uniprot

Name: uniprot
Author: adaptyvbio

37installs20forks

How to install uniprot?

adaptyvbio/protein-design-skills/uniprot

$npx -y skills add adaptyvbio/protein-design-skills --skill uniprot

Installs into the current project.

Summary

Access UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional annotations, (3) Getting domain boundaries, (4) Finding homologs and variants, (5) Cross-referencing to PDB structures. For str

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SKILL.md

1	# UniProt Database Access
2
3	Note: This skill uses the UniProt REST API directly. No Modal deployment needed - all operations run locally via HTTP requests.
4
5	## Fetching Sequences
6
7	### By Accession
8	```bash
9	# FASTA format
10	curl "https://rest.uniprot.org/uniprotkb/P00533.fasta"
11
12	# JSON format with annotations
13	curl "https://rest.uniprot.org/uniprotkb/P00533.json"
14	```
15
16	### Using Python
17	```python
18	import requests
19
20	def get_uniprot_sequence(accession):
21	"""Fetch sequence from UniProt."""
22	url = f"https://rest.uniprot.org/uniprotkb/{accession}.fasta"
23	response = requests.get(url)
24	if response.ok:
25	lines = response.text.strip().split('\n')
26	header = lines[0]
27	sequence = ''.join(lines[1:])
28	return header, sequence
29	return None, None
30	```
31
32	## Getting Annotations
33
34	### Full Entry
35	```python
36	def get_uniprot_entry(accession):
37	"""Fetch full UniProt entry as JSON."""
38	url = f"https://rest.uniprot.org/uniprotkb/{accession}.json"
39	response = requests.get(url)
40	return response.json() if response.ok else None
41
42	entry = get_uniprot_entry("P00533")
43	print(f"Protein: {entry['proteinDescription']['recommendedName']['fullName']['value']}")
44	```
45
46	### Domain Boundaries
47	```python
48	def get_domains(accession):
49	"""Extract domain annotations."""
50	entry = get_uniprot_entry(accession)
51	domains = []
52
53	for feature in entry.get('features', []):
54	if feature['type'] == 'Domain':
55	domains.append({
56	'name': feature.get('description', ''),
57	'start': feature['location']['start']['value'],
58	'end': feature['location']['end']['value']
59	})
60
61	return domains
62
63	# Example: EGFR domains
64	domains = get_domains("P00533")
65	# [{'name': 'Kinase', 'start': 712, 'end': 979}, ...]
66	```
67
68	## Searching UniProt
69
70	### By Gene Name
71	```python
72	def search_uniprot(query, organism=None, limit=10):
73	"""Search UniProt by query."""
74	url = "https://rest.uniprot.org/uniprotkb/search"
75	params = {
76	"query": query,
77	"format": "json",
78	"size": limit
79	}
80	if organism:
81	params["query"] += f" AND organism_id:{organism}"
82
83	response = requests.get(url, params=params)
84	return response.json()['results']
85
86	# Search for human EGFR
87	results = search_uniprot("EGFR", organism=9606)
88	```
89
90	### By Sequence Similarity (BLAST)
91	```python
92	# Use UniProt BLAST
93	# https://www.uniprot.org/blast
94	```
95
96	## Cross-References
97
98	### Get PDB Structures
99	```python
100	def get_pdb_references(accession):
101	"""Get PDB structures for UniProt entry."""
102	entry = get_uniprot_entry(accession)
103	pdbs = []
104
105	for xref in entry.get('uniProtKBCrossReferences', []):
106	if xref['database'] == 'PDB':
107	pdbs.append({
108	'pdb_id': xref['id'],
109	'method': xref.get('properties', [{}])[0].get('value', ''),
110	'chains': xref.get('properties', [{}])[1].get('value', '')
111	})
112
113	return pdbs
114
115	# Example: PDB structures for EGFR
116	pdbs = get_pdb_references("P00533")
117	```
118
119	## Common Use Cases
120
121	### Target Selection
122	```python
123	# 1. Find protein by name
124	results = search_uniprot("insulin receptor", organism=9606)
125
126	# 2. Get accession
127	accession = results[0]['primaryAccession'] # e.g., P06213
128
129	# 3. Get domains
130	domains = get_domains(accession)
131
132	# 4. Find PDB structure
133	pdbs = get_pdb_references(accession)
134
135	# 5. Download best structure for design
136	```
137
138	### Sequence Alignment Info
139	```python
140	def get_sequence_variants(accession):
141	"""Get natural variants from UniProt."""
142	entry = get_uniprot_entry(accession)
143	variants = []
144
145	for feature in entry.get('features', []):
146	if feature['type'] == 'Natural variant':
147	variants.append({
148	'position': feature['location']['start']['value'],
149	'original': feature.get('alternativeSequence', {}).get('originalSequence', ''),
150	'variant': feature.get('alternativeSequence', {}).get('alternativeSequences', [''])[0],
151	'description': feature.get('description', '')
152	})
153
154	return variants
155	```
156
157	## API Reference
158
159	\| Endpoint \| Description \|
160	\|----------\|-------------\|
161	\| `/uniprotkb/{id}.fasta` \| FASTA sequence \|
162	\| `/uniprotkb/{id}.json` \| Full entry JSON \|
163	\| `/uniprotkb/search` \| Search entries \|
164	\| `/uniprotkb/stream` \| Batch download \|
165
166	## Troubleshooting
167
168	Entry not found: Check accession format (e.g., P00533)
169	Rate limits: Add delay between requests
170	Large downloads: Use stream endpoint with pagination
171
172	---
173
174	Next: Use s

