-
Notifications
You must be signed in to change notification settings - Fork 1
/
references.bib
1353 lines (1261 loc) · 51.1 KB
/
references.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
@article{callaway2020,
title = {Revolutionary cryo-EM is taking over structural biology},
author = {Callaway, Ewen},
year = {2020},
month = {02},
date = {2020-02-10},
journal = {Nature},
pages = {201--201},
volume = {578},
number = {7794},
doi = {10.1038/d41586-020-00341-9},
url = {https://www.nature.com/articles/d41586-020-00341-9}
}
@article{stollar2020,
title = {Uncovering protein structure},
author = {Stollar, Elliott J and Smith, David P},
year = {2020},
month = {09},
date = {2020-09-25},
journal = {Essays in Biochemistry},
pages = {649--680},
volume = {64},
number = {4},
doi = {10.1042/EBC20190042},
url = {https://doi.org/10.1042/EBC20190042}
}
@article{miller2020,
title = {Introducing Foldit Education Mode},
author = {Miller, Josh Aaron and Khatib, Firas and Hammond, Haley and Cooper, Seth and Horowitz, Scott},
year = {2020},
month = {09},
date = {2020-09},
journal = {Nature Structural & Molecular Biology},
pages = {769--770},
volume = {27},
number = {9},
doi = {10.1038/s41594-020-0485-6},
note = {PMID: 32807992
PMCID: PMC8518189},
langid = {eng}
}
@article{mirdita2022,
title = {ColabFold: making protein folding accessible to all},
author = {Mirdita, Milot and {Schütze}, Konstantin and Moriwaki, Yoshitaka and Heo, Lim and Ovchinnikov, Sergey and Steinegger, Martin},
year = {2022},
month = {06},
date = {2022-06},
journal = {Nature Methods},
pages = {679--682},
volume = {19},
number = {6},
doi = {10.1038/s41592-022-01488-1},
note = {PMID: 35637307},
langid = {eng}
}
@article{jumper2021,
title = {Highly accurate protein structure prediction with AlphaFold},
author = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and {{\v{Z}}ídek}, Augustin and Potapenko, Anna and Bridgland, Alex and Meyer, Clemens and Kohl, Simon A. A. and Ballard, Andrew J. and Cowie, Andrew and Romera-Paredes, Bernardino and Nikolov, Stanislav and Jain, Rishub and Adler, Jonas and Back, Trevor and Petersen, Stig and Reiman, David and Clancy, Ellen and Zielinski, Michal and Steinegger, Martin and Pacholska, Michalina and Berghammer, Tamas and Bodenstein, Sebastian and Silver, David and Vinyals, Oriol and Senior, Andrew W. and Kavukcuoglu, Koray and Kohli, Pushmeet and Hassabis, Demis},
year = {2021},
month = {08},
date = {2021-08},
journal = {Nature},
pages = {583--589},
volume = {596},
number = {7873},
doi = {10.1038/s41586-021-03819-2},
url = {https://www.nature.com/articles/s41586-021-03819-2},
note = {Number: 7873
Publisher: Nature Publishing Group},
langid = {en}
}
@article{manjasetty2008,
title = {Automated technologies and novel techniques to accelerate protein crystallography for structural genomics},
author = {Manjasetty, Babu A. and Turnbull, Andrew P. and Panjikar, Santosh and {Büssow}, Konrad and Chance, Mark R.},
year = {2008},
date = {2008},
journal = {PROTEOMICS},
pages = {612--625},
volume = {8},
number = {4},
doi = {10.1002/pmic.200700687},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pmic.200700687},
note = {{\_}eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/pmic.200700687},
langid = {en}
}
@article{schultz2000,
title = {Illuminating folding intermediates},
author = {Schultz, Christian P.},
year = {2000},
month = {01},
date = {2000-01},
journal = {Nature Structural Biology},
pages = {7--10},
volume = {7},
number = {1},
doi = {10.1038/71197},
url = {https://www.nature.com/articles/nsb0100_7},
note = {Number: 1
Publisher: Nature Publishing Group},
langid = {en}
}
@article{radford2000,
title = {Protein folding: progress made and promises ahead},
author = {Radford, Sheena E.},
year = {2000},
month = {12},
date = {2000-12-01},
journal = {Trends in Biochemical Sciences},
pages = {611--618},
volume = {25},
number = {12},
doi = {10.1016/S0968-0004(00)01707-2},
url = {https://www.sciencedirect.com/science/article/pii/S0968000400017072},
langid = {en}
}
@article{anfinsen1973,
title = {Principles that govern the folding of protein chains},
author = {Anfinsen, C. B.},
year = {1973},
month = {07},
date = {1973-07-20},
journal = {Science (New York, N.Y.)},
pages = {223--230},
volume = {181},
number = {4096},
doi = {10.1126/science.181.4096.223},
note = {PMID: 4124164},
langid = {eng}
}
@article{muhammed2019,
