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absplit

(c) 2021 UCL, Andrew C.R. Martin

Code to take an antibody PDB file and split it into separate Fvs

Known issues

  1. The code needs to retain the PDB header for downstream steps
  2. Code needs to apply symmetry operators (e.g. 1b0w, 2rhe)
    • decided to do this first with pdbsymm
  3. Some truncated sequences won't score highly enough to be flagged as antibodies - just score over the aligned region.
  4. Crystal packing sometimes identified as a complex. e.g. 1shm_1

Algorithm

  1. Read the PDB file and split into chains
  2. For each chain, scan with a library of VH and VL domains to locate these. This is done by alignment and the standard interface positions are recorded.
  3. For each VH/VL domain, find the CoG
  4. For each VH/VL domain measure the CofG distance to all others. If within a cutoff, then this is a potential VH/VL pair.
  5. For each potential VH/VL pair (note that these can be VL/VL or VH/VL and may be within the same chain) check the standard interface residues (assigned from the alignment) and ensure that they are close together
  6. Add back HETATMs (other than water)
  7. We now have assigned VH/VL pairs, so check those against other chains to look for antibody/antigen interactions. Note that an 'antigen' may be a different antibody.
  8. Now check the HETATMs for HET antigens
  9. Output the VH/VL domains together with any contacted antigen

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absplit's Issues

SEQRES shorter than ATMSEQ

Length SEQRES < ATMSEQ

pdb1dee_2    (both HL)
pdb1dee_1P   (both HL)
pdb3j42_1    (L)
pdb3j42_2P   (L) 
pdb3j42_0P   (L)

special case: 7jz4

CDR-H3 in 7jz4_0 and 7jz4_1H is insertion of a LAIR1 domain (~109 residue long)

Current assignment is a slice of LAIR1

Need to use different contact counts for haptens

6n35_0 and 6n35_1H are both complexes with a hapten, but only 6n35_1H is identified as such.

I assume it isn't passing some of the count cutoffs for an antigen, so these should be tweaked for haptens.

Currently:

  • >=30 CDR contacts within 6A -or-
  • >=14 CDR contacts within 6A and the number of contacts with CDRs is greater than the number with framework

antigen chain miss labelled (h becomes H in ATOM records)

Dataset /serv/data/abdb_newdata_20200719

Entry: pdb6ao0_0P.mar

REMARK 950 CHAIN-TYPE  LABEL ORIGINAL
REMARK 950 CHAIN L     L     L
REMARK 950 CHAIN A     h     H

antigen chain label h miss labelled as H in ATOM records

ATOM    820  NH1 ARG L 110      27.317   8.919  -7.357  1.00 85.33           N  
ATOM    821  NH2 ARG L 110      26.525  11.069  -7.214  1.00 83.62           N  
TER     822      ARG L 110                                                      
ATOM    823  N   GLU H   1     -31.765  -2.083   2.986  1.00 56.89           N  
ATOM    824  CA  GLU H   1     -32.346  -3.410   3.146  1.00 58.64           C  
ATOM    825  C   GLU H   1     -31.360  -4.493   2.720  1.00 53.94           C

NR Code

Sort out the non-redundancy code

Chothia files empty or missing

Empty:

pdb1p7k_0H.cho
pdb1s78_0P.cho
pdb1xct_0P.cho
pdb1ahw_0P.cho

Missing:

pdb6e9q_2
pdb6e9q_3
pdb5dt1_0
pdb4rqq_2
pdb4rqq_1
pdb3mug_1
pdb3mug_4
pdb3mug_3
pdb3mug_0
pdb5uy3_0
pdb4toy_0
pdb6uum_1
pdb6v6w_1H
pdb6uuh_0
pdb6uuh_1
pdb5ud9_0
pdb3q6f_0
pdb3q6f_3
pdb3q6f_2
pdb3q6f_5
pdb5mp6_0
pdb3mlt_2
pdb3mlt_3
pdb5w1g_0
pdb6w5a_0
pdb6bjz_0
pdb5ywf_0
pdb5ywf_1
pdb6qd6_1
pdb6qd6_0
pdb6xv8_0
pdb5wb1_0
pdb6qb4_0
pdb6qf9_0
pdb6qfc_0
pdb6qb9_1
pdb6qb9_0
pdb6qf9_1
pdb5kov_10
pdb5kov_3
pdb5kov_1
pdb5kov_7
pdb5kov_5
pdb3wbd_3
pdb3wbd_1
pdb5nm0_2
pdb5d9q_8
pdb5wdu_1
pdb5d9q_2
pdb5d9q_5
pdb5wdu_5
pdb5gru_3
pdb2znx_1
pdb2znx_3
pdb6y1r_3
pdb1i3v_0
pdb6y0e_1
pdb6y0e_0
pdb4b50_0

Present but no H/L chains:

pdb6e9q_1P
pdb6e9q_0P
pdb6vtt_0PH
pdb4rqq_0P
pdb3mug_5PH
pdb3mug_2PH
pdb5uy3_1P
pdb5uty_0PH
pdb5u7o_0PH
pdb5fyj_0PH
pdb5fyl_0PH
pdb4tvp_1PH
pdb5wdu_11PH
pdb6de7_0PH
pdb5utf_1PH
pdb5fyk_0PH
pdb5u7m_0PH
pdb5wdu_9PH
pdb6uum_0
pdb6v6w_3H
pdb6utk_1PH
pdb6chb_0P
pdb6ch9_1PH
pdb6chb_3P
pdb6ch8_1PH
pdb6chb_5P
pdb6ch7_1PH
pdb3q6f_4P
pdb3q6f_1P
pdb5mp6_1P
pdb3mlt_1P
pdb3mls_3P
pdb3mlr_0P
pdb3mls_1P
pdb3mls_0P
pdb3mlt_0P
pdb3mls_2P
pdb5w1m_1P
pdb5w1m_2P
pdb5w1m_3P
pdb5w1m_0P
pdb6w9g_0P
pdb6w9g_2P
pdb6w9g_1P
pdb5ywp_0P
pdb5ywp_1P
pdb6qd6_2P
pdb6xv8_1P
pdb7kqy_1P
pdb5vm4_4P
pdb5vm4_1P
pdb5vm4_0P
pdb5kov_8P
pdb3lrh_2P
pdb3lrh_3P
pdb3lrh_0P
pdb2znx_0PH
pdb2znx_2PH
pdb6y1r_0P
pdb6y1r_4P
pdb6y1r_1P
pdb6y1r_2P
pdb1i3v_1P
pdb1i3u_0H
pdb6xzf_0P
pdb7aej_0P

