pdb

Name: pdb
Author: adaptyvbio

43installs20forks

How to install pdb?

adaptyvbio/protein-design-skills/pdb

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

Installs into the current project.

Summary

Fetch and analyze protein structures from RCSB PDB. Use this skill when: (1) Need to download a structure by PDB ID, (2) Search for similar structures, (3) Prepare target for binder design, (4) Extract specific chains or domains, (5) Get structure metadata. For sequence lookup, u

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SKILL.md

1	# PDB Database Access
2
3	Note: This skill uses the RCSB PDB web API directly. No Modal deployment needed - all operations run locally via HTTP requests.
4
5	## Fetching Structures
6
7	### By PDB ID
8	```bash
9	# Download PDB file
10	curl -o 1alu.pdb "https://files.rcsb.org/download/1ALU.pdb"
11
12	# Download mmCIF
13	curl -o 1alu.cif "https://files.rcsb.org/download/1ALU.cif"
14	```
15
16	### Using Python
17	```python
18	from Bio.PDB import PDBList
19
20	pdbl = PDBList()
21	pdbl.retrieve_pdb_file("1ABC", pdir="structures/", file_format="pdb")
22	```
23
24	### Using RCSB API
25	```python
26	import requests
27
28	def fetch_pdb(pdb_id: str, format: str = "pdb") -> str:
29	"""Fetch structure from RCSB PDB."""
30	url = f"https://files.rcsb.org/download/{pdb_id}.{format}"
31	response = requests.get(url)
32	response.raise_for_status()
33	return response.text
34
35	def fetch_fasta(pdb_id: str) -> str:
36	"""Fetch sequence in FASTA format."""
37	url = f"https://www.rcsb.org/fasta/entry/{pdb_id}"
38	return requests.get(url).text
39
40	# Example usage
41	pdb_content = fetch_pdb("1ALU")
42	with open("1ALU.pdb", "w") as f:
43	f.write(pdb_content)
44	```
45
46	## Structure Preparation
47
48	### Selecting Chains
49	```python
50	from Bio.PDB import PDBParser, PDBIO, Select
51
52	class ChainSelect(Select):
53	def __init__(self, chain_id):
54	self.chain_id = chain_id
55
56	def accept_chain(self, chain):
57	return chain.id == self.chain_id
58
59	# Extract chain A
60	parser = PDBParser()
61	structure = parser.get_structure("protein", "1abc.pdb")
62	io = PDBIO()
63	io.set_structure(structure)
64	io.save("chain_A.pdb", ChainSelect("A"))
65	```
66
67	### Trimming to Binding Region
68	```python
69	def trim_around_residues(pdb_file, center_residues, buffer=10.0):
70	"""Trim structure to region around specified residues."""
71	parser = PDBParser()
72	structure = parser.get_structure("protein", pdb_file)
73
74	# Get center coordinates
75	center_coords = []
76	for res in structure.get_residues():
77	if res.id[1] in center_residues:
78	center_coords.extend([a.coord for a in res.get_atoms()])
79
80	center = np.mean(center_coords, axis=0)
81
82	# Keep residues within buffer
83	class RegionSelect(Select):
84	def accept_residue(self, res):
85	for atom in res.get_atoms():
86	if np.linalg.norm(atom.coord - center) < buffer:
87	return True
88	return False
89
90	io = PDBIO()
91	io.set_structure(structure)
92	io.save("trimmed.pdb", RegionSelect())
93	```
94
95	## Searching PDB
96
97	### RCSB Search API
98	```python
99	import requests
100
101	query = {
102	"query": {
103	"type": "terminal",
104	"service": "full_text",
105	"parameters": {
106	"value": "EGFR kinase domain"
107	}
108	},
109	"return_type": "entry"
110	}
111
112	response = requests.post(
113	"https://search.rcsb.org/rcsbsearch/v2/query",
114	json=query
115	)
116	results = response.json()
117	```
118
119	### By Sequence Similarity
120	```python
121	query = {
122	"query": {
123	"type": "terminal",
124	"service": "sequence",
125	"parameters": {
126	"value": "MKTAYIAKQRQISFVK...",
127	"evalue_cutoff": 1e-10,
128	"identity_cutoff": 0.9
129	}
130	}
131	}
132	```
133
134	## Structure Analysis
135
136	### Get Chain Info
137	```python
138	def get_structure_info(pdb_file):
139	parser = PDBParser(QUIET=True)
140	structure = parser.get_structure("protein", pdb_file)
141
142	info = {
143	"chains": [],
144	"total_residues": 0
145	}
146
147	for model in structure:
148	for chain in model:
149	residues = list(chain.get_residues())
150	info["chains"].append({
151	"id": chain.id,
152	"length": len(residues),
153	"first_res": residues[0].id[1],
154	"last_res": residues[-1].id[1]
155	})
156	info["total_residues"] += len(residues)
157
158	return info
159	```
160
161	### Find Interface Residues
162	```python
163	def find_interface_residues(pdb_file, chain_a, chain_b, distance=4.0):
164	"""Find residues at interface between two chains."""
165	parser = PDBParser(QUIET=True)
166	structure = parser.get_structure("complex", pdb_file)
167
168	interface_a = set()
169	interface_b = set()
170
171	for res_a in structure[0][chain_a].get_residues():
172	for res_b in structure[0][chain_b].get_residues():
173	for atom_a in res_a.get_atoms():
174	for atom_b in res_b.get_atoms():
175	if atom_a - atom_b < distance:
176	interface_a.add(res_a.id[1])
177	interface_b.add(res_b.id[1])
178
179	return interface_a, interface_b
180	```
181
182	## Common Tasks for Binder Design
183
184	### Target Preparation Checklist
185	1. Download structure:

