_version == "3.10"
-Requires-Dist: matplotlib~=3.5.3; python_version == "3.10"
+Requires-Dist: matplotlib~=3.5; python_version == "3.10"
 Requires-Dist: numpy~=1.26.4; python_version == "3.10"
-Requires-Dist: pandas~=1.5.3; python_version == "3.10"
-Requires-Dist: pomegranate~=0.14; python_version == "3.10"
-Requires-Dist: requests~=2.31.0; python_version == "3.10"
+Requires-Dist: pandas~=2.0; python_version == "3.10"
+Requires-Dist: requests~=2.31; python_version == "3.10"
 Requires-Dist: scikit-learn~=1.0.2; python_version == "3.10"
 Requires-Dist: scipy~=1.12.0; python_version == "3.10"
-Requires-Dist: torch~=1.13.1; python_version == "3.10"
-Requires-Dist: torchvision~=0.14.1; python_version == "3.10"
-Requires-Dist: urllib3~=1.26.6; python_version == "3.10"
+Requires-Dist: torch~=1.13; python_version == "3.10"
+Requires-Dist: urllib3~=1.26; python_version == "3.10"
 Requires-Dist: biopython~=1.83; python_version == "3.11"
-Requires-Dist: matplotlib~=3.8.3; python_version == "3.11"
+Requires-Dist: matplotlib~=3.8; python_version == "3.11"
 Requires-Dist: numpy~=1.26.4; python_version == "3.11"
-Requires-Dist: pandas~=1.5.3; python_version == "3.11"
-Requires-Dist: pomegranate~=0.14.9; python_version == "3.11"
-Requires-Dist: requests~=2.31.0; python_version == "3.11"
-Requires-Dist: scikit-learn~=1.4.1.post1; python_version == "3.11"
+Requires-Dist: pandas~=2.0; python_version == "3.11"
+Requires-Dist: requests~=2.31; python_version == "3.11"
+Requires-Dist: scikit-learn~=1.1.0; python_version == "3.11"
 Requires-Dist: scipy~=1.12.0; python_version == "3.11"
 Requires-Dist: torch~=2.2.0; python_version == "3.11"
-Requires-Dist: urllib3~=1.26.18; python_version == "3.11"
-Requires-Dist: biopython~=1.83; python_version == "3.12"
-Requires-Dist: matplotlib~=3.8.3; python_version == "3.12"
-Requires-Dist: numpy~=1.26.4; python_version == "3.12"
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-Requires-Dist: requests~=2.31.0; python_version == "3.12"
-Requires-Dist: scikit-learn~=1.4.1.post1; python_version == "3.12"
+Requires-Dist: urllib3~=1.26; python_version == "3.11"
+Requires-Dist: biopython~=1.87.0; python_version == "3.12"
+Requires-Dist: matplotlib~=3.10.9; python_version == "3.12"
+Requires-Dist: numpy~=1.26.0; python_version == "3.12"
+Requires-Dist: pandas~=2.2.3; python_version == "3.12"
+Requires-Dist: requests~=2.33.1; python_version == "3.12"
+Requires-Dist: scikit-learn~=1.4.0; python_version == "3.12"
 Requires-Dist: scipy~=1.12.0; python_version == "3.12"
-Requires-Dist: torch~=2.2.0; python_version == "3.12"
-Requires-Dist: urllib3~=1.26.6; python_version == "3.12"
+Requires-Dist: torch~=2.2.2; python_version == "3.12"
+Requires-Dist: urllib3~=1.26.20; python_version == "3.12"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: maintainer
+Dynamic: maintainer-email
+Dynamic: project-url
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 <h1 align="center">
   <a href="bio2byte.be/b2btools" target="_blank" ref="noreferrer noopener">
@@ -142,7 +142,13 @@ To install the latest version of this package:
 $ pip install b2bTools
 ```
 
-**⚠️ Important notes:** [Hmmer](http://hmmer.org) and [T-Coffee](https://tcoffee.crg.eu) are required to run several features. Please install them following their official guidelines.
+Supported Python versions: `>=3.7, <3.13` (Python 3.7, 3.8, 3.9, 3.10, 3.11 and 3.12).
+
+**⚠️ Important notes:** [HMMER](http://hmmer.org) is required by PSPer, and [T-Coffee](https://tcoffee.crg.eu) is required by alignment-generation workflows. Please install them following their official guidelines.
+
+**Performance notes:** DisoMine can use Apple MPS acceleration for the PyTorch inference step when running on supported Apple hardware. This is disabled by default because CPU execution is the deterministic baseline and is safer when multiple Python environments run predictions in parallel. From the command line, enable it with `--enable-mps`; Python API usage remains CPU-based unless acceleration is enabled by the CLI entrypoint.
+
+PSPer calls HMMER through `subprocess` and automatically passes a bounded `--cpu` value based on available CPU cores, capped to avoid oversubscribing shared machines. Predictor runtime differs substantially by tool and input size; see [PREDICTORS.md](PREDICTORS.md) for the dependency order, qualitative runtime ranking, and implementation notes.
 
 ### Single Sequence predictions
 
@@ -401,6 +407,16 @@ $ pip install b2bTools
 !pip install b2bTools
 ```
 