Summary of problem files

The following all have remaining problems:


5kov - problem with H chain - weird chain names
       0P - ok but chain duplicated
       1P - ok but chain duplicated
       2P - not numbered (.bad) - confused by chain labels
       3P - ok but chain duplicated
       4P - ok? perhaps missing partner chain
       5P - OK
       6  - ok? perhaps missing partner chain
       7P - ok but chain duplicated

5wb1 - OK but chain duplicated.
       HC only Ab with Nter fusion. absplit is working but
       numbering is duplicating the Ab 

6e9q 
       0  - heavy chain missing (in SEQRES but not in ATOM)
       1P - heavy chain missing (in SEQRES but not in ATOM)
       2  - heavy chain missing (in SEQRES but not in ATOM)
       3  - heavy chain missing (in SEQRES but not in ATOM)

These all fail in numbering - they are now correctly provided as un-numbered (.bad) files:

1i3u - lost Ab in numbering - fixed to create a .bad file
3mlr - lost Ab in numbering - fixed to create a .bad file
3mls - lost Ab in numbering - fixed to create a .bad file
5dt1 - lost Ab in numbering - fixed to create a .bad file
5w1m - lost Ab in numbering - fixed to create a .bad file
5ywp - lost Ab in numbering - fixed to create a .bad file
6utk - lost Ab in numbering - fixed to create a .bad file
6uuh - lost Ab in numbering - fixed to create a .bad file
6uum - lost Ab in numbering - fixed to create a .bad file
6v6w - lost Ab in numbering - fixed to create a .bad file
6xzf - lost Ab in numbering - fixed to create a .bad file
4b50 - lost all - fixed to create a .bad file
4rqq - lost all - fixed to create a .bad file
4toy - lost all - fixed to create a .bad file
5mp6 - lost all - fixed to create a .bad file
5w1g - lost all - fixed to create a .bad file
5ywf - lost all - fixed to create a .bad file
6y0e - lost all - fixed to create a .bad file
6vtt - lost Ab / lost all - fixed to create a .bad file
7aej - lost Ab / lost all - fixed to create a .bad file
1i3v - lost Ab / lost all - fixed to create a .bad file
3mlt - lost Ab / lost all - fixed to create a .bad file
6qd6 - lost Ab / lost all - 1,2,4,5,7,8 are .bad; 0,3,9 are OK
6y1r - lost Ab / lost all - fixed to create a .bad file
4tvp - fixed for some - fixed to create a .bad file for the bad ones
5fyj - fixed for some - fixed to create a .bad file for the bad ones
5fyk - fixed for some - fixed to create a .bad file for the bad ones
5fyl - fixed for some - fixed to create a .bad file for the bad ones
5u7m - fixed for some - fixed to create a .bad file for the bad ones
5u7o - fixed for some - fixed to create a .bad file for the bad ones
5utf - fixed for some - fixed to create a .bad file for the bad ones
5uty - fixed for some - fixed to create a .bad file for the bad ones
5wdu - fixed for some - fixed to create a .bad file for the bad ones
6ch7 - fixed for some - fixed to create a .bad file for the bad ones
6ch8 - fixed for some - fixed to create a .bad file for the bad ones
6ch9 - fixed for some - fixed to create a .bad file for the bad ones
6de7 - fixed for some - fixed to create a .bad file for the bad ones
6chb - fixed for some / lost all - fixed to create .bad for bad ones
5uy3 - fixed for some / lost all - fixed to create .bad for bad ones
       (The bad one finds one chain as antigen since it doesn't pair them)

The following that were broken are all now fixed:

3wbd
5d9q 
5gru
5ud9 
6qb4 
6qb9 
6qf9
6qfc
6w9g
6xv8 
5nm0
2znx

pdb2fr4_0PN: extra antigen "P"

antigen type should only contain nucleotides

Chain B in pdb2fr4_0PN.mar classified as antigen due to location close to CDRs in chain H

7fej - not recognizing the H/L pairing

This one has a Light and Heavy that are not recognized as being paired. Consequently it splits it into 2 files where one has L as antibody with H as antigen and the other has H as antibody and L as antigen.