title = {Homology modeling in drug discovery: Overview, current applications, and future perspectives},
author = {Muhammed, Muhammed Tilahun and Aki-Yalcin, Esin},
year = {2019},
month = {01},
date = {2019-01},
journal = {Chemical Biology & Drug Design},
pages = {12--20},
volume = {93},
number = {1},
doi = {10.1111/cbdd.13388},
note = {PMID: 30187647},
langid = {eng}
}
@article{haddad2020,
title = {Ten quick tips for homology modeling of high-resolution protein 3D structures},
author = {Haddad, Yazan and Adam, Vojtech and Heger, Zbynek},
year = {2020},
month = {04},
date = {2020-04-02},
journal = {PLOS Computational Biology},
pages = {e1007449},
volume = {16},
number = {4},
doi = {10.1371/journal.pcbi.1007449},
url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007449},
note = {Publisher: Public Library of Science},
langid = {en}
}
@article{waterhouse2018,
title = {SWISS-MODEL: homology modelling of protein structures and complexes},
author = {Waterhouse, Andrew and Bertoni, Martino and Bienert, Stefan and Studer, Gabriel and Tauriello, Gerardo and Gumienny, Rafal and Heer, Florian T and {de Beer}, {Tjaart A P} and Rempfer, Christine and Bordoli, Lorenza and Lepore, Rosalba and Schwede, Torsten},
year = {2018},
month = {07},
date = {2018-07-02},
journal = {Nucleic Acids Research},
pages = {W296--W303},
volume = {46},
number = {W1},
doi = {10.1093/nar/gky427},
url = {https://doi.org/10.1093/nar/gky427}
}
@article{remmert2011,
title = {HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment},
author = {Remmert, Michael and Biegert, Andreas and Hauser, Andreas and {Söding}, Johannes},
year = {2011},
month = {12},
date = {2011-12-25},
journal = {Nature Methods},
pages = {173--175},
volume = {9},
number = {2},
doi = {10.1038/nmeth.1818},
note = {PMID: 22198341},
langid = {eng}
}
@inbook{fiser2009,
title = {Comparative Protein Structure Modelling},
author = {Fiser, {András}},
editor = {Rigden, Daniel John},
year = {2009},
date = {2009},
publisher = {Springer Netherlands},
pages = {57--90},
doi = {10.1007/978-1-4020-9058-5_3},
url = {https://doi.org/10.1007/978-1-4020-9058-5_3},
note = {DOI: 10.1007/978-1-4020-9058-5{\_}3},
address = {Dordrecht},
langid = {en}
}
@inbook{kelley2009,
title = {Fold Recognition},
author = {Kelley, Lawrence A.},
editor = {Rigden, Daniel John},
year = {2009},
date = {2009},
publisher = {Springer Netherlands},
pages = {27--55},
doi = {10.1007/978-1-4020-9058-5_2},
url = {https://doi.org/10.1007/978-1-4020-9058-5_2},
note = {DOI: 10.1007/978-1-4020-9058-5{\_}2},
address = {Dordrecht},
langid = {en}
}
@article{haddad2020,
title = {Ten quick tips for homology modeling of high-resolution protein 3D structures},
author = {Haddad, Yazan and Adam, Vojtech and Heger, Zbynek},
year = {2020},
month = {04},
date = {2020-04-02},
journal = {PLOS Computational Biology},
pages = {e1007449},
volume = {16},
number = {4},
doi = {10.1371/journal.pcbi.1007449},
url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007449},
note = {Publisher: Public Library of Science},
langid = {en}
}
@article{janson2019,
title = {Revisiting the {\textquotedblleft}satisfaction of spatial restraints{\textquotedblright} approach of MODELLER for protein homology modeling},
author = {Janson, Giacomo and Grottesi, Alessandro and Pietrosanto, Marco and Ausiello, Gabriele and Guarguaglini, Giulia and Paiardini, Alessandro},
year = {2019},
month = {12},
date = {2019-12-17},
journal = {PLOS Computational Biology},
pages = {e1007219},
volume = {15},
number = {12},
doi = {10.1371/journal.pcbi.1007219},
url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007219},
note = {Publisher: Public Library of Science},
langid = {en}
}
@article{studer2020,
title = {QMEANDisCo-distance constraints applied on model quality estimation},
author = {Studer, Gabriel and Rempfer, Christine and Waterhouse, Andrew M. and Gumienny, Rafal and Haas, Juergen and Schwede, Torsten},
year = {2020},
month = {03},
date = {2020-03-01},
journal = {Bioinformatics (Oxford, England)},
pages = {1765--1771},
volume = {36},
number = {6},
doi = {10.1093/bioinformatics/btz828},
note = {PMID: 31697312
PMCID: PMC7075525},
langid = {eng}
}
@article{mcguffin2021,
title = {ModFOLD8: accurate global and local quality estimates for 3D protein models},
author = {McGuffin, Liam J. and Aldowsari, Fahd M. F. and Alharbi, Shuaa M. A. and Adiyaman, Recep},