+### Development and QA
+
+For local development from the repository root, run the maintained pytest suite through:
+
+```console
+$ make test
+```
+
+The test command uses explicit test directories and disables third-party pytest plugin autoloading for faster, more predictable collection. The full suite intentionally avoids `pytest-xdist` parallelism because predictor tests call external binaries and runtime caches that must remain deterministic across Python 3.7-3.12.
+
 ## 📦  Package content
 
 ### 🔍 General Tools
@@ -481,6 +497,9 @@ Given a predictor might be built on top of other, it is usual to get more output
 | EfoldMine | Dynamine              |
 | Disomine  | EfoldMine, Dynamine   |
 | AgMata    | EfoldMine, Dynamine   |
+| PSPer     | Disomine, EfoldMine, Dynamine |
+
+Requested predictors are executed in dependency order, so asking for a downstream predictor can also add prerequisite outputs. For example, requesting PSPer also produces the DynaMine, EFoldMine and DisoMine predictions it needs.
 
 These are all the available options to use inside the tools array parameter:
 
@@ -505,7 +524,7 @@ The next table shows all the available predictor values by predictor:
 | EfoldMine | `"earlyFolding"` | `[Float]`            |
 | Disomine  | `"disoMine"`     | `[Float]`            |
 | AgMata    | `"agmata"`       | `[Float]`            |
-| PSPer     | `"viterbi"`      | `[Float]`            |
+| PSPer     | `"viterbi"`      | `[String]`           |
 | PSPer     | `"complexity"`   | `[Float]`            |
 | PSPer     | `"tyr"`          | `[Float]`            |
 | PSPer     | `"arg"`          | `[Float]`            |
@@ -529,47 +548,45 @@ multiple_seq.get_all_predictions_msa_distrib()['results']
 | EfoldMine | `"earlyFolding"` | `['median', 'thirdQuartile', 'firstQuartile', 'topOutlier', 'bottomOutlier']`            |
 | Disomine  | `"disoMine"`     | `['median', 'thirdQuartile', 'firstQuartile', 'topOutlier', 'bottomOutlier']`            |
 | AgMata    | `"agmata"`       | `['median', 'thirdQuartile', 'firstQuartile', 'topOutlier', 'bottomOutlier']`            |
-| PSPer     | `"viterbi"`      | `['median', 'thirdQuartile', 'firstQuartile', 'topOutlier', 'bottomOutlier']`            |
 | PSPer     | `"complexity"`   | `['median', 'thirdQuartile', 'firstQuartile', 'topOutlier', 'bottomOutlier']`            |
 | PSPer     | `"tyr"`          | `['median', 'thirdQuartile', 'firstQuartile', 'topOutlier', 'bottomOutlier']`            |
 | PSPer     | `"arg"`          | `['median', 'thirdQuartile', 'firstQuartile', 'topOutlier', 'bottomOutlier']`            |
 | PSPer     | `"RRM"`          | `['median', 'thirdQuartile', 'firstQuartile', 'topOutlier', 'bottomOutlier']`            |
 | PSPer     | `"disorder"`     | `['median', 'thirdQuartile', 'firstQuartile', 'topOutlier', 'bottomOutlier']`            |
 