Issues associated with .cho files

  1. Empty .cho files
pdb1p7k_0H.cho, pdb1s78_0P.cho, pdb1xct_0P.cho, pdb1ahw_0P.cho
  1. .cho files not found: see below for a list of identifiers
pdb6e9q_2, pdb6e9q_3, pdb5dt1_0,  pdb4rqq_2, pdb4rqq_1, pdb3mug_1, pdb3mug_4, pdb3mug_3, pdb3mug_0,  pdb5uy3_0
pdb4toy_0, pdb6uum_1, pdb6v6w_1H, pdb6uuh_0, pdb6uuh_1, pdb5ud9_0, pdb3q6f_0, pdb3q6f_3, pdb3q6f_2,  pdb3q6f_5
pdb5mp6_0, pdb3mlt_2, pdb3mlt_3,  pdb5w1g_0, pdb6w5a_0, pdb6bjz_0, pdb5ywf_0, pdb5ywf_1, pdb6qd6_1,  pdb6qd6_0, 
pdb6xv8_0, pdb5wb1_0, pdb6qb4_0,  pdb6qf9_0, pdb6qfc_0, pdb6qb9_1, pdb6qb9_0, pdb6qf9_1, pdb5kov_10, pdb5kov_3, 
pdb5kov_1, pdb5kov_7, pdb5kov_5,  pdb3wbd_3, pdb3wbd_1, pdb5nm0_2, pdb5d9q_8, pdb5wdu_1, pdb5d9q_2,  pdb5d9q_5, 
pdb5wdu_5, pdb5gru_3, pdb2znx_1,  pdb2znx_3, pdb6y1r_3, pdb1i3v_0, pdb6y0e_1, pdb6y0e_0, pdb4b50_0
  1. .cho files that where neither Heavy nor Light chains are present
pdb6e9q_1P,  pdb6e9q_0P,  pdb6vtt_0PH, pdb4rqq_0P,   pdb3mug_5PH, pdb3mug_2PH, pdb5uy3_1P,  pdb5uty_0PH, pdb5u7o_0PH, 
pdb5fyj_0PH, pdb5fyl_0PH, pdb4tvp_1PH, pdb5wdu_11PH, pdb6de7_0PH, pdb5utf_1PH, pdb5fyk_0PH, pdb5u7m_0PH, pdb5wdu_9PH, 
pdb6uum_0,   pdb6v6w_3H,  pdb6utk_1PH, pdb6chb_0P,   pdb6ch9_1PH, pdb6chb_3P,  pdb6ch8_1PH, pdb6chb_5P,  pdb6ch7_1PH, 
pdb3q6f_4P,  pdb3q6f_1P,  pdb5mp6_1P,  pdb3mlt_1P,   pdb3mls_3P,  pdb3mlr_0P,  pdb3mls_1P,  pdb3mls_0P,  pdb3mlt_0P, 
pdb3mls_2P,  pdb5w1m_1P,  pdb5w1m_2P,  pdb5w1m_3P,   pdb5w1m_0P,  pdb6w9g_0P,  pdb6w9g_2P,  pdb6w9g_1P,  pdb5ywp_0P,  
pdb5ywp_1P,  pdb6qd6_2P,  pdb6xv8_1P,  pdb7kqy_1P,   pdb5vm4_4P,  pdb5vm4_1P,  pdb5vm4_0P,  pdb5kov_8P,  pdb3lrh_2P,  
pdb3lrh_3P,  pdb3lrh_0P,  pdb2znx_0PH, pdb2znx_2PH,  pdb6y1r_0P,  pdb6y1r_4P,  pdb6y1r_1P,  pdb6y1r_2P,  pdb1i3v_1P,  
pdb1i3u_0H,  pdb6xzf_0P,  pdb7aej_0P
  1. .cho file where Length SEQRES < ATMSEQ:
pdb1dee_2 (both HL), pdb1dee_1P (both HL),
pdb3j42_1 (L), pdb3j42_2P (L), pdb3j42_0P (L)
e.g. pdb1dee_2.cho alignment with original chain
  • pdb1dee_2.cho chain H vs. original 1dee chain F
CLUSTAL O(1.2.3) multiple sequence alignment


pdb1dee_2.cho_H      QVQLVESGGGVVQPGKSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVALISYDESNKYY
1dee_F               QVQLVESGGGVVQPGKSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVALISYDESNKYY
                     ************************************************************

pdb1dee_2.cho_H      ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVKFYDPTAPNDYWGQGTLVTVS
1dee_F               ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVKFYDPTAPNDYWGQGTLVTVS
                     ************************************************************

pdb1dee_2.cho_H      QVQLVES------GGGVVQPGKSLRLSCAASGFTFSGYGMHWVRQAPGKGLEWVALISYD
1dee_F               SGSASAPTLFPLVSCENSNPSSTVAVGCLAQDFLPDSITFSWKYKNNSDISSTRGFPSVL
                     . .          .    :*..:: :.* *..*  ..  : *  :  ..  .  .: *  

pdb1dee_2.cho_H      ESNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKVKFYDPTAPNDYWGQG
1dee_F               RGGKYAATS--------------QVLLPSKDVAQGTNEHVVCKV-Q--H---PNGNKEKD
                     ...** * *               : *  :.:    .    *   :  .   **.   :.

pdb1dee_2.cho_H      TLVTVS
1dee_F               VPL---
                     . :
  • pdb1dee_2.cho chain L vs. original 1dee chain E
CLUSTAL O(1.2.3) multiple sequence alignment


pdb1dee_2.cho_L      DIQMTQSPSSLSASVGDRVTITCRTSQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS
1dee_E               DIQMTQSPSSLSASVGDRVTITCRTSQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPS
                     ************************************************************

pdb1dee_2.cho_L      RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSAPRTFGQGTKVEIKRTDIQMTQ---SP
1dee_E               RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSAPRTFGQGTKVEIKRTVAAPSVFIFPP
                     *************************************************    :     *

pdb1dee_2.cho_L      SSLSASVGDRVTITCRTSQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSG
1dee_E               SDEQLKSG-TASVVCL-------LNNFYPREAK----VQWKVDNALQSGNSQESVTEQDS
                     *. . . *  .::.*          *:* ::      :   . .:****  ..   . ..

pdb1dee_2.cho_L      T------DFTLTISSLQPEDFATYYCQQSY---SA--PRTFGQGTKVEIKRT
1dee_E               KDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC------
                     .      . ***:*. : *.. .* *: ::   *:   ::*.:*

The 2nd half of heavy and light chains cannot align with the original chain, does it suggest some issues with the trauncation process?

  1. special case: 4hjj_1P

4HJJ is a Dual Variable Domain Immunoglobulin (DVD-Ig)

pdb4hjj_1P.cho variable domain CDR is not interacting with the antigen.

In the original PDB file of 4HJJ, based on its structure, H126-H246 and L114-L224 looks like the second variable domain and is interacting with the antigen, is the correct variable domain to trauncate.

Change FAA files to be two entries

Currently there is one header followed by L and H chains.
Change to generate separate headers for each (in process.sh)
Also need to change nr.pl to handle the new files

pdb6ca6_0P and pdb6ca6_1P: no antigen present, chain-splitting issue

6ca6 contains two antibodies and no antigen is present in this PDB file except for two small molecules (ether and glycerol)

  • Fab 1: chian A and B
  • Fab 2: chain H and L

In preliminary version of the new release (/serv/data/abdb_newdata): pdb6ca6_0P.mar and pdb6ca6_1P.mar each contains a single heavy chain.

