UCSF banner
Vendor Summary

"PubChem" subset (# 122) - 15467019 entries

Contents: General Information   Property Distributions   Clustering and Diversity   Downloads

General Information

Website: http://pubchem.ncbi.nlm.nih.gov
E-mail: email
Phone: phone
Fax: fax

Subset Info
Catalog Version Catalog Count Num. Filtered Free Purchasable Pubchem Depleted
2011-05-17 31453252 3193633 Yes (1) No No No

"Usual" Subset Downloads: mol2 | SDF | Flexibase | more…

Property Distributions

Clustering and Diversity

We sort the ligands by molecular weight as a proxy for complexity. We then use the algorithm of Bienfait to incrementally select compounds that differ from all previous by the given Tanimoto cutoff. This is a very cheap clustering technique that scales well with set size and gives some indication of the amount of chemical redundancy in the dataset at various Tanimoto levels. N/A indicates that clustering is pending.

All15467019
90%151237
80%95784
70%38943
60%13299

Downloads

Molecules are available in four formats: isomeric SMILES, mol2, SDF and flexibase. Molecules are represented as a single pH=7 form. Additional representations (protonation variants and tautomers) are available in three incremental subsets to augment the single representative: medium pH (5.75 to 8.25), high pH 7.0-9.5 (e.g. for docking to metals), and low pH 4.5-7.0 (e.g. for docking to a positively charged binding site).
Larger files are broken up into slices to faciliate downloading. You may download individual slices or use c-shell scripts to download a single representation (pH 7.0), all Usual ligands (pH 5.75 to 8.25), ligands for metals (5.75-9.5) or All. Note that these sets are overlapping so you do not want to download both Metals and All.

We expect dockers will want to just download the "Usual" subset. Chemical informaticists who require only a single form of each molecule may want just the "Single" representation. If files appear to be missing or incomplete, please try again tomorrow as the export may still be in progress. If problems persist for 48 hours please complain to comments at docking dot org