+`viterbi` is categorical and is intentionally excluded from MSA distribution statistics.
+
 The method `get_all_predictions` will return a dictionary with the following structure:
 
 ```python
 {
-  "SEQUENCE_ID_000": {
-    "seq": "the input sequence 0",
-    "result001": [0.001, 0.002, ..., 0.00],
-    "result002": [0.001, 0.002, ..., 0.00],
-    "...": [...],
-    "resultN": [0.001, 0.002, ..., 0.00]
-  },
-  "SEQUENCE_ID_001": {
-    "seq": "the input sequence 1",
-    "result001": [0.001, 0.002, ..., 0.00],
-    "result002": [0.001, 0.002, ..., 0.00],
-    "...": [...],
-    "resultN": [0.001, 0.002, ..., 0.00]
-  },
-  "...": { ... },
-  "SEQUENCE_ID_N": {
-    "seq": "the input sequence N",
-    "result001": [0.001, 0.002, ..., 0.00],
-    "result002": [0.001, 0.002, ..., 0.00],
-    "...": [...],
-    "resultN": [0.001, 0.002, ..., 0.00]
+  "proteins": {
+    "SEQUENCE_ID_000": {
+      "seq": ["M", "A", "K", "..."],
+      "backbone": [0.001, 0.002, "..."],
+      "sidechain": [0.001, 0.002, "..."],
+      "...": ["..."]
+    },
+    "SEQUENCE_ID_001": {
+      "seq": ["M", "E", "T", "..."],
+      "backbone": [0.001, 0.002, "..."],
+      "sidechain": [0.001, 0.002, "..."],
+      "...": ["..."]
+    }
   },
+  "metadata": {
+    "title": "...",
+    "tools": ["dynamine", "..."],
+    "...": "..."
+  }
 }
 ```
 
 You are ready to use the sequence and predictions to work with them. Here is an example of plotting the data.
 
 ```python
-backbone_pred = predictions['SEQ001']['backbone']
-sidechain_pred = predictions['SEQ001']['sidechain']
+backbone_pred = predictions['proteins']['SEQ001']['backbone']
+sidechain_pred = predictions['proteins']['SEQ001']['sidechain']
 
 plt.plot(range(len(backbone_pred)), backbone_pred, label = "Backbone")
 plt.plot(range(len(sidechain_pred)), sidechain_pred, label = "Sidechain")
@@ -588,12 +605,15 @@ You are able to use this package directly from your console session with no Pyth
 usage: b2bTools [-h] [-v] -i INPUT_FILE -o OUTPUT_JSON_FILE
                 [-t OUTPUT_TABULAR_FILE] [-m METADATA_FILE]
                 [-dj DISTRIBUTION_JSON_FILE] [-dt DISTRIBUTION_TABULAR_FILE]
-                [-s {comma,tab}] [--short_ids] [--mode {single_seq,msa}]
-                [--dynamine] [--disomine] [--efoldmine] [--agmata] [--psper]
+                [-s {comma,tab}] [--short_ids]
+                [--log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
+                [--mode {single_seq,msa}]
+                [--enable-mps] [--dynamine] [--disomine] [--efoldmine]
+                [--agmata] [--psper] [-id SEQUENCE_ID]
 
 Bio2Byte Tool - Command Line Interface
 
-optional arguments:
+options:
   -h, --help            show this help message and exit
   -v, --version         show program's version number and exit
   -i INPUT_FILE, --input_file INPUT_FILE
@@ -607,19 +627,28 @@ optional arguments:
   -dj DISTRIBUTION_JSON_FILE, --distribution_json_file DISTRIBUTION_JSON_FILE
                         Path to distribution output JSON file
   -dt DISTRIBUTION_TABULAR_FILE, --distribution_tabular_file DISTRIBUTION_TABULAR_FILE
-                        Path to distribution output JSON file
+                        Path to distribution output tabular file
   -s {comma,tab}, --sep {comma,tab}
                         Tabular separator
   --short_ids           Trim sequence ids (up to 20 chars per seq)
+  --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --verbose-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
+                        Logger verbosity level
   --mode {single_seq,msa}
                         Execution mode: Single Sequence or MSA Analysis
+  --enable-mps          Enable Apple MPS acceleration where supported. Disabled
+                        by default for deterministic parallel runs.
   --dynamine            Run DynaMine predictor
   --disomine            Run DisoMine predictor
   --efoldmine           Run EFoldMine predictor
   --agmata              Run AgMata predictor
   --psper               Run PSPer predictor
+  -id SEQUENCE_ID, --sequence_id SEQUENCE_ID
+                        Sequence to extract results instead of getting all the
+                        results
 ```
 
