Ligand Extraction

This example shows how to align structures of the same protein and extract bound ligands from these structures.

matchAlign() function can be used for aligning protein structures. This example shows how to use it to extract ligands from multiple PDB structures after superposing the structures onto a reference. Output will be PDB files that contain ligands superposed onto the reference structure.

Parse reference and blast search

We start by importing everything from the ProDy package:

In [1]: from prody import *

In [2]: from pylab import *

In [3]: ion()

First, we parse the reference structure and blast search PDB for similar structure:

In [4]: p38 = parsePDB('1p38')

In [5]: seq = p38['A'].getSequence()

In [6]: blast_record = blastPDB(seq)

It is a good practice to save this record on disk, as NCBI may not respond to repeated searches for the same sequence. We can do this using Python standard library pickle as follows:

In [7]: import pickle

Record is save using dump() function into an open file:

In [8]: pickle.dump(blast_record, open('p38_blast_record.pkl', 'wb'))

Then, it can be loaded using load() function:

In [9]: blast_record = pickle.load(open('p38_blast_record.pkl', 'rb'))

Align structures and extract ligands

Then, we parse the hits one-by-one, superpose them onto the reference structure, and extract ligands:

In [10]: for pdb_id in blast_record.getHits(90, 70):
   ....:     try:
   ....:         pdb = parsePDB(pdb_id)
   ....:         pdb = matchAlign(pdb, p38)[0]
   ....:     except:
   ....:         continue
   ....:     else:
   ....:         ligand = pdb.select('not protein and not water')
   ....:         repr(ligand)
   ....:         if ligand:
   ....:             writePDB(pdb_id + '_ligand.pdb', ligand)
   ....: 

