Here we post issues or news for the following purposes:
- revision or importing of entries to mavisp database
- issues to fix with the toolkit for mavisp
- ideas for new development and methods to use in the framework
- news on changes in the mavisp_templates and protocols
NEWS
02/12/2025 mavisp_automatization has been revised to allow for collection of only essential modules for importing - useful when there is planned downtime from external resources not needed for the basic importing
25/11/2025 New module to cover variants impacting on native ss-bond or for de novo ss-bond upon mutation Fixed mavisp.py and dot_plot.py for GEMME thresholds and implemented options to choose different VEP for the discovery workflow Introduced a step in downstream_analysis for flagging variants with mechanistic indicators and low pLDDT scores
30/10/2025 Fixed issue in mavisp_automatization to write in the final simple_mode folder the ted folder
29/10/2025 Fixed the miscalculation of the average change in allosteric free energy (avg_dG) among response sites induced by each mutation in the filtering step of the AlloSigMA workflow.
21/10/2025 update of mavisp automatization for compatibility with version 6 of AFDB and to include full support to PPI2PDB and TED annotations support to IDPs in automatization
15/10/2025 update of slimfast for compatibility with version 6 of AFDB
09/10/2025 update on mutatex automatization pipeline for compatibility with version 6 of the AF database
08/09/2025
All proteins have been updated with a new long-range protocol in simple mode
Modified the aggregate script’s parsing of PDBminer_complexes output to correctly handle cases where the target protein has multiple chains in the complex structure
14/07/2025
We have updated the data from ELM that gget uses for the detection of short linear motifs in the protein sequences using Cancermuts
02/07/2025
New programmatic solution to generate gitbook reports available in the mavisp_templates for curators. This generates a Markdown template file of the report that can be further customized and then curators can ask an import to the MAVISp gitbook through this github space.
02/07/2025
We updated the templates for the psn-path analysis in simulations_analysis (ensemble mode) as edge cases were not correctly concatenated
26/06/2025 Introduction in structure_selection of uniprot2refseq.py to support the identification of the proper RefSeq ID for the given uniprot AC of the protein target. We are also updating some entries with wrong RefSeq ID and we will release the updates publicly in October 2025
19/06/2025 In mavisp_automatization, improved support for curating entries without specifying a RefSeq ID
13/06/2025
We have fixed a recent bug in mentha2pdb.py: replaced usage of pypdb with direct RCSB API queries to restore PDB extraction, as pypdb was incompatible with the current RCSB API.
12/06/2025
We have updated mavisp_automatization snakemake. Now there is a new feature that automatically generates metadata.yaml, importing.yaml, and a simple_mode/ folder for each curated protein. This ensures all essential content is structured and ready for direct import into the MAVISP database.
06/06/2025
A new version of the AlloSigMA2 workflow for the simple mode LONG_RANGE module is available aligned with the benchmark study under revision for JMB. Each new entry should be using this workflow. We will annotate method and relevant cutoffs in the metadata. The updates of old entries will be carried out during the yearly updates of 2025 (June-August 2025). We also revised one of the scripts of the LONG_RANGE module in ensemble mode for the psn-path analysis for a modification that make the calculation independent from the starting structure. Use new templates for new runs and the update of the old entries is also ongoing.
The pdbminer_complexes tool was updated to enhance the binding-interface flag, now allowing detection of target chain(s) interfaces across all other chains in the complex, especially useful for multimeric complexes.