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uniprot

37installs20forks

View on GitHub

How to install uniprot?

adaptyvbio/protein-design-skills/uniprot

$npx -y skills add adaptyvbio/protein-design-skills --skill uniprot

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# UniProt Database Access
2
3	Note: This skill uses the UniProt REST API directly. No Modal deployment needed - all operations run locally via HTTP requests.
4
5	## Fetching Sequences
6
7	### By Accession
8	```bash
9	# FASTA format
10	curl "https://rest.uniprot.org/uniprotkb/P00533.fasta"
11
12	# JSON format with annotations
13	curl "https://rest.uniprot.org/uniprotkb/P00533.json"
14	```
15
16	### Using Python
17	```python
18	import requests
19
20	def get_uniprot_sequence(accession):
21	"""Fetch sequence from UniProt."""
22	url = f"https://rest.uniprot.org/uniprotkb/{accession}.fasta"
23	response = requests.get(url)
24	if response.ok:
25	lines = response.text.strip().split('\n')
26	header = lines[0]
27	sequence = ''.join(lines[1:])
28	return header, sequence
29	return None, None
30	```
31
32	## Getting Annotations
33
34	### Full Entry
35	```python
36	def get_uniprot_entry(accession):
37	"""Fetch full UniProt entry as JSON."""
38	url = f"https://rest.uniprot.org/uniprotkb/{accession}.json"
39	response = requests.get(url)
40	return response.json() if response.ok else None
41
42	entry = get_uniprot_entry("P00533")
43	print(f"Protein: {entry['proteinDescription']['recommendedName']['fullName']['value']}")
44	```
45
46	### Domain Boundaries
47	```python
48	def get_domains(accession):
49	"""Extract domain annotations."""
50	entry = get_uniprot_entry(accession)
51	domains = []
52
53	for feature in entry.get('features', []):
54	if feature['type'] == 'Domain':
55	domains.append({
56	'name': feature.get('description', ''),
57	'start': feature['location']['start']['value'],
58	'end': feature['location']['end']['value']
59	})
60
61	return domains
62
63	# Example: EGFR domains
64	domains = get_domains("P00533")
65	# [{'name': 'Kinase', 'start': 712, 'end': 979}, ...]
66	```
67
68	## Searching UniProt
69
70	### By Gene Name
71	```python
72	def search_uniprot(query, organism=None, limit=10):
73	"""Search UniProt by query."""
74	url = "https://rest.uniprot.org/uniprotkb/search"
75	params = {
76	"query": query,
77	"format": "json",
78	"size": limit
79	}
80	if organism:
81	params["query"] += f" AND organism_id:{organism}"
82
83	response = requests.get(url, params=params)
84	return response.json()['results']
85
86	# Search for human EGFR
87	results = search_uniprot("EGFR", organism=9606)
88	```
89
90	### By Sequence Similarity (BLAST)
91	```python
92	# Use UniProt BLAST
93	# https://www.uniprot.org/blast
94	```
95
96	## Cross-References
97
98	### Get PDB Structures
99	```python
100	def get_pdb_references(accession):
101	"""Get PDB structures for UniProt entry."""
102	entry = get_uniprot_entry(accession)
103	pdbs = []
104
105	for xref in entry.get('uniProtKBCrossReferences', []):
106	if xref['database'] == 'PDB':
107	pdbs.append({
108	'pdb_id': xref['id'],
109	'method': xref.get('properties', [{}])[0].get('value', ''),
110	'chains': xref.get('properties', [{}])[1].get('value', '')
111	})
112
113	return pdbs
114
115	# Example: PDB structures for EGFR
116	pdbs = get_pdb_references("P00533")
117	```
118
119	## Common Use Cases
120
121	### Target Selection
122	```python
123	# 1. Find protein by name
124	results = search_uniprot("insulin receptor", organism=9606)
125
126	# 2. Get accession
127	accession = results[0]['primaryAccession'] # e.g., P06213
128
129	# 3. Get domains
130	domains = get_domains(accession)
131
132	# 4. Find PDB structure
133	pdbs = get_pdb_references(accession)
134
135	# 5. Download best structure for design
136	```
137
138	### Sequence Alignment Info
139	```python
140	def get_sequence_variants(accession):
141	"""Get natural variants from UniProt."""
142	entry = get_uniprot_entry(accession)
143	variants = []
144
145	for feature in entry.get('features', []):
146	if feature['type'] == 'Natural variant':
147	variants.append({
148	'position': feature['location']['start']['value'],
149	'original': feature.get('alternativeSequence', {}).get('originalSequence', ''),
150	'variant': feature.get('alternativeSequence', {}).get('alternativeSequences', [''])[0],
151	'description': feature.get('description', '')
152	})
153
154	return variants
155	```
156
157	## API Reference
158
159	\| Endpoint \| Description \|
160	\|----------\|-------------\|
161	\| `/uniprotkb/{id}.fasta` \| FASTA sequence \|
162	\| `/uniprotkb/{id}.json` \| Full entry JSON \|
163	\| `/uniprotkb/search` \| Search entries \|
164	\| `/uniprotkb/stream` \| Batch download \|
165
166	## Troubleshooting
167
168	Entry not found: Check accession format (e.g., P00533)
169	Rate limits: Add delay between requests
170	Large downloads: Use stream endpoint with pagination
171
172	---
173
174	Next: Use s

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