year = {2021},
month = {07},
date = {2021-07-02},
journal = {Nucleic Acids Research},
pages = {W425--W430},
volume = {49},
number = {W1},
doi = {10.1093/nar/gkab321},
note = {PMID: 33963867
PMCID: PMC8218196},
langid = {eng}
}
@article{olechnovi2017,
title = {VoroMQA: Assessment of protein structure quality using interatomic contact areas},
author = {{Olechnovi{\v{c}}}, Kliment and Venclovas, {{\v{C}}eslovas}},
year = {2017},
month = {06},
date = {2017-06},
journal = {Proteins},
pages = {1131--1145},
volume = {85},
number = {6},
doi = {10.1002/prot.25278},
note = {PMID: 28263393},
langid = {eng}
}
@article{yang2020,
title = {Improved protein structure prediction using predicted interresidue orientations},
author = {Yang, Jianyi and Anishchenko, Ivan and Park, Hahnbeom and Peng, Zhenling and Ovchinnikov, Sergey and Baker, David},
year = {2020},
month = {01},
date = {2020-01-21},
journal = {Proceedings of the National Academy of Sciences},
pages = {1496--1503},
volume = {117},
number = {3},
doi = {10.1073/pnas.1914677117},
url = {https://www.pnas.org/content/117/3/1496},
note = {Publisher: National Academy of Sciences
Section: Biological Sciences
PMID: 31896580},
langid = {en}
}
@article{zheng2019,
title = {Detecting distant-homology protein structures by aligning deep neural-network based contact maps},
author = {Zheng, Wei and Wuyun, Qiqige and Li, Yang and Mortuza, S. M. and Zhang, Chengxin and Pearce, Robin and Ruan, Jishou and Zhang, Yang},
year = {2019},
month = {10},
date = {2019-10-17},
journal = {PLOS Computational Biology},
pages = {e1007411},
volume = {15},
number = {10},
doi = {10.1371/journal.pcbi.1007411},
url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007411},
note = {Publisher: Public Library of Science},
langid = {en}
}
@article{bhattacharya2022,
title = {DisCovER: distance- and orientation-based covariational threading for weakly homologous proteins},
author = {Bhattacharya, Sutanu and Roche, Rahmatullah and Moussad, Bernard and Bhattacharya, Debswapna},
year = {2022},
date = {2022},
journal = {Proteins: Structure, Function, and Bioinformatics},
pages = {579--588},
volume = {90},
number = {2},
doi = {10.1002/prot.26254},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.26254},
note = {{\_}eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.26254},
langid = {en}
}
@article{wang2017,
title = {Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model},
author = {Wang, Sheng and Sun, Siqi and Li, Zhen and Zhang, Renyu and Xu, Jinbo},
year = {2017},
month = {01},
date = {2017-01},
journal = {PLoS computational biology},
pages = {e1005324},
volume = {13},
number = {1},
doi = {10.1371/journal.pcbi.1005324},
note = {PMID: 28056090
PMCID: PMC5249242},
langid = {eng}
}
@article{senior2020,
title = {Improved protein structure prediction using potentials from deep learning},
author = {Senior, Andrew W. and Evans, Richard and Jumper, John and Kirkpatrick, James and Sifre, Laurent and Green, Tim and Qin, Chongli and {{\v{Z}}ídek}, Augustin and Nelson, Alexander W. R. and Bridgland, Alex and Penedones, Hugo and Petersen, Stig and Simonyan, Karen and Crossan, Steve and Kohli, Pushmeet and Jones, David T. and Silver, David and Kavukcuoglu, Koray and Hassabis, Demis},
year = {2020},
month = {01},
date = {2020-01},
journal = {Nature},
pages = {706--710},
volume = {577},
number = {7792},
doi = {10.1038/s41586-019-1923-7},
note = {PMID: 31942072},
langid = {eng}
}
@article{jumper2021a,
title = {Highly accurate protein structure prediction with AlphaFold},
author = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and {{\v{Z}}ídek}, Augustin and Potapenko, Anna and Bridgland, Alex and Meyer, Clemens and Kohl, Simon A. A. and Ballard, Andrew J. and Cowie, Andrew and Romera-Paredes, Bernardino and Nikolov, Stanislav and Jain, Rishub and Adler, Jonas and Back, Trevor and Petersen, Stig and Reiman, David and Clancy, Ellen and Zielinski, Michal and Steinegger, Martin and Pacholska, Michalina and Berghammer, Tamas and Bodenstein, Sebastian and Silver, David and Vinyals, Oriol and Senior, Andrew W. and Kavukcuoglu, Koray and Kohli, Pushmeet and Hassabis, Demis},
year = {2021},
month = {08},
date = {2021-08},
journal = {Nature},
pages = {583--589},
volume = {596},
number = {7873},
doi = {10.1038/s41586-021-03819-2},
url = {https://www.nature.com/articles/s41586-021-03819-2},