Avoid xtal packing as complexes

When two Abs interacts where the sequences are the same, flag them as making xtal contacts instead of being complexes.

e.g. 1DVF is a genuine anti-id antibody
1SHM is not

missing antibody chains in some AbDb entries

I went through all AbDb in which the antigen type contains "P" (7402 entries), and found the following entries where antibody chains are missing.

mAb entries in which both H and L chains are missing (197 entries) 
5fyk_0PH 5um8_1PH 3csy_3P  5u7o_0PH 6de7_0PH 5ywp_0P  4r4n_5P  5w1k_4PH 3u2s_0PH 6wix_0PH
4y5y_1P  6w9g_2P  3mug_5PH 3mls_1P  6ch7_0PH 6ieq_1PH 5u1f_0P  6mdt_0PH 5v8l_3PH 6e4y_0P 
3u4e_0PH 5wdu_7PH 3mls_0P  5uy3_1P  5w1k_0PH 6e5p_3P  6v8z_1P  4y5y_0P  5v8l_2P  6ck9_0PH
4xnz_2P  7k7i_4P  6vtt_0PH 5fyj_0PH 5ywp_1P  4r4n_4P  5w1k_2PH 3csy_2P  6nm6_2P  6chb_0P 
6nnj_2P  3q6f_1P  6ch7_1PH 6u0n_2P  4dqo_0PH 6mu7_0PH 6t3j_3P  4org_2P  5kan_0P  5v8m_1P 
3u2s_1PH 6nnf_2P  7lf8_0P  6mug_0PH 5w1m_1P  6e5p_8P  7kgv_1P  6ca6_1P  7ly9_2P  6nnf_0PH
6w4m_0P  5wdu_11PH 6mtn_0PH 5uxq_0P  5w1k_7PH 4rx4_0PH 4r4n_3P  6ujc_0P  7k7i_3P  6x1w_0P 
7k7i_2P  4r4n_2P  6mv5_0P  5uxq_1P  3mug_2PH 4rqq_0P  5v7j_1PH 7ly9_3P  6ca6_0P  7kgv_0P 
5w1m_0P  5u7m_0PH 4lsq_0PH 3mlu_0P  6mu6_0PH 3u4e_1PH 6u0l_2P  4cc8_2P  5kan_1P  5v8m_0P 
4org_3P  6e5p_5P  5d1q_1P  6muf_0PH 6vi0_0PH 4yaq_0P  6u0l_1P  4cc8_1P  5kan_2P  3se8_0P 
4org_0P  6t3j_1P  5d1x_1P  6xrt_0PH 6urh_0PH 6u0n_0P  7k7i_1P  4r4n_1P  6mtj_0PH 5mp6_1P 
7kfe_0P  6e9q_1P  4lsr_0P  4s1q_0P  7ly9_0P  6vi0_2PH 5w1m_3P  5fyl_0PH 2qad_0P  6chb_5P 
6ch9_0PH 2qad_1P  5w1m_2P  5w6d_1PH 7ly9_1P  7kfe_1P  6e9q_0P  6ch8_0PH 6dfg_2PH 4r4n_0P 
7k7i_0P  3mlr_0P  6v8z_5P  6e4z_0P  6dfg_0PH 4org_1P  6nnj_0PH 5v8m_2P  4cc8_0P  6u0l_0P 
4jb9_0P  6opa_0PH 6utk_0PH 4yaq_1P  7lg6_2PH 4xnz_1P  4r4n_7P  4jpv_0P  5ywo_0P  4r4f_0P 
5wdu_9PH 6ch9_1PH 3csy_1P  5uty_0PH 7kmd_0PH 6chb_3P  7lf7_1P  3mlt_1P  6vi0_1PH 6vzi_0PH
6nij_0PH 3mls_3P  5t3s_1PH 6w9g_0P  3mlv_0P  7lg6_0PH 5v8l_1P  4tvp_1PH 5utf_1PH 3q6f_4P 
6u0n_1PH 5v8l_0P  6v8z_3P  3mlv_1P  6w9g_1P  3mls_2P  6dfg_1PH 7lg6_4PH 6nm6_0PH 3mlt_0P 
6v6w_2PH 6utk_1PH 6w03_0PH 6v6w_0PH 6zqk_0PH 6mco_0PH 4lsv_0P  3csy_0P  5cez_1PH 5vj6_0P 
6mu8_0PH 6ch8_1PH 5ywo_1P  4r4n_6P  4rx4_1P  6ce0_0PH 4xnz_0P
mAb entries in which H chain is missing (3 entries) 
6e8v_6P  6e8v_3P  6e8v_4P
mAb entries in which L chain is missing (3 entries) 
4lsp_0PH 5gs2_0P  4rwy_0PH
L only Ab in which L chain is missing (239 entries) 
4nik_0P  5gry_1P  6ikm_13P 6kr0_1P  7l1u_0P  5aaw_2P  5yax_1P  5npj_1P  7ldd_0P  4f9p_0P 
6oao_2P  5grw_0P  3lrh_3P  5jym_1P  6oij_0P  5gs1_1P  6z1o_3P  5u0u_3P  6vms_0P  3uzq_0P 
5lx9_0PH 5yd5_0P  6omm_0P  6ek2_1P  5gs3_0P  7db6_0P  6ikm_2P  6uup_2P  3uze_0P  6o8d_0P 
6ic3_3P  6njl_0P  6ic3_2P  3uze_1P  6uup_3P  7cmu_0P  6ikm_3P  5fhx_1P  5gs3_1P  7f4f_0P 
5yd5_1P  6ek2_0P  7aue_0P  6njn_0P  7f4h_1P  7ew4_0P  7ezm_0P  6os9_0P  6z1o_2P  5u0u_2P 
6kpf_0P  5grw_1P  3lrh_2P  5jym_0P  6lml_0P  6oao_3P  5j75_0PH 5npj_0P  4f9p_1P  5aaw_3P 
6kr0_0P  6xbm_0P  5a2l_0P  5gry_0P  6ikm_12P 5lxa_0PH 5gs1_7P  6z1o_5P  5yd3_0P  6yxf_0PH
7ew0_0P  4kv5_2P  4unt_3P  7e32_0P  6ikm_4P  5yd4_2P  5kov_8P  6ic3_5P  7rk1_0P  6ikm_15P
1lmk_2P  5u68_2P  7jum_0P  7k93_0P  6k42_0P  6wwz_0P  6ikm_8P  7jtr_3P  6dzy_1P  7deo_0P 
6oao_4P  7evz_0P  7deu_0P  6oao_5P  7deo_1P  5j75_1PH 6ikm_9P  7jtr_2P  6xbk_0P  7k93_1P 
7jum_1P  1lmk_3P  7rk1_1P  6ikm_14P 6crk_0P  6dde_0P  7ew2_0P  6xox_0P  5yd4_3P  6qf6_2P 
6ikm_5P  4unt_2P  7d77_0P  6yxg_0PH 7eb2_0P  7e9h_0P  7f2o_0P  4kv5_3P  6pt0_0P  5gs1_10P
5gs1_6P  6z1o_4P  5yd3_1P  5yd4_0P  6ikm_6P  7ew7_0P  6g8r_0P  4unt_1P  5dfw_0P  6oik_0P 
4kv5_0P  7cmv_0P  7cu5_1P  7dw9_1P  5yd3_2P  5gs1_5P  6vun_0PH 6o89_1P  5owp_0P  5iwl_0P 
5grz_0P  6ejm_0P  5iwl_1PH 1dzb_1P  7jtr_1P  5jyl_1P  5j74_0P  7k93_2P  6vrp_0PH 5wn9_0P 
5grx_1P  7jum_2P  6tou_0P  5npi_0P  5u68_0P  1lmk_0P  5gs1_9P  6ikm_17P 5yy4_0P  6ikm_16P
7dfl_0P  5gs1_8P  1lmk_1P  5npi_1P  5u68_1P  5grx_0P  6xbl_0P  7k93_3P  6n4b_0P  1dzb_0P 
7jtr_0P  5jyl_0P  5grz_1P  6ejm_1P  7l1v_0P  5yd3_3P  5gs1_4P  7cu5_0P  6kpg_0P  7jhj_0P 
4kv5_1P  4unt_0P  6ikm_7P  6qf6_0P  5yd4_1P  6wha_0P  6vuo_0PH 7exd_0P  6vrp_1P  3lrh_1P 
6ehy_1P  6oao_0P  7det_1P  7kh0_0P  7ldd_2P  6dzw_0PH 5aaw_0P  7evy_0P  6kr0_3P  6ikm_11P
7jvr_0P  6njl_2P  7e33_0P  7e9g_0P  4h0h_0P  6ikm_0P  3uzv_0P  6lfm_0P  6vun_1PH 3uyp_0P 
6yye_0P  6z1o_1P  5u0u_1P  5gs1_3P  7ezh_0P  7ew1_0P  2ghw_0P  2ghw_1P  2gki_1P  6z1o_0P 
5u0u_0P  5gs1_2P  6yye_1P  7ew3_0P  6ikm_1P  6vuo_1PH 6lfo_0P  2znx_2PH 6ikm_10P 6kr0_2P 
2znx_0PH 6y6c_1P  5aaw_1P  6k41_0P  7det_0P  6oao_1P  5aam_0P  6xbj_0P  3lrh_0P
H only Ab in which H chain is missing (90 entries) 
6gk4_2P  6qfa_2PH 1i3v_1P  5uk4_19P 6qd6_2P  6rvc_1P  6qfa_0PH 5uk4_6P  2p42_0P  5uk4_15P
5uk4_14P 2p42_1P  6xzf_0P  5uk4_7P  6ul6_0P  6qfa_4PH 6rvc_0P  6ui1_1P  6gkd_2P  5uk4_18P
6z20_0P  6y1r_4P  6gkd_10P 6xw5_1P  6qfa_1PH 2p48_0P  2p44_0P  6dbd_0P  2p46_1P  5uk4_0P 
6z20_1PH 5uk4_13P 5vm4_0P  7a5v_0PH 4f9l_1P  7a48_0P  6hup_0P  6huj_0P  6y1r_2P  6xvi_0P 
4f9l_0P  6pcu_2P  5vm4_1P  6gkd_8P  5uk4_12P 2p46_0P  5uk4_1P  6gjs_0P  6v7z_1PH 6xw5_0P 
7aej_0P  6gkd_4P  6qkd_0P  5uk4_11P 5uk4_2P  2p43_0P  4pfe_1P  6xym_1P  6huo_0P  6y1r_1P 
6pcu_1P  6pcu_0P  6v7z_0P  6y1r_0P  7kqy_1P  6xym_0P  6gkd_6P  4pfe_0P  5uk4_3P  5uk4_10P
5uk4_8P  3k3q_0P  5vm4_4P  6gk4_0P  5uk4_17P 5uk4_4P  6i07_0P  2p45_0P  6gkd_0P  6rvc_2P 
6i07_1P  2p47_0P  5f21_0P  5uk4_5P  6xv8_1P  5uk4_16P 6huk_0P  5l21_0P  6hug_0P  5uk4_9P