+By default the CLI runs DynaMine. Add `--disomine`, `--efoldmine`, `--agmata` and/or `--psper` to request additional predictors. Prerequisite predictors are still executed automatically when a selected tool depends on them.
+
 ##### To display the help section
 
 ```console
@@ -641,7 +670,21 @@ b2bTools \
   --input_file /path/to/input/example_toy.fasta \
   --output_json_file /path/to/output/example_toy.json \
   --output_tabular_file /path/to/output/example_toy.csv \
-  --metadata_file /path/to/output/example_toy.meta.csv
+  --metadata_file /path/to/output/example_toy.meta.csv \
+  --disomine \
+  --efoldmine \
+  --agmata \
+  --psper
+```
+
+To enable Apple MPS acceleration for supported DisoMine inference from the CLI, add `--enable-mps`:
+
+```console
+b2bTools \
+  --input_file /path/to/input/example_toy.fasta \
+  --output_json_file /path/to/output/example_toy.json \
+  --disomine \
+  --enable-mps
 ```
 
 Expected output:
@@ -649,7 +692,7 @@ Expected output:
 ```console
 2023-07-04 16:04:23,630 [b2bTools v3.0.6 INFO] Arguments parsed with success
 2023-07-04 16:04:23,630 [b2bTools v3.0.6 INFO] Reading sequences from: /path/to/input/example_toy.fasta
-2023-07-04 16:04:23,630 [b2bTools v3.0.6 INFO] Tools to execute: ['dynamine']
+2023-07-04 16:04:23,630 [b2bTools v3.0.6 INFO] Tools to execute: ['dynamine', 'disomine', 'efoldmine', 'agmata', 'psper']
 2023-07-04 16:04:23,630 [b2bTools v3.0.6 INFO] Predicting sequence(s)
 ...
 2023-07-04 16:04:23,986 [b2bTools v3.0.6 INFO] Saving results in JSON format in: /path/to/output/example_toy.json
@@ -666,14 +709,18 @@ b2bTools \
   --input_file /path/to/input/example_toy.fasta \
   --output_json_file /path/to/output/example_toy.json \
   --output_tabular_file /path/to/output/example_toy.csv \
-  --metadata_file /path/to/output/example_toy.meta.csv
+  --metadata_file /path/to/output/example_toy.meta.csv \
+  --disomine \
+  --efoldmine \
+  --agmata \
+  --psper
 ```
 
 ```console
 2023-07-04 16:25:35,486 [b2bTools v3.0.6 INFO] Arguments parsed with success
 2023-07-04 16:25:35,486 [b2bTools v3.0.6 INFO] Reading sequences from: /path/to/input/example_toy.fasta
 2023-07-04 16:25:35,486 [b2bTools v3.0.6 INFO] Sequence to filter: Q647G9
-2023-07-04 16:25:35,486 [b2bTools v3.0.6 INFO] Tools to execute: ['dynamine']
+2023-07-04 16:25:35,486 [b2bTools v3.0.6 INFO] Tools to execute: ['dynamine', 'disomine', 'efoldmine', 'agmata', 'psper']
 2023-07-04 16:25:35,486 [b2bTools v3.0.6 INFO] Predicting sequence(s)
 ...
 2023-07-04 16:25:35,842 [b2bTools v3.0.6 INFO] Saving results for Q647G9 in JSON format in: /path/to/output/example_toy.json
@@ -694,7 +741,11 @@ b2bTools \
   --output_tabular_file /path/to/output/small_alignment.clustal.csv \
   --metadata_file /path/to/output/small_alignment.clustal.meta.csv \
   --distribution_json_file /path/to/output/small_alignment.clustal.distrib.json \
-  --distribution_tabular_file /path/to/output/small_alignment.clustal.distrib.csv
+  --distribution_tabular_file /path/to/output/small_alignment.clustal.distrib.csv \
+  --disomine \
+  --efoldmine \
+  --agmata \
+  --psper
 ```
 
