Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 20 of 23

1.

Survey of Machine Learning Techniques in Drug Discovery.

Stephenson N, Shane E, Chase J, Rowland J, Ries D, Justice N, Zhang J, Chan L, Cao R.

Curr Drug Metab. 2018 Aug 19. doi: 10.2174/1389200219666180820112457. [Epub ahead of print]

PMID:
30124147
2.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

Keasar C, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D; Foldit Players consortium, Crivelli SN.

Sci Rep. 2018 Jul 2;8(1):9939. doi: 10.1038/s41598-018-26812-8.

3.

ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network.

Cao R, Freitas C, Chan L, Sun M, Jiang H, Chen Z.

Molecules. 2017 Oct 17;22(10). pii: E1732. doi: 10.3390/molecules22101732.

4.

QAcon: single model quality assessment using protein structural and contact information with machine learning techniques.

Cao R, Adhikari B, Bhattacharya D, Sun M, Hou J, Cheng J.

Bioinformatics. 2017 Feb 15;33(4):586-588. doi: 10.1093/bioinformatics/btw694.

5.

DeepQA: improving the estimation of single protein model quality with deep belief networks.

Cao R, Bhattacharya D, Hou J, Cheng J.

BMC Bioinformatics. 2016 Dec 5;17(1):495.

6.

Assessing Predicted Contacts for Building Protein Three-Dimensional Models.

Adhikari B, Bhattacharya D, Cao R, Cheng J.

Methods Mol Biol. 2017;1484:115-126. doi: 10.1007/978-1-4939-6406-2_9.

7.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

8.

UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling.

Bhattacharya D, Cao R, Cheng J.

Bioinformatics. 2016 Sep 15;32(18):2791-9. doi: 10.1093/bioinformatics/btw316. Epub 2016 Jun 3.

9.

3Drefine: an interactive web server for efficient protein structure refinement.

Bhattacharya D, Nowotny J, Cao R, Cheng J.

Nucleic Acids Res. 2016 Jul 8;44(W1):W406-9. doi: 10.1093/nar/gkw336. Epub 2016 Apr 29.

10.

Protein single-model quality assessment by feature-based probability density functions.

Cao R, Cheng J.

Sci Rep. 2016 Apr 4;6:23990. doi: 10.1038/srep23990.

11.

GMOL: An Interactive Tool for 3D Genome Structure Visualization.

Nowotny J, Wells A, Oluwadare O, Xu L, Cao R, Trieu T, He C, Cheng J.

Sci Rep. 2016 Feb 12;6:20802. doi: 10.1038/srep20802.

12.
13.

A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11.

Li J, Cao R, Cheng J.

BMC Bioinformatics. 2015 Oct 23;16:337. doi: 10.1186/s12859-015-0775-x.

14.

Iterative reconstruction of three-dimensional models of human chromosomes from chromosomal contact data.

Nowotny J, Ahmed S, Xu L, Oluwadare O, Chen H, Hensley N, Trieu T, Cao R, Cheng J.

BMC Bioinformatics. 2015 Oct 23;16:338. doi: 10.1186/s12859-015-0772-0.

15.
16.

Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11.

Cao R, Bhattacharya D, Adhikari B, Li J, Cheng J.

Proteins. 2016 Sep;84 Suppl 1:247-59. doi: 10.1002/prot.24924. Epub 2015 Sep 29.

17.

Large-scale model quality assessment for improving protein tertiary structure prediction.

Cao R, Bhattacharya D, Adhikari B, Li J, Cheng J.

Bioinformatics. 2015 Jun 15;31(12):i116-23. doi: 10.1093/bioinformatics/btv235.

18.

CONFOLD: Residue-residue contact-guided ab initio protein folding.

Adhikari B, Bhattacharya D, Cao R, Cheng J.

Proteins. 2015 Aug;83(8):1436-49. doi: 10.1002/prot.24829. Epub 2015 Jun 6.

19.

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines.

Cao R, Wang Z, Wang Y, Cheng J.

BMC Bioinformatics. 2014 Apr 28;15:120. doi: 10.1186/1471-2105-15-120.

20.

Designing and evaluating the MULTICOM protein local and global model quality prediction methods in the CASP10 experiment.

Cao R, Wang Z, Cheng J.

BMC Struct Biol. 2014 Apr 15;14:13. doi: 10.1186/1472-6807-14-13.

Supplemental Content

Loading ...
Support Center