note = {Number: 7873
Publisher: Nature Publishing Group},
langid = {en}
}
@article{baek2021,
title = {Accurate prediction of protein structures and interactions using a three-track neural network},
author = {Baek, Minkyung and DiMaio, Frank and Anishchenko, Ivan and Dauparas, Justas and Ovchinnikov, Sergey and Lee, Gyu Rie and Wang, Jue and Cong, Qian and Kinch, Lisa N. and Schaeffer, R. Dustin and {Millán}, Claudia and Park, Hahnbeom and Adams, Carson and Glassman, Caleb R. and DeGiovanni, Andy and Pereira, Jose H. and Rodrigues, Andria V. and van Dijk, Alberdina A. and Ebrecht, Ana C. and Opperman, Diederik J. and Sagmeister, Theo and Buhlheller, Christoph and Pavkov-Keller, Tea and Rathinaswamy, Manoj K. and Dalwadi, Udit and Yip, Calvin K. and Burke, John E. and Garcia, K. Christopher and Grishin, Nick V. and Adams, Paul D. and Read, Randy J. and Baker, David},
year = {2021},
month = {08},
date = {2021-08-20},
journal = {Science (New York, N.Y.)},
pages = {871--876},
volume = {373},
number = {6557},
doi = {10.1126/science.abj8754},
note = {PMID: 34282049
PMCID: PMC7612213},
langid = {eng}
}
@article{zheng2021,
title = {Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations},
author = {Zheng, Wei and Zhang, Chengxin and Li, Yang and Pearce, Robin and Bell, Eric W. and Zhang, Yang},
year = {2021},
month = {07},
date = {2021-07-26},
journal = {Cell Reports Methods},
pages = {100014},
volume = {1},
number = {3},
doi = {10.1016/j.crmeth.2021.100014},
note = {PMID: 34355210
PMCID: PMC8336924},
langid = {eng}
}
@article{mirdita2022a,
title = {ColabFold: making protein folding accessible to all},
author = {Mirdita, Milot and {Schütze}, Konstantin and Moriwaki, Yoshitaka and Heo, Lim and Ovchinnikov, Sergey and Steinegger, Martin},
year = {2022},
month = {06},
date = {2022-06},
journal = {Nature Methods},
pages = {679--682},
volume = {19},
number = {6},
doi = {10.1038/s41592-022-01488-1},
note = {PMID: 35637307},
langid = {eng}
}
@article{adiyaman2019,
title = {Methods for the Refinement of Protein Structure 3D Models},
author = {Adiyaman, Recep and McGuffin, Liam James},
year = {2019},
month = {05},
date = {2019-05-09},
journal = {International Journal of Molecular Sciences},
pages = {E2301},
volume = {20},
number = {9},
doi = {10.3390/ijms20092301},
note = {PMID: 31075942
PMCID: PMC6539982},
langid = {eng}
}
@article{peng2011,
title = {A multiple-template approach to protein threading},
author = {Peng, Jian and Xu, Jinbo},
year = {2011},
date = {2011},
journal = {Proteins: Structure, Function, and Bioinformatics},
pages = {1930--1939},
volume = {79},
number = {6},
doi = {10.1002/prot.23016},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.23016},
note = {{\_}eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.23016},
langid = {en}
}
@article{meier2015,
title = {Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling},
author = {Meier, Armin and {Söding}, Johannes},
year = {2015},
month = {10},
date = {2015-10},
journal = {PLoS computational biology},
pages = {e1004343},
volume = {11},
number = {10},
doi = {10.1371/journal.pcbi.1004343},
note = {PMID: 26496371
PMCID: PMC4619893},
langid = {eng}
}
@article{roy2010,
title = {I-TASSER: a unified platform for automated protein structure and function prediction},
author = {Roy, A. and Kucukural, A. and Zhang, Y.},
year = {2010},
date = {2010},
journal = {Nat Protoc},
pages = {725--38},
volume = {5},
number = {4},
doi = {nprot.2010.5 [pii] 10.1038/nprot.2010.5},
langid = {eng}
}
@article{olmea1997,
title = {Improving contact predictions by the combination of correlated mutations and other sources of sequence information},
author = {Olmea, O. and Valencia, A.},
year = {1997},
date = {1997},
journal = {Folding & Design},
pages = {S25--32},
volume = {2},
number = {3},
doi = {10.1016/s1359-0278(97)00060-6},
note = {PMID: 9218963},
langid = {eng}
}
@article{jones2012,
title = {PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments},
author = {Jones, David T. and Buchan, Daniel W. A. and Cozzetto, Domenico and Pontil, Massimiliano},
year = {2012},
month = {01},
date = {2012-01-15},
journal = {Bioinformatics (Oxford, England)},
pages = {184--190},
volume = {28},
number = {2},
doi = {10.1093/bioinformatics/btr638},
note = {PMID: 22101153},
langid = {eng}
}
@article{kamisetty2013,
title = {Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era},