 Expected output:
@@ -702,7 +753,7 @@ Expected output:
 ```console
 2023-07-04 16:06:40,524 [b2bTools v3.0.6 INFO] Arguments parsed with success
 2023-07-04 16:06:40,524 [b2bTools v3.0.6 INFO] Reading sequences from: /path/to/input/small_alignment.clustal
-2023-07-04 16:06:40,524 [b2bTools v3.0.6 INFO] Tools to execute: ['dynamine']
+2023-07-04 16:06:40,524 [b2bTools v3.0.6 INFO] Tools to execute: ['dynamine', 'disomine', 'efoldmine', 'agmata', 'psper']
 2023-07-04 16:06:40,524 [b2bTools v3.0.6 INFO] Predicting sequence(s)
 ...
 2023-07-04 16:06:40,749 [b2bTools v3.0.6 INFO] Saving results in JSON format in: /path/to/output/small_alignment.clustal.json
@@ -718,20 +769,24 @@ Otherwise, if you need to extract only one sequence from the input file:
 ```console
 b2bTools \
   --mode msa \
-  --sequence_id SEQ_1
+  --sequence_id SEQ_1 \
   --input_file /path/to/input/small_alignment.clustal \
   --output_json_file /path/to/output/small_alignment.clustal.json \
   --output_tabular_file /path/to/output/small_alignment.clustal.csv \
   --metadata_file /path/to/output/small_alignment.clustal.meta.csv \
   --distribution_json_file /path/to/output/small_alignment.clustal.distrib.json \
-  --distribution_tabular_file /path/to/output/small_alignment.clustal.distrib.csv
+  --distribution_tabular_file /path/to/output/small_alignment.clustal.distrib.csv \
+  --disomine \
+  --efoldmine \
+  --agmata \
+  --psper
 ```
 
