1a07 1a0q 1a1b 1a1e 1a28 1a42 1a4g 1a4k 1a4q 1a6w 1a9u 1aaq 1abe 1abf 1acj 1acl 1acm 1aco 1aec 1aha 1ai5 1aj7 1ake 1aoe 1apt 1apu 1aqw 1ase 1atl 1azm 1b58 1b59 1b6n 1b9v 1baf 1bbp 1bgo 1bl7 1blh 1bma 1bmq 1byb 1byg 1c12 1c1e 1c2t 1c5c 1c5x 1c83 1cbs 1cbx 1cdg 1cf8 1cil 1cin 1ckp 1cle 1com 1coy 1cps 1cqp 1ctr 1ctt 1cvu 1cx2 1d0l 1d3h 1d4p 1dbb 1dbj 1dbm 1dd7 1dg5 1dhf 1did 1die 1dmp 1dog 1dr1 1dwb 1dwc 1dwd 1dy9 1eap 1ebg 1eed 1ei1 1ejn 1ela 1elb 1elc 1eld 1ele 1eoc 1epb 1epo 1eta 1etr 1ets 1ett 1etz 1f0r 1f0s 1f3d 1fax 1fbl 1fen 1fgi 1fig 1fkg 1fki 1fl3 1flr 1frp 1ghb 1glp 1glq 1gpy 1hak 1hdc 1hdy 1hef 1hfc 1hiv 1hos 1hpv 1hri 1hsb 1hsl 1htf 1hti 1hvr 1hyt 1ibg 1icn 1ida 1igj 1imb 1ivb 1ivc 1ivd 1ive 1ivq 1jao 1jap 1kel 1kno 1lah 1lcp 1ldm 1lic 1lkk 1lmo 1lna 1lpm 1lst 1lyb 1lyl 1mbi 1mcq 1mcr 1mdr 1ml1 1mld 1mmb 1mmq 1mnc 1mrg 1mrk 1mts 1mtw 1mup 1nco 1ngp 1nis 1nsd 1okl 1okm 1pbd 1pdz 1pgp 1pha 1phd 1phf 1phg 1poc 1ppc 1pph 1ppi 1ppl 1pso 1ptv 1qbr 1qbt 1qbu 1qcf 1qh7 1ql7 1qpe 1qpq 1rbp 1rds 1rne 1rnt 1rob 1rt2 1sln 1slt 1snc 1srf 1srg 1srh 1srj 1stp 1tdb 1tka 1tlp 1tmn 1tng 1tnh 1tni 1tnl 1tph 1tpp 1trk 1tyl 1ukz 1ulb 1uvs 1uvt 1vgc 1vrh 1wap 1xid 1xie 1xkb 1ydr 1yds 1ydt 1yee 25c8 2aad 2ack 2ada 2ak3 2cgr 2cht 2cmd 2cpp 2ctc 2dbl 2er7 2fox 2gbp 2h4n 2ifb 2lgs 2mcp 2mip 2pcp 2phh 2pk4 2plv 2qwk 2r04 2r07 2sim 2tmn 2tsc 2yhx 2ypi 3cla 3cpa 3erd 3ert 3gch 3gpb 3hvt 3mth 3nos 3pgh 3ptb 3tpi 4aah 4cox 4cts 4dfr 4er2 4est 4fab 4fbp 4lbd 4phv 4tpi 5abp 5cpp 5er1 5p2p 6abp 6cpa 6rnt 6rsa 7cpa 7tim 8gch

Table 1. Entries in the complete test set

Application of filters to the complete test set results in a list of clean entries. This list of entries can be restricted further on the basis of crystal structure resolution. Tables 2-4 contain the clean lists that are recommended for use in docking experiments. Tables 3 and 4 contain subsets of the entries contained in Table 2 limited to resolutions of 2.5 and 2.0 Å respectively.

1a28 1a42 1a4g 1a4q 1a6w 1a9u 1aaq 1abe 1abf 1acj 1acl 1acm 1aco 1aec 1ai5 1aoe 1apt 1apu 1aqw 1ase 1atl 1azm 1b58 1b59 1b9v 1baf 1bbp 1bgo 1bl7 1blh 1bma 1bmq 1byb 1byg 1c12 1c1e 1c5c 1c5x 1c83 1cbs 1cbx 1cdg 1cil 1ckp 1cle 1com 1coy 1cps 1cqp 1cvu 1cx2 1d0l 1d3h 1d4p 1dbb 1dbj 1dd7 1dg5 1dhf 1did 1dmp 1dog 1dr1 1dwb 1dwc 1dwd 1dy9 1eap 1ebg 1eed 1ei1 1ejn 1eoc 1epb 1epo 1eta 1etr 1ets 1ett 1f0r 1f0s 1f3d 1fax 1fen 1fgi 1fkg 1fki 1fl3 1flr 1frp 1glp 1glq 1hak 1hdc 1hfc 1hiv 1hos 1hpv 1hri 1hsb 1hsl 1htf 1hvr 1hyt 1ibg 1ida 1imb 1ivb 1ivq 1jap 1kel 1lah 1lcp 1ldm 1lic 1lna 1lpm 1lst 1lyb 1lyl 1mbi 1mcq 1mdr 1mld 1mmq 1mrg 1mrk 1mts 1mup 1nco 1ngp 1nis 1okl 1okm 1pbd 1pdz 1phd 1phg 1poc 1ppc 1pph 1ppi 1pso 1ptv 1qbr 1qbu 1qcf 1qpe 1qpq 1rds 1rne 1rnt 1rob 1rt2 1slt 1snc 1srj 1tdb 1tlp 1tmn 1tng 1tnh 1tni 1tnl 1tpp 1trk 1tyl 1ukz 1ulb 1uvs 1uvt 1vgc 1wap 1xid 1xie 1ydr 1ydt 1yee 25c8 2aad 2ack 2ada 2ak3 2cht 2cmd 2cpp 2ctc 2dbl 2fox 2gbp 2h4n 2ifb 2lgs 2mcp 2pcp 2phh 2pk4 2qwk 2r07 2tmn 2tsc 2yhx 2ypi 3cla 3cpa 3erd 3ert 3gpb 3hvt 3tpi 4aah 4cox 4cts 4dfr 4est 4fbp 4lbd 4phv 5abp 5cpp 5er1 6rnt 6rsa 7tim