author = {Kamisetty, Hetunandan and Ovchinnikov, Sergey and Baker, David},
year = {2013},
month = {09},
date = {2013-09-24},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
pages = {15674--15679},
volume = {110},
number = {39},
doi = {10.1073/pnas.1314045110},
note = {PMID: 24009338
PMCID: PMC3785744},
langid = {eng}
}
@article{jones2015,
title = {MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins},
author = {Jones, David T. and Singh, Tanya and Kosciolek, Tomasz and Tetchner, Stuart},
year = {2015},
month = {04},
date = {2015-04-01},
journal = {Bioinformatics (Oxford, England)},
pages = {999--1006},
volume = {31},
number = {7},
doi = {10.1093/bioinformatics/btu791},
note = {PMID: 25431331
PMCID: PMC4382908},
langid = {eng}
}
@article{ma2015a,
title = {Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning},
author = {Ma, Jianzhu and Wang, Sheng and Wang, Zhiyong and Xu, Jinbo},
year = {2015},
month = {11},
date = {2015-11-01},
journal = {Bioinformatics (Oxford, England)},
pages = {3506--3513},
volume = {31},
number = {21},
doi = {10.1093/bioinformatics/btv472},
note = {PMID: 26275894
PMCID: PMC4838177},
langid = {eng}
}
@article{ma2015,
title = {Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning},
author = {Ma, Jianzhu and Wang, Sheng and Wang, Zhiyong and Xu, Jinbo},
year = {2015},
month = {11},
date = {2015-11-01},
journal = {Bioinformatics (Oxford, England)},
pages = {3506--3513},
volume = {31},
number = {21},
doi = {10.1093/bioinformatics/btv472},
note = {PMID: 26275894
PMCID: PMC4838177},
langid = {eng}
}
@article{engelberger2021,
title = {Developing and Implementing Cloud-Based Tutorials That Combine Bioinformatics Software, Interactive Coding, and Visualization Exercises for Distance Learning on Structural Bioinformatics},
author = {Engelberger, Felipe and Galaz-Davison, Pablo and Bravo, Graciela and Rivera, Maira and {Ramírez-Sarmiento}, {César A.}},
year = {2021},
month = {05},
date = {2021-05-11},
journal = {Journal of Chemical Education},
pages = {1801--1807},
volume = {98},
number = {5},
doi = {10.1021/acs.jchemed.1c00022},
url = {https://doi.org/10.1021/acs.jchemed.1c00022},
note = {Publisher: American Chemical Society}
}
@article{baker2001,
title = {Protein Structure Prediction and Structural Genomics},
author = {Baker, David and Sali, Andrej},
year = {2001},
month = {10},
date = {2001-10-05},
journal = {Science},
pages = {93--96},
volume = {294},
number = {5540},
doi = {10.1126/science.1065659},
url = {https://www.science.org/doi/10.1126/science.1065659},
note = {Publisher: American Association for the Advancement of Science}
}
@article{radford2000,
title = {Protein folding: progress made and promises ahead},
author = {Radford, Sheena E.},
year = {2000},
month = {12},
date = {2000-12-01},
journal = {Trends in Biochemical Sciences},
pages = {611--618},
volume = {25},
number = {12},
doi = {10.1016/S0968-0004(00)01707-2},
url = {https://www.sciencedirect.com/science/article/pii/S0968000400017072},
langid = {en}
}
@article{baek2021a,
title = {Accurate prediction of protein structures and interactions using a three-track neural network},
author = {Baek, Minkyung and DiMaio, Frank and Anishchenko, Ivan and Dauparas, Justas and Ovchinnikov, Sergey and Lee, Gyu Rie and Wang, Jue and Cong, Qian and Kinch, Lisa N. and Schaeffer, R. Dustin and {Millán}, Claudia and Park, Hahnbeom and Adams, Carson and Glassman, Caleb R. and DeGiovanni, Andy and Pereira, Jose H. and Rodrigues, Andria V. and van Dijk, Alberdina A. and Ebrecht, Ana C. and Opperman, Diederik J. and Sagmeister, Theo and Buhlheller, Christoph and Pavkov-Keller, Tea and Rathinaswamy, Manoj K. and Dalwadi, Udit and Yip, Calvin K. and Burke, John E. and Garcia, K. Christopher and Grishin, Nick V. and Adams, Paul D. and Read, Randy J. and Baker, David},
year = {2021},
month = {08},
date = {2021-08-20},
journal = {Science (New York, N.Y.)},
pages = {871--876},
volume = {373},
number = {6557},
doi = {10.1126/science.abj8754},
note = {PMID: 34282049
PMCID: PMC7612213},
langid = {eng}
}
@article{zheng2021a,
title = {Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations},
author = {Zheng, Wei and Zhang, Chengxin and Li, Yang and Pearce, Robin and Bell, Eric W. and Zhang, Yang},
year = {2021},
month = {07},
date = {2021-07-26},
journal = {Cell Reports Methods},
pages = {100014},
volume = {1},
number = {3},