pdb6xun_2PH.mar: chain mapping, repeated HETATM, antigen type

Current 6xun_2PH chain mapping:

REMARK 950 CHAIN-TYPE  LABEL ORIGINAL
REMARK 950 CHAIN L     L     D
REMARK 950 CHAIN H     H     C
REMARK 950 CHAIN A     B     B
SEQRES   1 L  116  GLN SER VAL LEU THR GLN PRO PRO SER ALA SER GLY THR

Hapten is in chain G, might be clearer to add

REMARK 950 CHAIN A     G     G

Also, HETATM lines were repeated in pdb6xun_2PH.mar compared with original PDB file.
In the original PDB file (56 HETATM in chain G)

HETATM section 
HETATM10097  C1  NAG G   1     -29.496  -5.180 -10.475  1.00 36.52           C  
HETATM10098  C2  NAG G   1     -29.832  -6.201 -11.559  1.00 39.31           C  
HETATM10099  C3  NAG G   1     -29.808  -7.616 -10.978  1.00 38.49           C  
HETATM10100  C4  NAG G   1     -28.488  -7.870 -10.258  1.00 41.60           C  
HETATM10101  C5  NAG G   1     -28.233  -6.765  -9.239  1.00 37.27           C  
HETATM10102  C6  NAG G   1     -26.902  -6.879  -8.537  1.00 40.53           C  
HETATM10103  C7  NAG G   1     -31.220  -5.567 -13.469  1.00 41.32           C  
HETATM10104  C8  NAG G   1     -32.609  -5.308 -13.974  1.00 31.95           C  
HETATM10105  N2  NAG G   1     -31.114  -5.920 -12.184  1.00 39.35           N  
HETATM10106  O1  NAG G   1     -29.506  -3.874 -10.960  1.00 40.28           O  
HETATM10107  O3  NAG G   1     -29.983  -8.563 -12.027  1.00 40.36           O  
HETATM10108  O4  NAG G   1     -28.501  -9.130  -9.596  1.00 43.78           O  
HETATM10109  O5  NAG G   1     -28.241  -5.495  -9.904  1.00 42.13           O  
HETATM10110  O6  NAG G   1     -26.898  -6.121  -7.335  1.00 47.52           O  
HETATM10111  O7  NAG G   1     -30.236  -5.459 -14.191  1.00 45.35           O  
HETATM10112  C1  GAL G   2     -31.215  -9.175 -12.071  1.00 42.90           C  
HETATM10113  C2  GAL G   2     -31.247  -9.706 -13.512  1.00 37.51           C  
HETATM10114  C3  GAL G   2     -32.527 -10.446 -13.786  1.00 42.73           C  
HETATM10115  C4  GAL G   2     -32.776 -11.550 -12.714  1.00 42.43           C  
HETATM10116  C5  GAL G   2     -32.643 -10.960 -11.320  1.00 36.22           C  
HETATM10117  C6  GAL G   2     -32.646 -12.011 -10.227  1.00 40.51           C  
HETATM10118  O2  GAL G   2     -31.213  -8.669 -14.466  1.00 40.36           O  
HETATM10119  O3  GAL G   2     -32.454 -11.056 -15.060  1.00 41.78           O  
HETATM10120  O4  GAL G   2     -31.873 -12.626 -12.859  1.00 40.52           O  
HETATM10121  O5  GAL G   2     -31.411 -10.267 -11.163  1.00 45.23           O  
HETATM10122  O6  GAL G   2     -32.665 -11.422  -8.956  1.00 45.75           O  
HETATM10123  C1  SIA G   3     -34.962 -11.322 -15.249  1.00 49.54           C  
HETATM10124  C2  SIA G   3     -33.522 -11.183 -15.914  1.00 44.89           C  
HETATM10125  C3  SIA G   3     -33.167 -12.252 -16.951  1.00 41.38           C  
HETATM10126  C4  SIA G   3     -33.917 -12.060 -18.266  1.00 41.89           C  
HETATM10127  C5  SIA G   3     -33.714 -10.643 -18.812  1.00 43.46           C  
HETATM10128  C6  SIA G   3     -34.086  -9.592 -17.742  1.00 43.34           C  
HETATM10129  C7  SIA G   3     -33.705  -8.128 -18.103  1.00 43.83           C  
HETATM10130  C8  SIA G   3     -33.978  -7.198 -16.893  1.00 41.99           C  
HETATM10131  C9  SIA G   3     -34.132  -5.731 -17.279  1.00 36.85           C  
HETATM10132  C10 SIA G   3     -33.893 -10.170 -21.219  1.00 43.77           C  
HETATM10133  C11 SIA G   3     -34.798 -10.024 -22.441  1.00 36.77           C  
HETATM10134  N5  SIA G   3     -34.488 -10.470 -20.038  1.00 43.23           N  
HETATM10135  O1A SIA G   3     -35.530 -10.201 -15.067  1.00 49.22           O  
HETATM10136  O1B SIA G   3     -35.368 -12.484 -14.980  1.00 47.67           O  
HETATM10137  O4  SIA G   3     -33.459 -12.983 -19.265  1.00 46.64           O  
HETATM10138  O6  SIA G   3     -33.361  -9.864 -16.545  1.00 42.37           O  
HETATM10139  O7  SIA G   3     -32.347  -8.074 -18.525  1.00 39.67           O  
HETATM10140  O8  SIA G   3     -35.126  -7.670 -16.184  1.00 47.23           O  
HETATM10141  O9  SIA G   3     -34.617  -5.662 -18.617  1.00 50.75           O  
HETATM10142  O10 SIA G   3     -32.683 -10.011 -21.319  1.00 47.56           O  
HETATM10143  C1  FUC G   4     -27.472 -10.020  -9.794  1.00 40.57           C  
HETATM10144  C2  FUC G   4     -27.585 -11.275  -8.964  1.00 39.65           C  
HETATM10145  C3  FUC G   4     -28.633 -12.197  -9.578  1.00 37.71           C  
HETATM10146  C4  FUC G   4     -28.234 -12.516 -11.003  1.00 39.49           C  
HETATM10147  C5  FUC G   4     -28.089 -11.205 -11.777  1.00 39.90           C  
HETATM10148  C6  FUC G   4     -27.564 -11.391 -13.202  1.00 34.71           C  
HETATM10149  O2  FUC G   4     -27.894 -10.981  -7.630  1.00 32.37           O  
HETATM10150  O3  FUC G   4     -28.688 -13.423  -8.870  1.00 39.12           O  
HETATM10151  O4  FUC G   4     -27.002 -13.219 -11.011  1.00 37.02           O  
HETATM10152  O5  FUC G   4     -27.181 -10.312 -11.113  1.00 38.92           O

In pdb6xun_2PH.mar (112 HETATM in chain G)

