PMADS

Database introduction

PMADS workflow

We developed a literature mining pipeline using search terms derived from the dbPTM vocabulary and automated article retrieval via NCBI E-Utilities (EDirect) combined with Biopython. To broaden our corpus, we utilized the NCBI TranslationSet for thesaurus expansion of both PTM and keyword ontologies. Entity recognition was performed using PubTator and bespoke regular expressions to capture multi‑class biomedical entities, underpinned by pretrained natural language processing models (Stanza and CRAFT) for relation extraction. Candidate associations were filtered via manually curated inter‑entity rules, followed by expert review for final validation. To date, the data pipeline has processed 20,310,267 documents. Through rigorous manual curation, over 4,500 post-translational modification (PTM)-drug associations have been identified, among which more than 2,500 are cancer-related.

Workflow of PMADS

PTM types in PMADS

Diseases in PMADS

Disease category

Key features

AI-Driven Literature Mining

Curated from 2+ million biomedical publications using advanced natural language processing (NLP) and large language models (LLMs), with dual validation by domain experts.

Multi-Omics Integration

Integrates experimental mass spectrometry data from PRIDE Database (via rigorous computational pipelines) with text-mined PTM-drug associations. Provides residue-level PTM sites, regulatory pathways, and drug response correlations.

Clinically Actionable Insights

Annotates 4,500+ experimentally validated PTM-drug relationships and 500+ cross-species modification sites linked to 1000+ therapeutic agents. Supports biomarker discovery, drug repositioning, and therapy response prediction tools.

Dynamic Knowledge Expansion

Continuously updated with real-time literature surveillance and AI-predicted PTM-drug interactions.

Applications

Basic Research: Elucidate molecular networks of PTM-regulated drug mechanisms.

Drug Development: Guide targeted drug design by mapping "druggable" PTM hotspots.

Precision Medicine: Identify patient-specific PTM signatures for personalized treatment optimization.

Usage

The database provides a variety of data query and browsing strategies. All search fields support auto-complete functionality for user convenience.

Quick search

Located in the upper-right corner of every page, the quick search interface offers a unified portal with four clickable icons that enable rapid access to distinct categories: PTM sites, proteins, genes, and drugs. Users can initiate searches with minimal input, and the system returns matched entries enriched with PTM types, counts, and contextual annotations.

Fig. 1 Quick search entry

Quick search for protein

Click the protein icon (selected by default) to switch the search box to protein quick search, which supports searching by protein name or Uniprot ID, and will return fuzzy search results.

Fig. 2 Quick search for protein

On the search results page (using VEGFR2 as an example), the search statistics and categorized PTM statistics results page will be displayed (Fig.3). The results page splits the data by protein name, ID, and species, and displays the types and categories of post-translational modifications for different proteins on the right side. P denotes phosphorylation, Me denotes methylation, Ub denotes ubiquitination, and Misc denotes other types. You can view detailed records by clicking on the protein name or different PTMs (Fig. 4).

Fig. 3 Results of quick search for protein

Fig. 4 Results of PTM (phosphorylation of VEGFR2)

Quick search for gene

Gene quick search can be switched by clicking on the gene icon, and supports fuzzy input and auto-complete (e.g., SMAD3).

Fig. 5 Quick search for gene

Fig. 6 Results of quick search for gene

Quick search for drug

Drug quick search can be switched by clicking on the drug icon (e.g., imatinib).

Fig. 7 Quick search for drug

Fig. 8 Quick search results of drug

Quick search for PTM site

The rapid search function of the Site enables the retrieval of proteins and residue positions. Searches can be conducted using either the protein name followed by the amino acid residue and its position (e.g., EGFR-Tyr1068) or the UniProt ID along with the amino acid residue and its position (e.g., P00533-Tyr1068).

Fig. 9 Quick search for PTM site

Fig. 10 Results of quick search of PTM site

Advanced search

Available under the Search page, supporting combinatorial queries across multiple dimensions (Drug, Protein, Disease, Species, PTM type and Site ). The "DEMO" button can automatically populate search examples, and clicking the "SEARCH" button will allow access to the search results.