doi = {10.1016/j.crmeth.2021.100014},
note = {PMID: 34355210
PMCID: PMC8336924},
langid = {eng}
}
@article{evans,
title = {Protein complex prediction with AlphaFold-Multimer},
author = {Evans, Richard and {O{\textquoteright}Neill}, Michael and Pritzel, Alexander and Antropova, Natasha and Senior, Andrew and Green, Tim and {{\v{Z}}ídek}, Augustin and Bates, Russ and Blackwell, Sam and Yim, Jason and Ronneberger, Olaf and Bodenstein, Sebastian and Zielinski, Michal and Bridgland, Alex and Potapenko, Anna and Cowie, Andrew and Tunyasuvunakool, Kathryn and Jain, Rishub and Clancy, Ellen and Kohli, Pushmeet and Jumper, John and Hassabis, Demis},
doi = {10.1101/2021.10.04.463034},
langid = {en}
}
@article{mirdita2022b,
title = {ColabFold: making protein folding accessible to all},
author = {Mirdita, Milot and {Schütze}, Konstantin and Moriwaki, Yoshitaka and Heo, Lim and Ovchinnikov, Sergey and Steinegger, Martin},
year = {2022},
month = {06},
date = {2022-06},
journal = {Nature Methods},
pages = {679--682},
volume = {19},
number = {6},
doi = {10.1038/s41592-022-01488-1},
note = {PMID: 35637307},
langid = {eng}
}
@article{pakhrin2021,
title = {Deep Learning-Based Advances in Protein Structure Prediction},
author = {Pakhrin, Subash C. and Shrestha, Bikash and Adhikari, Badri and Kc, Dukka B.},
year = {2021},
month = {01},
date = {2021-01},
journal = {International Journal of Molecular Sciences},
pages = {5553},
volume = {22},
number = {11},
doi = {10.3390/ijms22115553},
url = {https://www.mdpi.com/1422-0067/22/11/5553},
note = {Number: 11
Publisher: Multidisciplinary Digital Publishing Institute},
langid = {en}
}
@article{jumper2021b,
title = {Highly accurate protein structure prediction with AlphaFold},
author = {Jumper, John and Evans, Richard and Pritzel, Alexander and Green, Tim and Figurnov, Michael and Ronneberger, Olaf and Tunyasuvunakool, Kathryn and Bates, Russ and {{\v{Z}}ídek}, Augustin and Potapenko, Anna and Bridgland, Alex and Meyer, Clemens and Kohl, Simon A. A. and Ballard, Andrew J. and Cowie, Andrew and Romera-Paredes, Bernardino and Nikolov, Stanislav and Jain, Rishub and Adler, Jonas and Back, Trevor and Petersen, Stig and Reiman, David and Clancy, Ellen and Zielinski, Michal and Steinegger, Martin and Pacholska, Michalina and Berghammer, Tamas and Bodenstein, Sebastian and Silver, David and Vinyals, Oriol and Senior, Andrew W. and Kavukcuoglu, Koray and Kohli, Pushmeet and Hassabis, Demis},
year = {2021},
month = {08},
date = {2021-08},
journal = {Nature},
pages = {583--589},
volume = {596},
number = {7873},
doi = {10.1038/s41586-021-03819-2},
url = {https://www.nature.com/articles/s41586-021-03819-2},
note = {Number: 7873
Publisher: Nature Publishing Group},
langid = {en}
}
@article{portapardo2022,
title = {The structural coverage of the human proteome before and after AlphaFold},
author = {Porta-Pardo, Eduard and Ruiz-Serra, Victoria and Valentini, Samuel and Valencia, Alfonso},
year = {2022},
month = {01},
date = {2022-01-24},
journal = {PLOS Computational Biology},
pages = {e1009818},
volume = {18},
number = {1},
doi = {10.1371/journal.pcbi.1009818},
url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009818},
note = {Publisher: Public Library of Science},
langid = {en}
}
@article{pederson2021,
title = {Protein structure: Has Levinthal's paradox {\textquotedblleft}folded{\textquotedblright}?},
author = {Pederson, Thoru},
year = {2021},
date = {2021},
journal = {The FASEB Journal},
pages = {e21416},
volume = {35},
number = {3},
doi = {10.1096/fj.202100136},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1096/fj.202100136},
note = {{\_}eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1096/fj.202100136},
langid = {en}
}
@article{outeiral,
title = {Current protein structure predictors do not produce meaningful folding pathways},
author = {Outeiral, Carlos and Nissley, Daniel A. and Deane, Charlotte M.},
doi = {10.1101/2021.09.20.461137},
langid = {en}
}
@article{aljanabi2022,
title = {Has DeepMind's AlphaFold solved the protein folding problem?},
author = {Al-Janabi, Aisha},
year = {2022},
month = {03},
date = {2022-03},
journal = {BioTechniques},
pages = {73--76},
volume = {72},
number = {3},
doi = {10.2144/btn-2022-0007},
url = {https://www.future-science.com/doi/full/10.2144/btn-2022-0007},
note = {Publisher: Future Science}
}
@article{bhattacharya2021,