HETATM section 
HETATM 3467  C1  SIA G   1     -34.962 -11.322 -15.249  1.00 49.54           C  
HETATM 3468  C2  SIA G   1     -33.522 -11.183 -15.914  1.00 44.89           C  
HETATM 3469  C3  SIA G   1     -33.167 -12.252 -16.951  1.00 41.38           C  
HETATM 3470  C4  SIA G   1     -33.917 -12.060 -18.266  1.00 41.89           C  
HETATM 3471  C5  SIA G   1     -33.714 -10.643 -18.812  1.00 43.46           C  
HETATM 3472  C6  SIA G   1     -34.086  -9.592 -17.742  1.00 43.34           C  
HETATM 3473  C7  SIA G   1     -33.705  -8.128 -18.103  1.00 43.83           C  
HETATM 3474  C8  SIA G   1     -33.978  -7.198 -16.893  1.00 41.99           C  
HETATM 3475  C9  SIA G   1     -34.132  -5.731 -17.279  1.00 36.85           C  
HETATM 3476  C10 SIA G   1     -33.893 -10.170 -21.219  1.00 43.77           C  
HETATM 3477  C11 SIA G   1     -34.798 -10.024 -22.441  1.00 36.77           C  
HETATM 3478  N5  SIA G   1     -34.488 -10.470 -20.038  1.00 43.23           N  
HETATM 3479  O1A SIA G   1     -35.530 -10.201 -15.067  1.00 49.22           O  
HETATM 3480  O1B SIA G   1     -35.368 -12.484 -14.980  1.00 47.67           O  
HETATM 3481  O4  SIA G   1     -33.459 -12.983 -19.265  1.00 46.64           O  
HETATM 3482  O6  SIA G   1     -33.361  -9.864 -16.545  1.00 42.37           O  
HETATM 3483  O7  SIA G   1     -32.347  -8.074 -18.525  1.00 39.67           O  
HETATM 3484  O8  SIA G   1     -35.126  -7.670 -16.184  1.00 47.23           O  
HETATM 3485  O9  SIA G   1     -34.617  -5.662 -18.617  1.00 50.75           O  
HETATM 3486  O10 SIA G   1     -32.683 -10.011 -21.319  1.00 47.56           O  
HETATM 3487  C1  FUC G   2     -27.472 -10.020  -9.794  1.00 40.57           C  
HETATM 3488  C2  FUC G   2     -27.585 -11.275  -8.964  1.00 39.65           C  
HETATM 3489  C3  FUC G   2     -28.633 -12.197  -9.578  1.00 37.71           C  
HETATM 3490  C4  FUC G   2     -28.234 -12.516 -11.003  1.00 39.49           C  
HETATM 3491  C5  FUC G   2     -28.089 -11.205 -11.777  1.00 39.90           C  
HETATM 3492  C6  FUC G   2     -27.564 -11.391 -13.202  1.00 34.71           C  
HETATM 3493  O2  FUC G   2     -27.894 -10.981  -7.630  1.00 32.37           O  
HETATM 3494  O3  FUC G   2     -28.688 -13.423  -8.870  1.00 39.12           O  
HETATM 3495  O4  FUC G   2     -27.002 -13.219 -11.011  1.00 37.02           O  
HETATM 3496  O5  FUC G   2     -27.181 -10.312 -11.113  1.00 38.92           O  
HETATM 3497  C1  NAG G   3     -29.496  -5.180 -10.475  1.00 36.52           C  
HETATM 3498  C2  NAG G   3     -29.832  -6.201 -11.559  1.00 39.31           C  
HETATM 3499  C3  NAG G   3     -29.808  -7.616 -10.978  1.00 38.49           C  
HETATM 3500  C4  NAG G   3     -28.488  -7.870 -10.258  1.00 41.60           C  
HETATM 3501  C5  NAG G   3     -28.233  -6.765  -9.239  1.00 37.27           C  
HETATM 3502  C6  NAG G   3     -26.902  -6.879  -8.537  1.00 40.53           C  
HETATM 3503  C7  NAG G   3     -31.220  -5.567 -13.469  1.00 41.32           C  
HETATM 3504  C8  NAG G   3     -32.609  -5.308 -13.974  1.00 31.95           C  
HETATM 3505  N2  NAG G   3     -31.114  -5.920 -12.184  1.00 39.35           N  
HETATM 3506  O1  NAG G   3     -29.506  -3.874 -10.960  1.00 40.28           O  
HETATM 3507  O3  NAG G   3     -29.983  -8.563 -12.027  1.00 40.36           O  
HETATM 3508  O4  NAG G   3     -28.501  -9.130  -9.596  1.00 43.78           O  
HETATM 3509  O5  NAG G   3     -28.241  -5.495  -9.904  1.00 42.13           O  
HETATM 3510  O6  NAG G   3     -26.898  -6.121  -7.335  1.00 47.52           O  
HETATM 3511  O7  NAG G   3     -30.236  -5.459 -14.191  1.00 45.35           O  
HETATM 3512  C1  GAL G   4     -31.215  -9.175 -12.071  1.00 42.90           C  
HETATM 3513  C2  GAL G   4     -31.247  -9.706 -13.512  1.00 37.51           C  
HETATM 3514  C3  GAL G   4     -32.527 -10.446 -13.786  1.00 42.73           C  
HETATM 3515  C4  GAL G   4     -32.776 -11.550 -12.714  1.00 42.43           C  
HETATM 3515  C4  GAL G   4     -32.776 -11.550 -12.714  1.00 42.43           C  
HETATM 3516  C5  GAL G   4     -32.643 -10.960 -11.320  1.00 36.22           C  
HETATM 3517  C6  GAL G   4     -32.646 -12.011 -10.227  1.00 40.51           C  
HETATM 3518  O2  GAL G   4     -31.213  -8.669 -14.466  1.00 40.36           O  
HETATM 3519  O3  GAL G   4     -32.454 -11.056 -15.060  1.00 41.78           O  
HETATM 3520  O4  GAL G   4     -31.873 -12.626 -12.859  1.00 40.52           O  
HETATM 3521  O5  GAL G   4     -31.411 -10.267 -11.163  1.00 45.23           O  
