Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 119

1.

Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications.

Fine J, Lackner R, Samudrala R, Chopra G.

Sci Rep. 2019 Sep 11;9(1):13155. doi: 10.1038/s41598-019-49515-0.

2.

Exploration of interaction scoring criteria in the CANDO platform.

Falls Z, Mangione W, Schuler J, Samudrala R.

BMC Res Notes. 2019 Jun 7;12(1):318. doi: 10.1186/s13104-019-4356-3.

3.

Association of cutaneous adverse drug reactions due to antiepileptic drugs with HLA alleles in a North Indian population.

Ihtisham K, Ramanujam B, Srivastava S, Mehra NK, Kaur G, Khanna N, Jain S, Kumar S, Kaul B, Samudrala R, Tripathi M.

Seizure. 2019 Mar;66:99-103. doi: 10.1016/j.seizure.2019.02.011. Epub 2019 Feb 20.

PMID:
30826555
4.

In vitro bioactivity and degradation behaviour of β-wollastonite derived from natural waste.

Palakurthy S, K VGR, Samudrala RK, P AA.

Mater Sci Eng C Mater Biol Appl. 2019 May;98:109-117. doi: 10.1016/j.msec.2018.12.101. Epub 2018 Dec 29.

PMID:
30812993
5.
6.

Photochemistry of the 1,6-Dideuterio-1,3,5-hexatrienes in Solution: Efficient Terminal Bond Photoisomerization in One-Bond-Twist and Bicycle Pedal Ways.

Saltiel J, Redwood CE, Laohhasurayotin K, Samudrala R.

J Phys Chem A. 2018 Nov 1;122(43):8477-8489. doi: 10.1021/acs.jpca.8b08288. Epub 2018 Oct 18.

PMID:
30277763
7.

A Systematic Review of Computational Drug Discovery, Development, and Repurposing for Ebola Virus Disease Treatment.

Schuler J, Hudson ML, Schwartz D, Samudrala R.

Molecules. 2017 Oct 20;22(10). pii: E1777. doi: 10.3390/molecules22101777. Review.

8.

Cytocompatibility studies of titania-doped calcium borosilicate bioactive glasses in-vitro.

Samudrala R, Abdul Azeem P, Penugurti V, Manavathi B.

Mater Sci Eng C Mater Biol Appl. 2017 Aug 1;77:772-779. doi: 10.1016/j.msec.2017.03.245. Epub 2017 Mar 27.

PMID:
28532092
9.

Combating Ebola with Repurposed Therapeutics Using the CANDO Platform.

Chopra G, Kaushik S, Elkin PL, Samudrala R.

Molecules. 2016 Nov 25;21(12). pii: E1537.

10.

Mycobacterium Cytidylate Kinase Appears to Be an Undruggable Target.

Craig JK, Risler JK, Loesch KA, Dong W, Baker D, Barrett LK, Subramanian S, Samudrala R, Van Voorhis WC.

J Biomol Screen. 2016 Aug;21(7):695-700. doi: 10.1177/1087057116646702. Epub 2016 May 4.

PMID:
27146385
11.

Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform.

Chopra G, Samudrala R.

Curr Pharm Des. 2016;22(21):3109-23. Review.

12.

Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development.

Manocheewa S, Mittler JE, Samudrala R, Mullins JI.

Viruses. 2015 Nov 4;7(11):5718-35. doi: 10.3390/v7112901.

13.
14.

Data access for the 1,000 Plants (1KP) project.

Matasci N, Hung LH, Yan Z, Carpenter EJ, Wickett NJ, Mirarab S, Nguyen N, Warnow T, Ayyampalayam S, Barker M, Burleigh JG, Gitzendanner MA, Wafula E, Der JP, dePamphilis CW, Roure B, Philippe H, Ruhfel BR, Miles NW, Graham SW, Mathews S, Surek B, Melkonian M, Soltis DE, Soltis PS, Rothfels C, Pokorny L, Shaw JA, DeGironimo L, Stevenson DW, Villarreal JC, Chen T, Kutchan TM, Rolf M, Baucom RS, Deyholos MK, Samudrala R, Tian Z, Wu X, Sun X, Zhang Y, Wang J, Leebens-Mack J, Wong GK.

Gigascience. 2014 Oct 27;3:17. doi: 10.1186/2047-217X-3-17. eCollection 2014. Review.

15.

Preferential Promotion of Lycopersicon esculentum (Tomato) Growth by Plant Growth Promoting Bacteria Associated with Tomato.

Vaikuntapu PR, Dutta S, Samudrala RB, Rao VR, Kalam S, Podile AR.

Indian J Microbiol. 2014 Dec;54(4):403-12. doi: 10.1007/s12088-014-0470-z. Epub 2014 May 15.

16.

CANDO and the infinite drug discovery frontier.

Minie M, Chopra G, Sethi G, Horst J, White G, Roy A, Hatti K, Samudrala R.