title = {Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading},
author = {Bhattacharya, Sutanu and Roche, Rahmatullah and Shuvo, Md Hossain and Bhattacharya, Debswapna},
year = {2021},
date = {2021},
journal = {Frontiers in Molecular Biosciences},
pages = {643752},
volume = {8},
doi = {10.3389/fmolb.2021.643752},
note = {PMID: 34046429
PMCID: PMC8148041},
langid = {eng}
}
@article{baek2021b,
title = {Accurate prediction of protein structures and interactions using a three-track neural network},
author = {Baek, Minkyung and DiMaio, Frank and Anishchenko, Ivan and Dauparas, Justas and Ovchinnikov, Sergey and Lee, Gyu Rie and Wang, Jue and Cong, Qian and Kinch, Lisa N. and Schaeffer, R. Dustin and {Millán}, Claudia and Park, Hahnbeom and Adams, Carson and Glassman, Caleb R. and DeGiovanni, Andy and Pereira, Jose H. and Rodrigues, Andria V. and van Dijk, Alberdina A. and Ebrecht, Ana C. and Opperman, Diederik J. and Sagmeister, Theo and Buhlheller, Christoph and Pavkov-Keller, Tea and Rathinaswamy, Manoj K. and Dalwadi, Udit and Yip, Calvin K. and Burke, John E. and Garcia, K. Christopher and Grishin, Nick V. and Adams, Paul D. and Read, Randy J. and Baker, David},
year = {2021},
month = {08},
date = {2021-08-20},
journal = {Science (New York, N.Y.)},
pages = {871--876},
volume = {373},
number = {6557},
doi = {10.1126/science.abj8754},
note = {PMID: 34282049
PMCID: PMC7612213},
langid = {eng}
}
@article{baek2021c,
title = {Accurate prediction of protein structures and interactions using a three-track neural network},
author = {Baek, Minkyung and DiMaio, Frank and Anishchenko, Ivan and Dauparas, Justas and Ovchinnikov, Sergey and Lee, Gyu Rie and Wang, Jue and Cong, Qian and Kinch, Lisa N. and Schaeffer, R. Dustin and {Millán}, Claudia and Park, Hahnbeom and Adams, Carson and Glassman, Caleb R. and DeGiovanni, Andy and Pereira, Jose H. and Rodrigues, Andria V. and van Dijk, Alberdina A. and Ebrecht, Ana C. and Opperman, Diederik J. and Sagmeister, Theo and Buhlheller, Christoph and Pavkov-Keller, Tea and Rathinaswamy, Manoj K. and Dalwadi, Udit and Yip, Calvin K. and Burke, John E. and Garcia, K. Christopher and Grishin, Nick V. and Adams, Paul D. and Read, Randy J. and Baker, David},
year = {2021},
month = {08},
date = {2021-08-20},
journal = {Science (New York, N.Y.)},
pages = {871--876},
volume = {373},
number = {6557},
doi = {10.1126/science.abj8754},
note = {PMID: 34282049
PMCID: PMC7612213},
langid = {eng}
}
@article{evans2022,
title = {Protein complex prediction with AlphaFold-Multimer},
author = {Evans, Richard and {O{\textquoteright}Neill}, Michael and Pritzel, Alexander and Antropova, Natasha and Senior, Andrew and Green, Tim and {{\v{Z}}ídek}, Augustin and Bates, Russ and Blackwell, Sam and Yim, Jason and Ronneberger, Olaf and Bodenstein, Sebastian and Zielinski, Michal and Bridgland, Alex and Potapenko, Anna and Cowie, Andrew and Tunyasuvunakool, Kathryn and Jain, Rishub and Clancy, Ellen and Kohli, Pushmeet and Jumper, John and Hassabis, Demis},
year = {2022},
date = {2022},
url = {https://www.biorxiv.org/content/10.1101/2021.10.04.463034v2},
note = {Pages: 2021.10.04.463034
Section: New Results},
langid = {en}
}
@article{mirdita2022c,
title = {ColabFold: making protein folding accessible to all},
author = {Mirdita, Milot and {Schütze}, Konstantin and Moriwaki, Yoshitaka and Heo, Lim and Ovchinnikov, Sergey and Steinegger, Martin},
year = {2022},
month = {06},
date = {2022-06},
journal = {Nature Methods},
pages = {679--682},
volume = {19},
number = {6},
doi = {10.1038/s41592-022-01488-1},
note = {PMID: 35637307},
langid = {eng}
}
@article{varadi2022,
title = {AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models},
author = {Varadi, Mihaly and Anyango, Stephen and Deshpande, Mandar and Nair, Sreenath and Natassia, Cindy and Yordanova, Galabina and Yuan, David and Stroe, Oana and Wood, Gemma and Laydon, Agata and {{\v{Z}}ídek}, Augustin and Green, Tim and Tunyasuvunakool, Kathryn and Petersen, Stig and Jumper, John and Clancy, Ellen and Green, Richard and Vora, Ankur and Lutfi, Mira and Figurnov, Michael and Cowie, Andrew and Hobbs, Nicole and Kohli, Pushmeet and Kleywegt, Gerard and Birney, Ewan and Hassabis, Demis and Velankar, Sameer},
year = {2022},
month = {01},
date = {2022-01-07},
journal = {Nucleic Acids Research},
pages = {D439--D444},
volume = {50},
number = {D1},