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Type

pdb

43installs20forks

View on GitHub

How to install pdb?

adaptyvbio/protein-design-skills/pdb

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

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# PDB Database Access
2
3	Note: This skill uses the RCSB PDB web API directly. No Modal deployment needed - all operations run locally via HTTP requests.
4
5	## Fetching Structures
6
7	### By PDB ID
8	```bash
9	# Download PDB file
10	curl -o 1alu.pdb "https://files.rcsb.org/download/1ALU.pdb"
11
12	# Download mmCIF
13	curl -o 1alu.cif "https://files.rcsb.org/download/1ALU.cif"
14	```
15
16	### Using Python
17	```python
18	from Bio.PDB import PDBList
19
20	pdbl = PDBList()
21	pdbl.retrieve_pdb_file("1ABC", pdir="structures/", file_format="pdb")
22	```
23
24	### Using RCSB API
25	```python
26	import requests
27
28	def fetch_pdb(pdb_id: str, format: str = "pdb") -> str:
29	"""Fetch structure from RCSB PDB."""
30	url = f"https://files.rcsb.org/download/{pdb_id}.{format}"
31	response = requests.get(url)
32	response.raise_for_status()
33	return response.text
34
35	def fetch_fasta(pdb_id: str) -> str:
36	"""Fetch sequence in FASTA format."""
37	url = f"https://www.rcsb.org/fasta/entry/{pdb_id}"
38	return requests.get(url).text
39
40	# Example usage
41	pdb_content = fetch_pdb("1ALU")
42	with open("1ALU.pdb", "w") as f:
43	f.write(pdb_content)
44	```
45
46	## Structure Preparation
47
48	### Selecting Chains
49	```python
50	from Bio.PDB import PDBParser, PDBIO, Select
51
52	class ChainSelect(Select):
53	def __init__(self, chain_id):
54	self.chain_id = chain_id
55
56	def accept_chain(self, chain):
57	return chain.id == self.chain_id
58
59	# Extract chain A
60	parser = PDBParser()
61	structure = parser.get_structure("protein", "1abc.pdb")
62	io = PDBIO()
63	io.set_structure(structure)
64	io.save("chain_A.pdb", ChainSelect("A"))
65	```
66
67	### Trimming to Binding Region
68	```python
69	def trim_around_residues(pdb_file, center_residues, buffer=10.0):
70	"""Trim structure to region around specified residues."""
71	parser = PDBParser()
72	structure = parser.get_structure("protein", pdb_file)
73
74	# Get center coordinates
75	center_coords = []
76	for res in structure.get_residues():
77	if res.id[1] in center_residues:
78	center_coords.extend([a.coord for a in res.get_atoms()])
79
80	center = np.mean(center_coords, axis=0)
81
82	# Keep residues within buffer
83	class RegionSelect(Select):
84	def accept_residue(self, res):
85	for atom in res.get_atoms():
86	if np.linalg.norm(atom.coord - center) < buffer:
87	return True
88	return False
89
90	io = PDBIO()
91	io.set_structure(structure)
92	io.save("trimmed.pdb", RegionSelect())
93	```
94
95	## Searching PDB
96
97	### RCSB Search API
98	```python
99	import requests
100
101	query = {
102	"query": {
103	"type": "terminal",
104	"service": "full_text",
105	"parameters": {
106	"value": "EGFR kinase domain"
107	}
108	},
109	"return_type": "entry"
110	}
111
112	response = requests.post(
113	"https://search.rcsb.org/rcsbsearch/v2/query",
114	json=query
115	)
116	results = response.json()
117	```
118
119	### By Sequence Similarity
120	```python
121	query = {
122	"query": {
123	"type": "terminal",
124	"service": "sequence",
125	"parameters": {
126	"value": "MKTAYIAKQRQISFVK...",
127	"evalue_cutoff": 1e-10,
128	"identity_cutoff": 0.9
129	}
130	}
131	}
132	```
133
134	## Structure Analysis
135
136	### Get Chain Info
137	```python
138	def get_structure_info(pdb_file):
139	parser = PDBParser(QUIET=True)
140	structure = parser.get_structure("protein", pdb_file)
141
142	info = {
143	"chains": [],
144	"total_residues": 0
145	}
146
147	for model in structure:
148	for chain in model:
149	residues = list(chain.get_residues())
150	info["chains"].append({
151	"id": chain.id,
152	"length": len(residues),
153	"first_res": residues[0].id[1],
154	"last_res": residues[-1].id[1]
155	})
156	info["total_residues"] += len(residues)
157
158	return info
159	```
160
161	### Find Interface Residues
162	```python
163	def find_interface_residues(pdb_file, chain_a, chain_b, distance=4.0):
164	"""Find residues at interface between two chains."""
165	parser = PDBParser(QUIET=True)
166	structure = parser.get_structure("complex", pdb_file)
167
168	interface_a = set()
169	interface_b = set()
170
171	for res_a in structure[0][chain_a].get_residues():
172	for res_b in structure[0][chain_b].get_residues():
173	for atom_a in res_a.get_atoms():
174	for atom_b in res_b.get_atoms():
175	if atom_a - atom_b < distance:
176	interface_a.add(res_a.id[1])
177	interface_b.add(res_b.id[1])
178
179	return interface_a, interface_b
180	```
181
182	## Common Tasks for Binder Design
183
184	### Target Preparation Checklist
185	1. Download structure:

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Type