Table 2. List of 224 clean entries

1a28 1a42 1a4g 1a4q 1a6w 1abe 1abf 1aco 1aec 1ai5 1aoe 1apt 1apu 1aqw 1atl 1azm 1b58 1b59 1b9v 1bbp 1bgo 1blh 1bma 1byb 1byg 1c1e 1c5c 1c5x 1c83 1cbs 1cbx 1cdg 1cil 1ckp 1cle 1com 1coy 1cps 1cvu 1d0l 1d3h 1d4p 1dd7 1dg5 1dhf 1dmp 1dog 1dr1 1dy9 1ebg 1eed 1ei1 1ejn 1eoc 1epb 1epo 1eta 1etr 1ets 1f0r 1f0s 1f3d 1fen 1fkg 1fki 1fl3 1flr 1frp 1glp 1glq 1hdc 1hfc 1hiv 1hos 1hpv 1hsb 1hsl 1htf 1hvr 1hyt 1ida 1imb 1ivb 1jap 1kel 1lah 1lcp 1ldm 1lic 1lna 1lpm 1lst 1mbi 1mdr 1mld 1mmq 1mrg 1mrk 1mts 1mup 1nco 1ngp 1nis 1okl 1okm 1pbd 1pdz 1phd 1phg 1poc 1ppc 1pph 1ppi 1pso 1ptv 1qbr 1qbu 1qcf 1qpe 1qpq 1rds 1rne 1rnt 1rob 1slt 1snc 1srj 1tlp 1tmn 1tng 1tnh 1tni 1tnl 1tpp 1trk 1tyl 1ukz 1vgc 1wap 1xid 1xie 1ydr 1ydt 1yee 25c8 2aad 2ack 2ada 2ak3 2cht 2cmd 2cpp 2ctc 2fox 2gbp 2h4n 2ifb 2pcp 2pk4 2qwk 2tmn 2tsc 2yhx 3cla 3cpa 3erd 3ert 3gpb 3tpi 4aah 4dfr 4est 4lbd 4phv 5abp 5cpp 5er1 6rnt 6rsa 7tim

Table 3. Subset of clean entries with resolution less than 2.5 Å (180 entries)

1a28 1a4q 1a6w 1abe 1abf 1aec 1aoe 1apt 1apu 1aqw 1atl 1b58 1b59 1bma 1byb 1c1e 1c5c 1c5x 1c83 1cbs 1cil 1coy 1d0l 1d3h 1ejn 1eta 1f3d 1fen 1flr 1glp 1glq 1hfc 1hpv 1hsb 1hsl 1hvr 1hyt 1ida 1jap 1kel 1lcp 1lic 1lna 1lst 1mld 1mmq 1mrg 1mrk 1mts 1nco 1phd 1phg 1ppc 1pph 1qbr 1qbu 1rds 1rnt 1rob 1slt 1snc 1srj 1tmn 1tng 1tnh 1tni 1tnl 1tpp 1tyl 1ukz 1vgc 1wap 1xid 1xie 2ak3 2cmd 2cpp 2ctc 2fox 2gbp 2h4n 2qwk 2tmn 2tsc 3cla 3ert 3tpi 4dfr 4est 5abp 6rnt 7tim

Table 4. Subset of clean entries with resolution less than 2.0 Å (92 entries)

The filtered entries and the reasons for their omission can be found in Table 5. Table 6 lists the entries that have been omitted to ensure diversity of protein-ligand complexes within the test set.

Entry Reason Entry Reason Entry Reason 1a07 AC 1ppl A 1ivd B 1a0q A 1qbt A 1ive B 1a1b A 1ql7 A 1kno B 1a1e A 1sln A 1lmo B 1a4k A 1srf AB 1pha B 1aj7 A 1srg AB 2plv B 1ake A 1srh A 3gch B 1cf8 A 1stp A 3nos B 1ctt AB 1xkb A 3pgh B 1ela A 1yds A 4fab B 1elb A 2cgr A 5p2p B 1eld AB 2er7 A 8gch B 1ele A 2mip A 1b6n C 1etz A 3mth A 1qh7 DE 1fbl A 4er2 A 1dbm DE 1jao A 6cpa A 1ctr E 1lkk A 7cpa A 1icn E 1mmb A 1c2t A 1ivc E 1mnc A 1qhb A 1vrh E 1mtw A 1hdy A 1pqp A 1hef A

Table 5. Omitted entries and reasons for their omission:
    A: presence of contacts with crystallographically related chains
    B: significant clashes between protein and ligand atoms
    C: incorrect ligand representation
    D: dubious ligand geometry
    E: incongruity between ligand placement and electron density

1a07 1a1b 1aha 1cin 1dbm 1die 1elb 1elc 1eld 1fig 1gpy 1hti 1icn 1igj 1ive 1mcr 1ml1 1nsd 1phf 1rbp 1tka 1tph 1xkb 2r04 2sim 3ptb 4fab 4tpi 6abp

Table 6. Entries omitted to ensure diversity of validation set