Drug Discov Today. 2014 Sep;19(9):1353-63. doi: 10.1016/j.drudis.2014.06.018. Epub 2014 Jun 26. Review.

17.

fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data.

Hung LH, Samudrala R.

Bioinformatics. 2014 Jun 15;30(12):1774-6. doi: 10.1093/bioinformatics/btu098. Epub 2014 Feb 14.

18.

Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin.

Lertkiatmongkol P, Assawamakin A, White G, Chopra G, Rongnoparut P, Samudrala R, Tongsima S.

PLoS One. 2013 Sep 2;8(9):e74053. doi: 10.1371/journal.pone.0074053. eCollection 2013. Erratum in: PLoS One. 2013;8(9). doi:10.1371/annotation/416be1ef-f439-445a-96f8-b1d2f01c6957.

19.

Bicycle pedal photoisomerization of 1-phenyl-4-(4-pyridyl)-1,3-butadienes in glassy isopentane at 77 K.

Redwood CE, Kanvah S, Samudrala R, Saltiel J.

Photochem Photobiol Sci. 2013 Oct;12(10):1754-60. doi: 10.1039/c3pp50064k.

PMID:
23904008
20.

Structure prediction of partial-length protein sequences.

Laurenzi A, Hung LH, Samudrala R.

Int J Mol Sci. 2013 Jul 17;14(7):14892-907. doi: 10.3390/ijms140714892.

21.

Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens.

Afzal AJ, Srour A, Goil A, Vasudaven S, Liu T, Samudrala R, Dogra N, Kohli P, Malakar A, Lightfoot DA.

BMC Plant Biol. 2013 Mar 15;13:43. doi: 10.1186/1471-2229-13-43.

22.

The Promise and Challenge of Digital Biology.

Minie ME, Samudrala R.

J Bioeng Biomed Sci. 2013;3(3). pii: e118. doi: 10.4172/2155-9538.1000e118. Epub 2013 Dec 4. No abstract available.

23.

Synthesis of donor-σ-perylenebisimide-acceptor molecules having PEG swallowtails and sulfur anchors.

Kota R, Samudrala R, Mattern DL.

J Org Chem. 2012 Nov 2;77(21):9641-51. doi: 10.1021/jo301701a. Epub 2012 Oct 22.

PMID:
23051043
24.

Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils.

Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S.

Biomacromolecules. 2012 Nov 12;13(11):3494-502. doi: 10.1021/bm300942c. Epub 2012 Sep 28.

25.

The enzymatic and metabolic capabilities of early life.

Goldman AD, Baross JA, Samudrala R.

PLoS One. 2012;7(9):e39912. doi: 10.1371/journal.pone.0039912. Epub 2012 Sep 10.

26.

Strategic protein target analysis for developing drugs to stop dental caries.

Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD.

Adv Dent Res. 2012 Sep;24(2):86-93. doi: 10.1177/0022034512449837.

27.

Cementomimetics-constructing a cementum-like biomineralized microlayer via amelogenin-derived peptides.

Gungormus M, Oren EE, Horst JA, Fong H, Hnilova M, Somerman MJ, Snead ML, Samudrala R, Tamerler C, Sarikaya M.

Int J Oral Sci. 2012 Jun;4(2):69-77. doi: 10.1038/ijos.2012.40. Epub 2012 Jun 29.

28.

Accelerated protein structure comparison using TM-score-GPU.

Hung LH, Samudrala R.

Bioinformatics. 2012 Aug 15;28(16):2191-2. doi: 10.1093/bioinformatics/bts345. Epub 2012 Jun 19.

29.

LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates.

Moughon SE, Samudrala R.

BMC Bioinformatics. 2011 Sep 15;12:368. doi: 10.1186/1471-2105-12-368.

30.

GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition.

Hung LH, Guerquin M, Samudrala R.

BMC Res Notes. 2011 Apr 1;4:97. doi: 10.1186/1756-0500-4-97.

31.

Evolutionary transients in the rice transcriptome.

Wang J, Zhang J, Li R, Zheng H, Li J, Zhang Y, Li H, Ni P, Li S, Li S, Wang J, Liu D, McDermott J, Samudrala R, Liu S, Wang J, Yang H, Yu J, Wong GK.

Genomics Proteomics Bioinformatics. 2010 Dec;8(4):211-28. doi: 10.1016/S1672-0229(10)60023-X.

32.

Caries induced cytokine network in the odontoblast layer of human teeth.

Horst OV, Horst JA, Samudrala R, Dale BA.

BMC Immunol. 2011 Jan 24;12:9. doi: 10.1186/1471-2172-12-9.

33.

IGF1R variants associated with isolated single suture craniosynostosis.

Cunningham ML, Horst JA, Rieder MJ, Hing AV, Stanaway IB, Park SS, Samudrala R, Speltz ML.