 ```console
 2023-07-04 16:28:34,388 [b2bTools v3.0.6 INFO] Arguments parsed with success
 2023-07-04 16:28:34,388 [b2bTools v3.0.6 INFO] Reading sequences from: /path/to/input/small_alignment.clustal
 2023-07-04 16:28:34,388 [b2bTools v3.0.6 INFO] Sequence to filter: SEQ_1
-2023-07-04 16:28:34,388 [b2bTools v3.0.6 INFO] Tools to execute: ['dynamine']
+2023-07-04 16:28:34,388 [b2bTools v3.0.6 INFO] Tools to execute: ['dynamine', 'disomine', 'efoldmine', 'agmata', 'psper']
 2023-07-04 16:28:34,388 [b2bTools v3.0.6 INFO] Predicting sequence(s)
 ...
 2023-07-04 16:28:34,602 [b2bTools v3.0.6 INFO] Saving results for SEQ_1 in JSON format in: /path/to/output/small_alignment.clustal.json
@@ -928,7 +983,7 @@ If you use this package or data in this package, please cite:
 | Predictor | Authors | Cite | Digital Object Identifier (DOI) |
 | --------- | --------- | --------- | --------- |
 | Dynamine  | Elisa Cilia, Rita Pancsa, Peter Tompa, Tom Lenaerts, and Wim Vranken | _Elisa Cilia, Rita Pancsa, Peter Tompa, Tom Lenaerts, and Wim Vranken._ From protein sequence to dynamics and disorder with DynaMine **Nature Communications 4:2741 (2013)** | https://www.nature.com/articles/ncomms3741 |
-| Disomine  | Gabriele Orlando, Daniele Raimondi, Francesco Codice, Francesco Tabaro, Wim Vranken | _Gabriele Orlando, Daniele Raimondi, Francesco Codice, Francesco Tabaro, Wim Vranken._ Prediction of disordered regions in proteins with recurrent Neural Networks and protein dynamics. **bioRxiv 2020.05.25.115253 (2020)** | https://www.biorxiv.org/content/10.1101/2020.05.25.115253v1 |
+| Disomine  | Gabriele Orlando, Daniele Raimondi, Francesco Codice, Francesco Tabaro, Wim Vranken | _Gabriele Orlando, Daniele Raimondi, Francesco Codice, Francesco Tabaro, Wim Vranken._ Prediction of disordered regions in proteins with recurrent Neural Networks and protein dynamics. **bioRxiv 2020.05.25.115253 (2020)** | 10.1016/j.jmb.2022.167579 |
 | EfoldMine | Raimondi, D., Orlando, G., Pancsa, R. et al |  _Raimondi, D., Orlando, G., Pancsa, R. et al._ Exploring the Sequence-based Prediction of Folding Initiation Sites in Proteins. **Sci Rep 7, 8826 (2017)** | https://doi.org/10.1038/s41598-017-08366-3 |
 | AgMata    | Gabriele Orlando, Alexandra Silva, Sandra Macedo-Ribeiro, Daniele Raimondi, Wim Vranken | _Gabriele Orlando, Alexandra Silva, Sandra Macedo-Ribeiro, Daniele Raimondi, Wim Vranken._ Accurate prediction of protein beta-aggregation with generalized statistical potentials **Bioinformatics , Volume 36, Issue 7, 1 April 2020, Pages 2076–2081 (2020)** | https://academic.oup.com/bioinformatics/article/36/7/2076/5670527 |
 | PSPer    | Gabriele Orlando,  Daniele Raimondi,  Francesco Tabaro,  Francesco Codicè,  Yves Moreau, Wim F Vranken  | _Gabriele Orlando and others_, Computational identification of prion-like RNA-binding proteins that form liquid phase-separated condensates, **Bioinformatics, Volume 35, Issue 22, November 2019, Pages 4617–4623** | https://doi.org/10.1093/bioinformatics/btz274 |
@@ -944,7 +999,7 @@ Bio2Byte Tools is free and open-source software licensed under the Apache 2.0 Li
 1. The Bio2Byte group aims to promote open science by providing freely available online services, database and software relating to the life sciences, with focus on proteins. Where we present scientific data generated by others we impose no additional restriction on the use of the contributed data than those provided by the data owner.
 1. The Bio2Byte group expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice. The expected attribution will be indicated in 'How to cite' sections (or equivalent).
 1. The Bio2Byte group is not liable to you or third parties claiming through you, for any loss or damage.
-1. Any questions or comments concerning these Terms of Use can be addressed to [Wim Vranken](mailto:wim.vranken@vub.be).
+1. Any questions or comments concerning these Terms of Use can be addressed to [Wim Vranken](mailto:bio2byte@vub.be).
 
 <hr/>
 <p align="center">© Wim Vranken, Bio2Byte group, VUB, Belgium</p>