HETATM 3522  O6  GAL G   4     -32.665 -11.422  -8.956  1.00 45.75           O  
HETATM 3523  C1  SIA G   1     -34.962 -11.322 -15.249  1.00 49.54           C  
HETATM 3524  C2  SIA G   1     -33.522 -11.183 -15.914  1.00 44.89           C  
HETATM 3525  C3  SIA G   1     -33.167 -12.252 -16.951  1.00 41.38           C  
HETATM 3526  C4  SIA G   1     -33.917 -12.060 -18.266  1.00 41.89           C  
HETATM 3527  C5  SIA G   1     -33.714 -10.643 -18.812  1.00 43.46           C  
HETATM 3528  C6  SIA G   1     -34.086  -9.592 -17.742  1.00 43.34           C  
HETATM 3529  C7  SIA G   1     -33.705  -8.128 -18.103  1.00 43.83           C  
HETATM 3530  C8  SIA G   1     -33.978  -7.198 -16.893  1.00 41.99           C  
HETATM 3531  C9  SIA G   1     -34.132  -5.731 -17.279  1.00 36.85           C  
HETATM 3532  C10 SIA G   1     -33.893 -10.170 -21.219  1.00 43.77           C  
HETATM 3533  C11 SIA G   1     -34.798 -10.024 -22.441  1.00 36.77           C  
HETATM 3534  N5  SIA G   1     -34.488 -10.470 -20.038  1.00 43.23           N  
HETATM 3535  O1A SIA G   1     -35.530 -10.201 -15.067  1.00 49.22           O  
HETATM 3536  O1B SIA G   1     -35.368 -12.484 -14.980  1.00 47.67           O  
HETATM 3537  O4  SIA G   1     -33.459 -12.983 -19.265  1.00 46.64           O  
HETATM 3538  O6  SIA G   1     -33.361  -9.864 -16.545  1.00 42.37           O  
HETATM 3539  O7  SIA G   1     -32.347  -8.074 -18.525  1.00 39.67           O  
HETATM 3540  O8  SIA G   1     -35.126  -7.670 -16.184  1.00 47.23           O  
HETATM 3541  O9  SIA G   1     -34.617  -5.662 -18.617  1.00 50.75           O  
HETATM 3542  O10 SIA G   1     -32.683 -10.011 -21.319  1.00 47.56           O  
HETATM 3543  C1  FUC G   2     -27.472 -10.020  -9.794  1.00 40.57           C  
HETATM 3544  C2  FUC G   2     -27.585 -11.275  -8.964  1.00 39.65           C  
HETATM 3545  C3  FUC G   2     -28.633 -12.197  -9.578  1.00 37.71           C  
HETATM 3546  C4  FUC G   2     -28.234 -12.516 -11.003  1.00 39.49           C  
HETATM 3547  C5  FUC G   2     -28.089 -11.205 -11.777  1.00 39.90           C  
HETATM 3548  C6  FUC G   2     -27.564 -11.391 -13.202  1.00 34.71           C  
HETATM 3549  O2  FUC G   2     -27.894 -10.981  -7.630  1.00 32.37           O  
HETATM 3550  O3  FUC G   2     -28.688 -13.423  -8.870  1.00 39.12           O  
HETATM 3551  O4  FUC G   2     -27.002 -13.219 -11.011  1.00 37.02           O  
HETATM 3552  O5  FUC G   2     -27.181 -10.312 -11.113  1.00 38.92           O  
HETATM 3553  C1  NAG G   3     -29.496  -5.180 -10.475  1.00 36.52           C  
HETATM 3554  C2  NAG G   3     -29.832  -6.201 -11.559  1.00 39.31           C  
HETATM 3555  C3  NAG G   3     -29.808  -7.616 -10.978  1.00 38.49           C  
HETATM 3556  C4  NAG G   3     -28.488  -7.870 -10.258  1.00 41.60           C  
HETATM 3557  C5  NAG G   3     -28.233  -6.765  -9.239  1.00 37.27           C  
HETATM 3558  C6  NAG G   3     -26.902  -6.879  -8.537  1.00 40.53           C  
HETATM 3559  C7  NAG G   3     -31.220  -5.567 -13.469  1.00 41.32           C  
HETATM 3560  C8  NAG G   3     -32.609  -5.308 -13.974  1.00 31.95           C  
HETATM 3561  N2  NAG G   3     -31.114  -5.920 -12.184  1.00 39.35           N  
HETATM 3562  O1  NAG G   3     -29.506  -3.874 -10.960  1.00 40.28           O  
HETATM 3563  O3  NAG G   3     -29.983  -8.563 -12.027  1.00 40.36           O  
HETATM 3564  O4  NAG G   3     -28.501  -9.130  -9.596  1.00 43.78           O  
HETATM 3565  O5  NAG G   3     -28.241  -5.495  -9.904  1.00 42.13           O  
HETATM 3566  O6  NAG G   3     -26.898  -6.121  -7.335  1.00 47.52           O  
HETATM 3567  O7  NAG G   3     -30.236  -5.459 -14.191  1.00 45.35           O  
HETATM 3568  C1  GAL G   4     -31.215  -9.175 -12.071  1.00 42.90           C  
HETATM 3569  C2  GAL G   4     -31.247  -9.706 -13.512  1.00 37.51           C  
HETATM 3570  C3  GAL G   4     -32.527 -10.446 -13.786  1.00 42.73           C  
HETATM 3571  C4  GAL G   4     -32.776 -11.550 -12.714  1.00 42.43           C  
HETATM 3572  C5  GAL G   4     -32.643 -10.960 -11.320  1.00 36.22           C  
HETATM 3573  C6  GAL G   4     -32.646 -12.011 -10.227  1.00 40.51           C  
HETATM 3574  O2  GAL G   4     -31.213  -8.669 -14.466  1.00 40.36           O  
HETATM 3575  O3  GAL G   4     -32.454 -11.056 -15.060  1.00 41.78           O  
HETATM 3576  O4  GAL G   4     -31.873 -12.626 -12.859  1.00 40.52           O  
HETATM 3577  O5  GAL G   4     -31.411 -10.267 -11.163  1.00 45.23           O  
HETATM 3578  O6  GAL G   4     -32.665 -11.422  -8.956  1.00 45.75           O