02/06/2025
We have updated Mol_Analysis for the quality control of the MD simulations and pre-md steps so that the average rmsd matrix is calculated more efficiently
12/05/2025
Updated get_mutlist.py
11/04/2025
A new metadata template is available where also the source of structure should be reported
08/04/2025
We have fixed a problem that made the MAVISp_automatization crash when multiple Gene ID where found to be associated with a protein's RefSeq identifier
03/03/2025 revised version of mavisp_automatization snakemake to fix a bug with PTM module for multi-domai proteins
08/01/2025
revised version of mavisp_automatization snakemake to fix issues with PTM and RaSP experienced in December
18/01/2024
templates for step 6 of simulations_analysis corrected for the groups for rmsd calculation (i.e. mainchain)
05/12/2024
- new pancancer.py template for cases where cancermuts fail in retriving entrez ID
29/11/2024
- new templates available for custom analysis with long-range modules in simple and ensemble mode for cofactor bindign sites or catalytic sites of enzymes
28/11/2024
- fixed a bug in mavisp_automatization for the generation of the saturation mutlist
20/11/2024
- new version of Mol_Analysis.py with fixed labels in pdf and with option to perform gmindist using a slicing of the trajectory
19/11/2024
- new templates file for mutatex_automatization
- new version of mavisp_automatization with support to custom PDB file in input
14/11/2024
- updates in mavisp_automatization that requries to update the template folder for data colleciton - includes a fix for the folder name in cancermuts_data and in the script for the domain annotations
05/11/2024
- a new version of SLiMfast is available for data analysis which integrate the filtering step based on solvent accessibility
24/10/2024
- the procheck step within structure_selection has been implemented in mavisp_automatization, new templates available for data collection on the local server . a wrapper around simulations_analysis is available in the mavisp_templates on the local server
05/10/2024
-- we have introduced in dot_plot.py loss/gain of function for GEMME
- the default to assign damaging effect for GEMME have been changed with a default value of -3 (loss-of-function) and 3 (gain-of-function) and using the "GEMME Score"
- the default to assign damaging effect for DeMaSk have been changed with a default value of -0.25 (loss-of-function) and 0.25 (gain-of-function)
- we should not import results on variants in MET1 since a mutation in this code would interrupt transcription and do not result in a full-lenght protein
- the templates for mavisp automatization have been updated including the proper script for clinvar_gene
27/09/2024
- mavisp_automatization now includes also the pdbminer_complexes step
24/09/2024
- new procedure for selecting complexes for local interactions in the guideline document
13/09/2024
- we have introduced in dot_plot.py loss/gain of function for DeMaSk and efoldmine annotations
- the default to assign damaging effect for GEMME has been changed with a default value of 0.5
05/07/2024
- the first release of mavisp saturation is available (simple mode) - importing for the ensemble mode is ongoing
24/05/2024
- new clinvar.py version with support of genomic coordinates
29/04/2024
- updated pdbminer_complexes to solve this issue: https://github.com/ELELAB/CSB-scripts/issues/418
27/04/2024
- updated mavisp templates for long_range with distance cutoff set to 15 Ang after ASM publication and exploration of other similar cases
25/04/2024
- updated readme for step 7 of simulations_analysis to cover cases with residue type HISE, HISD and HISH from CHARMM36m simulations
22/04/2024
- step 5 of simulations_analysis has been updated including a script in python2 to add the chain identifier for mutatex calculations
- clinvar.py in clinvar_gene has been updated in light of this pull request: https://github.com/ELELAB/CSB-scripts/pull/371 - we have updated in both mavisp_templates and mavisp_automatization
- a new version of cancermuts is available in light of this PR: ELELAB/cancermuts#198 which allows to interact with a local version of ELM through the recently published gget elm: https://academic.oup.com/bioinformatics/article/40/3/btae095/7611647 - the template file for pancancer_clinvar_saturation.py has been modified in mavisp_templated and in mavisp_automatization since it is the one to use from now on.
15/04/2024
- templates for ptm.md have been added to mavisp_templates in shared_projects
12/04/2024
- metadata has been revised to include also a config file needed to the data manager to streamline the importing of new entries (importing.yalm) that needs to be filled in
- step 7 for simulations_analysis has been revised to include the right python module to use (python2.7)
- from now on on new entries we will only support data collected with the saturation mutlist and using pancancer_clinvar_saturation.py for cancermuts
- in structure_selection there is a new tool pdbminer_complexes to use to verify if there are structures available without missing residues to reconstructs for local_interaction. it needs a pdbminer output from at least early 2024.
11/04/2024
- denovo_phospho has been moved back to 'dev' since we need to include some changes in the design to make it less time consuming before starting a large data collection
10/04/2024
- the clinvar step after generation of mutlist is no longer needed and it has been archived
- the pocket_analysis step is no longer needed since allosigma workflow includes it
15/03/2024
- from today we switch in the data collection for stability as a default to only rasp and mutatex - rosetta will be used only in focused studies on specific protein targets