Debora S. Marks*, Lucy J. Colwell*, Robert Sheridan, Thomas A. Hopf, Andrea Pagnani, Riccardo Zecchina, Chris Sander
*Joint first
News report: Sciencedaily Focushms Eurekalert
| Appendix Name | Description | Appendix Name | Description |
|---|---|---|---|
| Appendix_A1 | 1. All DI scores 2. Top 500 filtered and ranked DIScores1 | Appendix_A6 | TM and GDT_TS scores |
| Appendix_A2 | Distance geometry and simulated annealing protocol | Appendix_A7 | Pymol rmsd scores |
| Appendix_A3 | All predicted structure coordinates for all proteins | Appendix_A8 | DI MI, BNM and SCA top 500 scores plus (i) cys, conservation and secondary structure clashes flagged, (ii) mapping to a crystal structure (iii) distance between predicted residues in a reference crystal structure |
| Appendix_A4 | Pymol sessions for a. All EIC top ranked predicted structures, the best TM score structure and a reference crystal structures. b. Best TM score BNM method predicted structures. | Appendix_A9 | Sequence, secondary structure prediction and residue mapping to crystal structure |
| Appendix_A5 | Discrimination scores | Appendix_A10 | Atom types used in applying residue-residue distance constraints (in addition to C-alpha and C-beta) |
1Selection of those rows with no annotation in columns 7, 8 or 9 gives EICs
Note: The Trypsin content in the appendicies above reflects a minor method adjustment. Follow this link for an explanation and additional resources.
All input files for CNS_solve available on request. These include formatted distance and dihedral constraints and the extended polypeptide coordinates
Higher resolution versions of the main text figures can be downloaded here: main text figures
| Pfam Family Id | Pfam Family Name | Uniprot Id | Uniprot Name | Pdb Id |
|---|---|---|---|---|
| PF00001 | 7tm_1 | P02699 | OPSD_BOVIN | 1hzx |
| PF00089 | Trypsin | P00763 | TRY2_RAT | 3tgi |
| PF00071 | Ras | P01112 | RASH_HUMAN | 5p21 |
| PF00075 | RNase_H | P0A7Y4 | RNH_ECOLI | 1f21 |
| PF00072 | Response_reg | P0AE67 | CHEY_ECOLI | 1e6k |
| PF00307 | CH | Q01082 | SPTB2_HUMAN | 1bkr |
| PF00059 | Lectin_C | Q9NNX6 | A8MVQ9_HUMAN | 2it6 |
| PF00085 | Thioredoxin | P80579 | THIO_ALIAC | 1rqm |
| PF00028 | Cadherin | P12830 | CADH1_HUMAN | 2o72 |
| PF00254 | FKBP_C | O45418 | O45418_CAEEL | 1r9h |
| PF00486 | Trans_reg_C | P0AA16 | OMPR_ECOLI | 1odd |
| PF00076 | RRM_1 | P26378 | ELAV4_HUMAN | 1g2e |
| PF00013 | KH_1 | Q15365 | PCBP1_HUMAN | 1wvn |
| PF00014 | Kunitz_BPTI | P00974 | BPT1_BOVIN | 5pti |
| PF00018 | SH3_1 | P07947 | YES_HUMAN | 2hda |