Am J Med Genet A. 2011 Jan;155A(1):91-7. doi: 10.1002/ajmg.a.33781.

34.

Viral entry inhibitors block dengue antibody-dependent enhancement in vitro.

Nicholson CO, Costin JM, Rowe DK, Lin L, Jenwitheesuk E, Samudrala R, Isern S, Michael SF.

Antiviral Res. 2011 Jan;89(1):71-4. doi: 10.1016/j.antiviral.2010.11.008. Epub 2010 Nov 18.

PMID:
21093488
35.

Computational prediction of type III and IV secreted effectors in gram-negative bacteria.

McDermott JE, Corrigan A, Peterson E, Oehmen C, Niemann G, Cambronne ED, Sharp D, Adkins JN, Samudrala R, Heffron F.

Infect Immun. 2011 Jan;79(1):23-32. doi: 10.1128/IAI.00537-10. Epub 2010 Oct 25. Review.

36.

Solution study of engineered quartz binding peptides using replica exchange molecular dynamics.

Notman R, Oren EE, Tamerler C, Sarikaya M, Samudrala R, Walsh TR.

Biomacromolecules. 2010 Dec 13;11(12):3266-74. doi: 10.1021/bm100646z. Epub 2010 Oct 22.

PMID:
20964422
37.

Disease risk of missense mutations using structural inference from predicted function.

Horst JA, Wang K, Horst OV, Cunningham ML, Samudrala R.

Curr Protein Pept Sci. 2010 Nov;11(7):573-88.

38.

A protein sequence meta-functional signature for calcium binding residue prediction.

Horst JA, Samudrala R.

Pattern Recognit Lett. 2010 Oct 15;31(14):2103-2112.

39.

Structural optimization and de novo design of dengue virus entry inhibitory peptides.

Costin JM, Jenwitheesuk E, Lok SM, Hunsperger E, Conrads KA, Fontaine KA, Rees CR, Rossmann MG, Isern S, Samudrala R, Michael SF.

PLoS Negl Trop Dis. 2010 Jun 22;4(6):e721. doi: 10.1371/journal.pntd.0000721.

40.

Probing the molecular mechanisms of quartz-binding peptides.

Oren EE, Notman R, Kim IW, Evans JS, Walsh TR, Samudrala R, Tamerler C, Sarikaya M.

Langmuir. 2010 Jul 6;26(13):11003-9. doi: 10.1021/la100049s.

PMID:
20499870
41.

The evolution and functional repertoire of translation proteins following the origin of life.

Goldman AD, Samudrala R, Baross JA.

Biol Direct. 2010 Apr 8;5:15. doi: 10.1186/1745-6150-5-15.

42.

Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix.

Borlee BR, Goldman AD, Murakami K, Samudrala R, Wozniak DJ, Parsek MR.

Mol Microbiol. 2010 Feb;75(4):827-42. doi: 10.1111/j.1365-2958.2009.06991.x. Epub 2010 Jan 17.

43.

Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea.

Goldman AD, Leigh JA, Samudrala R.

BMC Evol Biol. 2009 Aug 11;9:199. doi: 10.1186/1471-2148-9-199.

44.

A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction.

Liu T, Horst JA, Samudrala R.

Proteins. 2009 Oct;77(1):220-34. doi: 10.1002/prot.22434.

45.

Protinfo PPC: a web server for atomic level prediction of protein complexes.

Kittichotirat W, Guerquin M, Bumgarner RE, Samudrala R.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W519-25. doi: 10.1093/nar/gkp306. Epub 2009 May 6.

46.

Accurate prediction of secreted substrates and identification of a conserved putative secretion signal for type III secretion systems.

Samudrala R, Heffron F, McDermott JE.

PLoS Pathog. 2009 Apr;5(4):e1000375. doi: 10.1371/journal.ppat.1000375. Epub 2009 Apr 24.

47.

Inferring molecular interactions pathways from eQTL data.

Rashid I, McDermott J, Samudrala R.

Methods Mol Biol. 2009;541:211-23. doi: 10.1007/978-1-59745-243-4_10. Review.

PMID:
19381546
48.

The Bioverse API and web application.

Guerquin M, McDermott J, Frazier Z, Samudrala R.

Methods Mol Biol. 2009;541:511-34. doi: 10.1007/978-1-59745-243-4_22. Review.

PMID:
19381533
49.

Computational representation of biological systems.

Frazier Z, McDermott J, Guerquin M, Samudrala R.

Methods Mol Biol. 2009;541:535-49. doi: 10.1007/978-1-59745-243-4_23. Review.

PMID:
19381532
50.

Prediction and integration of regulatory and protein-protein interactions.

Wichadakul D, McDermott J, Samudrala R.

Methods Mol Biol. 2009;541:101-43. doi: 10.1007/978-1-59745-243-4_6. Review.

PMID:
19381527

Supplemental Content

Loading ...
Support Center