doi = {10.1093/nar/gkab1061},
url = {https://doi.org/10.1093/nar/gkab1061}
}
@article{porta-pardo2022a,
title = {The structural coverage of the human proteome before and after AlphaFold},
author = {Porta-Pardo, Eduard and Ruiz-Serra, Victoria and Valentini, Samuel and Valencia, Alfonso},
year = {2022},
month = {01},
date = {2022-01-24},
journal = {PLOS Computational Biology},
pages = {e1009818},
volume = {18},
number = {1},
doi = {10.1371/journal.pcbi.1009818},
url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009818},
note = {Publisher: Public Library of Science},
langid = {en}
}
@article{kempen,
title = {Foldseek: fast and accurate protein structure search},
author = {Kempen, Michel van and Kim, Stephanie S. and Tumescheit, Charlotte and Mirdita, Milot and Gilchrist, Cameron L. M. and {Söding}, Johannes and Steinegger, Martin},
doi = {10.1101/2022.02.07.479398},
langid = {en}
}
@article{holm2022,
title = {Dali server: structural unification of protein families},
author = {Holm, Liisa},
year = {2022},
month = {07},
date = {2022-07-05},
journal = {Nucleic Acids Research},
pages = {W210--W215},
volume = {50},
number = {W1},
doi = {10.1093/nar/gkac387},
url = {https://doi.org/10.1093/nar/gkac387}
}
@article{marks2011,
title = {Protein 3D Structure Computed from Evolutionary Sequence Variation},
author = {Marks, Debora S. and Colwell, Lucy J. and Sheridan, Robert and Hopf, Thomas A. and Pagnani, Andrea and Zecchina, Riccardo and Sander, Chris},
year = {2011},
month = {12},
date = {2011-12-07},
journal = {PLOS ONE},
pages = {e28766},
volume = {6},
number = {12},
doi = {10.1371/journal.pone.0028766},
url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028766},
note = {Publisher: Public Library of Science},
langid = {en}
}
@book{structur,
title = {Structural Bioinformatics, 2nd Edition | Wiley},
author = {Gu, J. and Bourne, P.E.},
year = {2009},
url = {https://www.wiley.com/en-us/Structural+Bioinformatics%2C+2nd+Edition-p-9780470181058},
langid = {en-us}
}
@article{kendrew1958,
title = {A three-dimensional model of the myoglobin molecule obtained by x-ray analysis},
author = {Kendrew, J. C. and Bodo, G. and Dintzis, H. M. and Parrish, R. G. and Wyckoff, H. and Phillips, D. C.},
year = {1958},
month = {03},
date = {1958-03-08},
journal = {Nature},
pages = {662--666},
volume = {181},
number = {4610},
doi = {10.1038/181662a0},
note = {PMID: 13517261},
langid = {eng}
}
@article{steinegger2018,
title = {Clustering huge protein sequence sets in linear time},
author = {Steinegger, Martin and {Söding}, Johannes},
year = {2018},
month = {06},
date = {2018-06-29},
journal = {Nature Communications},
pages = {2542},
volume = {9},
number = {1},
doi = {10.1038/s41467-018-04964-5},
note = {PMID: 29959318
PMCID: PMC6026198},
langid = {eng}
}
@article{blum2021,
title = {The InterPro protein families and domains database: 20 years on},
author = {Blum, Matthias and Chang, Hsin-Yu and Chuguransky, Sara and Grego, Tiago and Kandasaamy, Swaathi and Mitchell, Alex and Nuka, Gift and Paysan-Lafosse, Typhaine and Qureshi, Matloob and Raj, Shriya and Richardson, Lorna and Salazar, Gustavo A and Williams, Lowri and Bork, Peer and Bridge, Alan and Gough, Julian and Haft, Daniel H and Letunic, Ivica and Marchler-Bauer, Aron and Mi, Huaiyu and Natale, Darren A and Necci, Marco and Orengo, Christine A and Pandurangan, Arun P and Rivoire, Catherine and Sigrist, Christian J A and Sillitoe, Ian and Thanki, Narmada and Thomas, Paul D and Tosatto, Silvio C E and Wu, Cathy H and Bateman, Alex and Finn, Robert D},
year = {2021},
month = {01},
date = {2021-01-08},
journal = {Nucleic Acids Research},
pages = {D344--D354},
volume = {49},
number = {D1},
doi = {10.1093/nar/gkaa977},
url = {https://doi.org/10.1093/nar/gkaa977}
}
@article{mistry2020,
title = {Pfam: The protein families database in 2021},
author = {Mistry, Jaina and Chuguransky, Sara and Williams, Lowri and Qureshi, Matloob and Salazar, {Gustavo A} and Sonnhammer, Erik L L and Tosatto, Silvio C E and Paladin, Lisanna and Raj, Shriya and Richardson, Lorna J and Finn, Robert D and Bateman, Alex},
year = {2020},
month = {10},
date = {2020-10-30},
journal = {Nucleic Acids Research},
pages = {D412--D419},
volume = {49},
number = {D1},
doi = {10.1093/nar/gkaa913},
url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779014/},
note = {PMID: 33125078
PMCID: PMC7779014}
}