Fig. 11 Advanced search page

Result of record

The sole means of accessing detailed result data from PMADS is by clicking on the Record ID (e.g., acc0079) displayed on the search results page (Fig. 4).

Fig. 12 Record result page

On the PMADS record page, there is a detailed description of the record, including the following:

Basic description: Gene, Protein, Disease, Drug, PTM, etc.

Impact description: Effect keywords, Score, Effect description, etc. detail

Structural description: Sequence, 3D structure (PDB, AlphaFold).

Fig. 13 Sequence & structure

Known drugs: Known drugs targeting the protein, etc.

Fig. 14 Known drugs

Protein Tractability: Drug accessibility of the protein as a target, etc.

Fig. 15 Protein tractability

PTM intensity: Expression profile of the PTM site in cancer types, etc.

Fig. 16 PTM intensity

PTM-disease association: Records of disease associations with the site, etc.

Fig. 17 PTM-disease association

PTM-drug perturbation response: PTM response under drug perturbation, Response curves, etc.

Fig. 18 PTM-drug perturbation response

Function score: Phosphorylation function score of the protein, with emphasis on the site.

Fig. 19 Function score

Cross links: Associated links to other important databases, like dbPTM, Uniprot, DrugBank, etc.

Fig. 20 Cross links

FAQ

Citation

PMADS (Protein Modification and Drug Sensitivity). 2025. https://pmads.org/

Download

Currently, PMADS supports full database downloads, core data downloads, and annotation data downloads. You can select the desired download method by navigating to the Download page.

Abbreviations in PMADS

Provides amino acid abbreviations and other abbreviations for easy user lookup and use of PMADS.

Amino acid abbreviations

Name	Abbreviation
Alanine	Ala
Phenylalanine	Phe
Cysteine	Cys
Selenocysteine	Sec
Aspartic acid / Aspartate	Asp
Asparagine	Asn
Glutamic acid / Glutamate	Glu
Glutamine	Gln
Glycine	Gly
Histidine	His
Leucine	Leu
Isoleucine	Ile
Lysine	Lys
Pyrrolysine	Pyl
Methionine	Met
Proline	Pro
Arginine	Arg
Serine	Ser
Threonine	Thr
Valine	Val
Tryptophan	Trp
Tyrosine	Tyr

Other abbreviations

Name	Abbreviation
Post-Translational Modification	PTM
Over expression	OE
Knock out	KO

Effect & Score

In the detailed information of records in PMADS, Effect, Effect Info, Note, and Score are key record entries.

Effect: Describes the impact of increased PTM on the efficacy of drugs in diseases.

Effect Info: Provides a detailed description for each record, specifically indicating the influence of PTM at a certain site of a specific protein on the treatment of a particular disease with a specific drug.

Note: Serves as supplementary explanation to the Effect of the record, marking information such as combined medication, unconventional drugs, and whether it is a histone, etc.

Score: The impact score is used by PMADS to quantify the effect of PTM on the efficacy of drugs in diseases. The definition of this indicator is as shown in the following table:

Category	Score	Notes/Examples
Definite relationship	5	e.g. Phosphorylation of protein A sensitizes tumors to drug B.
Definite relationship (insufficient)	4.5	Definite relationship with insufficient: - Non-conventional drugs: radiation, ICB, etc.
Mutual influence	4	e.g. Drug A inhibits tumors by suppressing phosphorylation of protein B. e.g. Drug B in disease A enhances treatment efficacy by inhibiting protein C phosphorylation.
Weak influence	3	Mutual influence with insufficient: - Low credibility of articles: Article retraction, etc. - Unconventional proteins: Histone, etc. - Non-conventional drugs: Gene A KO, Gene B OE, etc.
No influence	2	e.g. Drug A inhibits phosphorylation of protein B, but no effect for disease. e.g. Drug A relieved the disease but did not affect protein B phosphorylation.
Not included	0	- Non-disease. - No PTM.

Contact us

If you have any questions, please feel free to contact us. Suggestions and bug reports are welcome.

E-mail: [email protected]

Telephone: +8621-65980233

Address: No. 1239, Siping Road, Yangpu Area, Shanghai, China