5wb1 special case

5wb1 is a fusion protein (X-VHH). It is handled OK (and just generates the VHH part)

HETATMs

The code requires that a HET group be at least 8 atoms in order to be considered as an antigen.

We need code like addhetv2 to add HETATMs back at the end.

Special case 4hjj

special case: 4hjj_1P
4HJJ is a Dual Variable Domain Immunoglobulin (DVD-Ig)

pdb4hjj_1P.cho variable domain CDR is not interacting with the antigen.

In the original PDB file of 4HJJ, based on its structure, H126-H246 and L114-L224 looks like the second variable domain and is interacting with the antigen, is the correct variable domain to trauncate.

6e9q - heavy chains in SEQRES but ATOM records missing

6e9q

       0  - heavy chain missing (in SEQRES but not in ATOM)
       1P - heavy chain missing (in SEQRES but not in ATOM)
       2  - heavy chain missing (in SEQRES but not in ATOM)
       3  - heavy chain missing (in SEQRES but not in ATOM)

5kov - problem with H chain

5kov - problem with H chain - weird chain names

       0P - ok but chain duplicated
       1P - ok but chain duplicated
       2P - not numbered (.bad) - confused by chain labels
       3P - ok but chain duplicated
       4P - ok? perhaps missing partner chain
       5P - OK
       6  - ok? perhaps missing partner chain
       7P - ok but chain duplicated

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