In [11]: !ls *_ligand.pdb
1a9u_ligand.pdb  2yix_ligand.pdb  3hv3_ligand.pdb  3p78_ligand.pdb
1bl6_ligand.pdb  2zaz_ligand.pdb  3hv4_ligand.pdb  3p79_ligand.pdb
1bl7_ligand.pdb  2zb0_ligand.pdb  3hv5_ligand.pdb  3p7a_ligand.pdb
1bmk_ligand.pdb  2zb1_ligand.pdb  3hv6_ligand.pdb  3p7b_ligand.pdb
1di9_ligand.pdb  3bv2_ligand.pdb  3hv7_ligand.pdb  3p7c_ligand.pdb
1ian_ligand.pdb  3bv3_ligand.pdb  3hvc_ligand.pdb  3pg3_ligand.pdb
1kv1_ligand.pdb  3bx5_ligand.pdb  3iph_ligand.pdb  3py3_ligand.pdb
1kv2_ligand.pdb  3c5u_ligand.pdb  3itz_ligand.pdb  3qud_ligand.pdb
1m7q_ligand.pdb  3ctq_ligand.pdb  3iw5_ligand.pdb  3que_ligand.pdb
1ouk_ligand.pdb  3d7z_ligand.pdb  3iw6_ligand.pdb  3rin_ligand.pdb
1ouy_ligand.pdb  3d83_ligand.pdb  3iw7_ligand.pdb  3roc_ligand.pdb
1ove_ligand.pdb  3ds6_ligand.pdb  3iw8_ligand.pdb  3s3i_ligand.pdb
1oz1_ligand.pdb  3dt1_ligand.pdb  3k3i_ligand.pdb  3s4q_ligand.pdb
1r39_ligand.pdb  3e92_ligand.pdb  3k3j_ligand.pdb  3u8w_ligand.pdb
1r3c_ligand.pdb  3e93_ligand.pdb  3kf7_ligand.pdb  3uvp_ligand.pdb
1w7h_ligand.pdb  3fc1_ligand.pdb  3kq7_ligand.pdb  3uvq_ligand.pdb
1w82_ligand.pdb  3fi4_ligand.pdb  3l8s_ligand.pdb  3uvr_ligand.pdb
1w83_ligand.pdb  3fkl_ligand.pdb  3l8x_ligand.pdb  3zs5_ligand.pdb
1w84_ligand.pdb  3fkn_ligand.pdb  3lfa_ligand.pdb  3zsg_ligand.pdb
1wbn_ligand.pdb  3fko_ligand.pdb  3lfb_ligand.pdb  3zsh_ligand.pdb
1wbo_ligand.pdb  3fl4_ligand.pdb  3lfc_ligand.pdb  3zsi_ligand.pdb
1wbs_ligand.pdb  3fln_ligand.pdb  3lfd_ligand.pdb  3zya_ligand.pdb
1wbt_ligand.pdb  3flq_ligand.pdb  3lfe_ligand.pdb  4a9y_ligand.pdb
1wbv_ligand.pdb  3fls_ligand.pdb  3lff_ligand.pdb  4aa0_ligand.pdb
1wbw_ligand.pdb  3flw_ligand.pdb  3lhj_ligand.pdb  4aa4_ligand.pdb
1yqj_ligand.pdb  3fly_ligand.pdb  3mgy_ligand.pdb  4aa5_ligand.pdb
1yw2_ligand.pdb  3flz_ligand.pdb  3mh0_ligand.pdb  4aac_ligand.pdb
1ywr_ligand.pdb  3fmh_ligand.pdb  3mh1_ligand.pdb  4dli_ligand.pdb
1zyj_ligand.pdb  3fmj_ligand.pdb  3mh2_ligand.pdb  4dlj_ligand.pdb
1zz2_ligand.pdb  3fmk_ligand.pdb  3mh3_ligand.pdb  4e6a_ligand.pdb
1zzl_ligand.pdb  3fml_ligand.pdb  3mpa_ligand.pdb  4e6c_ligand.pdb
2baj_ligand.pdb  3fmm_ligand.pdb  3mpt_ligand.pdb  4e8a_ligand.pdb
2bak_ligand.pdb  3fmn_ligand.pdb  3mvl_ligand.pdb  4eh2_ligand.pdb
2bal_ligand.pdb  3fsf_ligand.pdb  3mvm_ligand.pdb  4eh3_ligand.pdb
2baq_ligand.pdb  3fsk_ligand.pdb  3mw1_ligand.pdb  4eh4_ligand.pdb
2ewa_ligand.pdb  3gc7_ligand.pdb  3new_ligand.pdb  4eh5_ligand.pdb
2fsl_ligand.pdb  3gcp_ligand.pdb  3nnu_ligand.pdb  4eh6_ligand.pdb
2fsm_ligand.pdb  3gcq_ligand.pdb  3nnv_ligand.pdb  4eh7_ligand.pdb
2fso_ligand.pdb  3gcs_ligand.pdb  3nnw_ligand.pdb  4eh8_ligand.pdb
2fst_ligand.pdb  3gcu_ligand.pdb  3nnx_ligand.pdb  4eh9_ligand.pdb
2gfs_ligand.pdb  3gcv_ligand.pdb  3nww_ligand.pdb  4ehv_ligand.pdb
2ghl_ligand.pdb  3gfe_ligand.pdb  3o8p_ligand.pdb  4ewq_ligand.pdb
2ghm_ligand.pdb  3gi3_ligand.pdb  3o8t_ligand.pdb  4f9w_ligand.pdb
2gtm_ligand.pdb  3ha8_ligand.pdb  3o8u_ligand.pdb  4f9y_ligand.pdb
2gtn_ligand.pdb  3hec_ligand.pdb  3obg_ligand.pdb  4fa2_ligand.pdb
2i0h_ligand.pdb  3heg_ligand.pdb  3obj_ligand.pdb  4geo_ligand.pdb
2npq_ligand.pdb  3hl7_ligand.pdb  3oc1_ligand.pdb  4kin_ligand.pdb
2puu_ligand.pdb  3hll_ligand.pdb  3ocg_ligand.pdb  4kip_ligand.pdb
2qd9_ligand.pdb  3hp2_ligand.pdb  3od6_ligand.pdb  4kiq_ligand.pdb
2rg5_ligand.pdb  3hp5_ligand.pdb  3ody_ligand.pdb  4l8m_ligand.pdb
2rg6_ligand.pdb  3hrb_ligand.pdb  3odz_ligand.pdb  4loo_ligand.pdb
2yis_ligand.pdb  3hub_ligand.pdb  3oef_ligand.pdb  4lop_ligand.pdb
2yiw_ligand.pdb  3huc_ligand.pdb  3p5k_ligand.pdb  4loq_ligand.pdb

Ligands bound to p38 are outputted. Note that output PDB files may contain multiple ligands.

The output can be loaded into a molecular visualization tool for analysis.