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Items: 1 to 20 of 63

1.

Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.

Lee H, Baek M, Lee GR, Park S, Seok C.

Proteins. 2016 Oct 22. doi: 10.1002/prot.25192. [Epub ahead of print]

PMID:
27770545
2.

Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge.

Tofoleanu F, Lee J, Pickard Iv FC, König G, Huang J, Baek M, Seok C, Brooks BR.

J Comput Aided Mol Des. 2017 Jan;31(1):107-118. doi: 10.1007/s10822-016-9965-5.

PMID:
27696242
3.

Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge.

Lee J, Tofoleanu F, Pickard FC 4th, König G, Huang J, Damjanović A, Baek M, Seok C, Brooks BR.

J Comput Aided Mol Des. 2017 Jan;31(1):71-85. doi: 10.1007/s10822-016-9968-2.

PMID:
27677749
4.
5.

Galaxy7TM: flexible GPCR-ligand docking by structure refinement.

Lee GR, Seok C.

Nucleic Acids Res. 2016 Jul 8;44(W1):W502-6. doi: 10.1093/nar/gkw360.

6.

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.

Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.

Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007.

7.

Binding Site Prediction of Proteins with Organic Compounds or Peptides Using GALAXY Web Servers.

Heo L, Lee H, Baek M, Seok C.

Methods Mol Biol. 2016;1414:33-45. doi: 10.1007/978-1-4939-3569-7_3.

PMID:
27094284
8.

Crystal Structure of Streptococcus pyogenes Cas1 and Its Interaction with Csn2 in the Type II CRISPR-Cas System.

Ka D, Lee H, Jung YD, Kim K, Seok C, Suh N, Bae E.

Structure. 2016 Jan 5;24(1):70-9. doi: 10.1016/j.str.2015.10.019.

9.

Evaluation of GalaxyDock Based on the Community Structure-Activity Resource 2013 and 2014 Benchmark Studies.

Shin WH, Lee GR, Seok C.

J Chem Inf Model. 2016 Jun 27;56(6):988-95. doi: 10.1021/acs.jcim.5b00309.

PMID:
26583962
10.

Potential Application of Alchemical Free Energy Simulations to Discriminate GPCR Ligand Efficacy.

Lee HS, Seok C, Im W.

J Chem Theory Comput. 2015 Mar 10;11(3):1255-66. doi: 10.1021/ct5008907.

PMID:
26579772
11.

High-resolution protein-protein docking by global optimization: recent advances and future challenges.

Park H, Lee H, Seok C.

Curr Opin Struct Biol. 2015 Dec;35:24-31. doi: 10.1016/j.sbi.2015.08.001. Review.

PMID:
26295792
12.

Effective protein model structure refinement by loop modeling and overall relaxation.

Lee GR, Heo L, Seok C.

Proteins. 2016 Sep;84 Suppl 1:293-301. doi: 10.1002/prot.24858.

PMID:
26172288
13.

Measured and predicted affinities of binding and relative potencies to activate the AhR of PAHs and their alkylated analogues.

Lee S, Shin WH, Hong S, Kang H, Jung D, Yim UH, Shim WJ, Khim JS, Seok C, Giesy JP, Choi K.

Chemosphere. 2015 Nov;139:23-9. doi: 10.1016/j.chemosphere.2015.05.033.

PMID:
26037956
14.

Factors affecting redox potential and differential sensitivity of SoxR to redox-active compounds.

Lee KL, Singh AK, Heo L, Seok C, Roe JH.

Mol Microbiol. 2015 Sep;97(5):808-21. doi: 10.1111/mmi.13068.

PMID:
25998932
15.

GalaxyPepDock: a protein-peptide docking tool based on interaction similarity and energy optimization.

Lee H, Heo L, Lee MS, Seok C.

Nucleic Acids Res. 2015 Jul 1;43(W1):W431-5. doi: 10.1093/nar/gkv495.

16.

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

Park H, Lee GR, Heo L, Seok C.

PLoS One. 2014 Nov 24;9(11):e113811. doi: 10.1371/journal.pone.0113811.

17.

GalaxySite: ligand-binding-site prediction by using molecular docking.

Heo L, Shin WH, Lee MS, Seok C.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W210-4. doi: 10.1093/nar/gku321.

18.

Structure of vaccinia virus A46, an inhibitor of TLR4 signaling pathway, shows the conformation of VIPER motif.

Kim Y, Lee H, Heo L, Seok C, Choe J.

Protein Sci. 2014 Jul;23(7):906-14. doi: 10.1002/pro.2472.

19.

Is posterior delamination in arthroscopic rotator cuff repair hidden to the posterior viewing portal?

Han Y, Shin JH, Seok CW, Lee CH, Kim SH.

Arthroscopy. 2013 Nov;29(11):1740-7. doi: 10.1016/j.arthro.2013.08.021.

PMID:
24209671
20.

Blind prediction of interfacial water positions in CAPRI.

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ.

Proteins. 2014 Apr;82(4):620-32. doi: 10.1002/prot.24439.

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