File format Individual slicesScripts to download slices
SMILES Reference   mid pH   high pH   low pH  
mol2 0 1 10 100 101 102 103 104 105 106 107 108 109 11 110 111 112 113 114 115 116 117 118 119 12 120 121 122 123 124 125 126 127 128 129 13 130 131 132 133 134 135 136 137 138 139 14 140 141 142 143 144 145 146 147 148 149 15 150 151 152 153 154 155 156 157 158 159 16 160 161 162 163 164 165 166 167 168 169 17 170 171 172 173 174 175 176 177 178 179 18 180 181 182 183 184 185 186 187 188 189 19 190 191 192 193 194 195 196 197 198 199 2 20 200 201 202 203 204 205 206 207 208 209 21 210 211 212 213 214 215 216 217 218 219 22 220 221 222 223 224 225 226 227 228 229 23 230 231 232 233 234 235 236 237 238 239 24 240 241 242 243 244 245 246 247 248 249 25 250 251 252 253 254 255 256 257 258 259 26 260 261 262 263 264 265 266 267 268 269 27 270 271 272 273 274 275 276 277 278 279 28 280 281 282 283 284 285 286 287 288 289 29 290 291 292 293 294 295 296 297 298 299 3 30 300 301 302 303 304 305 306 307 308 309 31 310 311 312 313 314 315 316 317 318 319 32 320 321 322 323 324 325 326 327 328 329 33 330 331 332 333 334 335 336 337 338 339 34 340 341 342 343 344 345 346 347 348 349 35 350 351 352 353 354 355 356 357 358 359 36 360 361 362 363 364 365 366 367 368 369 37 370 371 372 373 374 375 376 377 378 379 38 380 381 382 383 384 385 386 387 388 389 39 390 391 392 393 394 395 396 397 398 399 4 40 400 401 402 403 404 405 406 407 408 409 41 410 411 412 413 414 415 416 417 418 419 42 420 421 422 423 424 425 426 427 428 429 43 430 431 432 433 434 435 436 437 438 439 44 440 441 442 443 444 445 446 447 448 449 45 450 451 452 453 454 455 456 457 458 459 46 460 461 462 463 464 465 466 467 468 469 47 470 471 472 473 474 475 476 477 478 479 48 480 481 482 483 484 485 486 487 488 489 49 490 491 492 493 494 495 496 497 498 499 5 50 500 501 502 503 504 505 506 507 508 509 51 510 511 512 513 514 515 516 517 518 519 52 520 521 522 523 524 525 526 527 528 529 53 530 531 532 533 534 535 536 537 538 539 54 540 541 542 543 544 545 546 547 548 549 55 550 551 552 553 554 555 556 557 558 559 56 560 561 562 563 564 565 566 567 568 569 57 570 571 572 573 574 575 576 577 578 579 58 580 581 582 583 584 585 586 587 588 589 59 590 591 592 593 594 595 596 597 598 599 6 60 600 601 602 603 604 605 606 607 608 609 61 610 611 612 613 614 615 616 617 618 619 62 620 621 622 623 624 625 626 627 628 629 63 630 631 632 633 634 635 636 637 638 639 64 640 641 642 643 644 645 646 647 648 649 65 650 651 652 653 654 655 656 657 658 659 66 660 661 662 663 664 665 666 667 668 669 67 670 671 672 673 674 675 676 677 678 679 68 680 681 682 683 684 685 686 687 688 689 69 690 691 692 693 694 695 696 697 698 699 7 70 700 701 702 703 704 705 706 707 708 709 71 710 711 712 713 714 715 716 717 718 719 72 720 721 722 723 724 725 726 727 728 729 73 730 731 732 733 734 735 736 74 75 76 77 78 79 8 80 81 82 83 84 85 86 87 88 89 9 90 91 92 93 94 95 96 97 98 99   0 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 4 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 57 58 59 6 60 61 62 63 64 65 66 67 68 69 7 70 71 72 73 74 75 76 77 78 79 8 80 81 82 83 9   0 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 4 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 57 58 59 6 60 7 8 9   0 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 4 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 6 7 8 9   Single Usual Metals All
SDF 0 1 10 100 101 102 103 104 105 106 107 108 109 11 110 111 112 113 114 115 116 117 118 119 12 120 121 122 123 124 125 126 127 128 129 13 130 131 132 133 134 135 136 137 138 139 14 140 141 142 143 144 145 146 147 148 149 15 150 151 152 153 154 155 156 157 158 159 16 160 161 162 163 164 165 166 167 168 169 17 170 171 172 173 174 175 176 177 178 179 18 180 181 182 183 184 185 186 187 188 189 19 190 191 192 193 194 195 196 197 198 199 2 20 200 201 202 203 204 205 206 207 208 209 21 210 211 212 213 214 215 216 217 218 219 22 220 221 222 223 224 225 226 227 228 229 23 230 231 232 233 234 235 236 237 238 239 24 240 241 242 243 244 245 246 247 248 249 25 250 251 252 253 254 255 256 257 258 259 26 260 261 262 263 264 265 266 267 268 269 27 270 271 272 273 274 275 276 277 278 279 28 280 281 282 283 284 285 286 287 288 289 29 290 291 292 293 294 295 296 297 298 299 3 30 300 301 302 303 304 305 306 307 308 309 31 310 311 312 313 314 315 316 317 318 319 32 320 321 322 323 324 325 326 327 328 329 33 330 331 332 333 334 335 336 337 338 339 34 340 341 342 343 344 345 346 347 348 349 35 350 351 352 353 354 355 356 357 358 359 36 360 361 362 363 364 365 366 367 368 369 37 370 371 372 373 374 375 376 377 378 379 38 380 381 382 383 384 385 386 387 388 389 39 390 391 392 393 394 395 396 397 398 399 4 40 400 401 402 403 404 405 406 407 408 409 41 410 411 412 413 414 415 416 417 418 419 42 420 421 422 423 424 425 426 427 428 429 43 430 431 432 433 434 435 436 437 438 439 44 440 441 442 443 444 445 446 447 448 449 45 450 451 452 453 454 455 456 457 458 459 46 460 461 462 463 464 465 466 467 468 469 47 470 471 472 473 474 475 476 477 478 479 48 480 481 482 483 484 485 486 487 488 489 49 490 491 492 493 494 495 496 497 498 499 5 50 500 501 502 503 504 505 506 507 508 509 51 510 511 512 513 514 515 516 517 518 519 52 520 521 522 523 524 525 526 527 528 529 53 530 531 532 533 534 535 536 537 538 539 54 540 541 542 543 544 545 546 547 548 549 55 550 551 552 553 554 555 556 557 558 559 56 560 561 562 563 564 565 566 567 568 569 57 570 571 572 573 574 575 576 577 578 579 58 580 581 582 583 584 585 586 587 588 589 59 590 591 592 593 594 595 596 597 598 599 6 60 600 601 602 603 604 605 606 607 608 609 61 610 611 612 613 614 615 616 617 618 619 62 620 621 622 623 624 625 626 627 628 629 63 630 631 632 633 634 635 636 637 638 639 64 640 641 642 643 644 645 646 647 648 649 65 650 651 652 653 654 655 656 657 658 659 66 660 661 662 663 664 665 666 667 668 669 67 670 671 672 673 674 675 676 677 678 679 68 680 681 682 683 684 685 686 687 688 689 69 690 691 692 693 694 695 696 697 698 699 7 70 700 701 702 703 704 705 706 707 708 709 71 710 711 712 713 714 715 716 717 718 719 72 720 721 722 723 724 725 726 727 728 729 73 730 731 732 733 734 735 736 74 75 76 77 78 79 8 80 81 82 83 84 85 86 87 88 89 9 90 91 92 93 94 95 96 97 98 99   0 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 4 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 57 58 59 6 60 61 62 63 64 65 66 67 68 69 7 70 71 72 73 74 75 76 77 78 79 8 80 81 82 83 9   0 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 4 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 57 58 59 6 60 7 8 9   0 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 23 24 25 26 27 28 29 3 30 31 32 33 34 35 36 37 38 39 4 40 41 42 43 44 45 46 47 48 49 5 50 51 52 53 54 55 56 6 7 8 9   Single Usual Metals All
Flexibase  Single Usual Metals All
A product of BCIRC, the Bioinfomatics and Chemical Informatics Research Center @ UCSF. Last updated Aug 6, 2009. questions and discussion to zinc-fans at docking.org; bug reports to support at docking.org; any other correspondence to comments at docking.org. Terms of use. Privacy policy.