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Items: 17

1.

Study of specific nanoenvironments containing α-helices in all-α and (α+β)+(α/β) proteins.

Mazoni I, Borro LC, Jardine JG, Yano IH, Salim JA, Neshich G.

PLoS One. 2018 Jul 10;13(7):e0200018. doi: 10.1371/journal.pone.0200018. eCollection 2018.

2.

Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows.

Sok D, Le KM, Vadnais M, Saye-Francisco KL, Jardine JG, Torres JL, Berndsen ZT, Kong L, Stanfield R, Ruiz J, Ramos A, Liang CH, Chen PL, Criscitiello MF, Mwangi W, Wilson IA, Ward AB, Smider VV, Burton DR.

Nature. 2017 Aug 3;548(7665):108-111. doi: 10.1038/nature23301. Epub 2017 Jul 20.

3.

Correction: Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design.

Jardine JG, Sok D, Julien JP, Briney B, Sarkar A, Liang CH, Scherer EM, Henry Dunand CJ, Adachi Y, Diwanji D, Hsueh J, Jones M, Kalyuzhniy O, Kubitz M, Spencer S, Pauthner M, Saye-Francisco KL, Sesterhenn F, Wilson PC, Galloway DA, Stanfield RL, Wilson IA, Burton DR, Schief WR.

PLoS Pathog. 2016 Sep 14;12(9):e1005905. doi: 10.1371/journal.ppat.1005905. eCollection 2016 Sep.

4.

Tailored Immunogens Direct Affinity Maturation toward HIV Neutralizing Antibodies.

Briney B, Sok D, Jardine JG, Kulp DW, Skog P, Menis S, Jacak R, Kalyuzhniy O, de Val N, Sesterhenn F, Le KM, Ramos A, Jones M, Saye-Francisco KL, Blane TR, Spencer S, Georgeson E, Hu X, Ozorowski G, Adachi Y, Kubitz M, Sarkar A, Wilson IA, Ward AB, Nemazee D, Burton DR, Schief WR.

Cell. 2016 Sep 8;166(6):1459-1470.e11. doi: 10.1016/j.cell.2016.08.005.

5.

Priming HIV-1 broadly neutralizing antibody precursors in human Ig loci transgenic mice.

Sok D, Briney B, Jardine JG, Kulp DW, Menis S, Pauthner M, Wood A, Lee EC, Le KM, Jones M, Ramos A, Kalyuzhniy O, Adachi Y, Kubitz M, MacPherson S, Bradley A, Friedrich GA, Schief WR, Burton DR.

Science. 2016 Sep 30;353(6307):1557-1560. Epub 2016 Sep 8.

6.

Minimally Mutated HIV-1 Broadly Neutralizing Antibodies to Guide Reductionist Vaccine Design.

Jardine JG, Sok D, Julien JP, Briney B, Sarkar A, Liang CH, Scherer EA, Henry Dunand CJ, Adachi Y, Diwanji D, Hsueh J, Jones M, Kalyuzhniy O, Kubitz M, Spencer S, Pauthner M, Saye-Francisco KL, Sesterhenn F, Wilson PC, Galloway DM, Stanfield RL, Wilson IA, Burton DR, Schief WR.

PLoS Pathog. 2016 Aug 25;12(8):e1005815. doi: 10.1371/journal.ppat.1005815. eCollection 2016 Aug. Erratum in: PLoS Pathog. 2016 Sep;12(9):e1005905.

7.

A Prominent Site of Antibody Vulnerability on HIV Envelope Incorporates a Motif Associated with CCR5 Binding and Its Camouflaging Glycans.

Sok D, Pauthner M, Briney B, Lee JH, Saye-Francisco KL, Hsueh J, Ramos A, Le KM, Jones M, Jardine JG, Bastidas R, Sarkar A, Liang CH, Shivatare SS, Wu CY, Schief WR, Wong CH, Wilson IA, Ward AB, Zhu J, Poignard P, Burton DR.

Immunity. 2016 Jul 19;45(1):31-45. doi: 10.1016/j.immuni.2016.06.026.

8.

Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins.

Salim JA, Borro L, Mazoni I, Yano I, Jardine JG, Neshich G.

Bioinformatics. 2016 Jun 15;32(12):1885-7. doi: 10.1093/bioinformatics/btw082. Epub 2016 Feb 15.

PMID:
27153716
9.

HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen.

Jardine JG, Kulp DW, Havenar-Daughton C, Sarkar A, Briney B, Sok D, Sesterhenn F, Ereño-Orbea J, Kalyuzhniy O, Deresa I, Hu X, Spencer S, Jones M, Georgeson E, Adachi Y, Kubitz M, deCamp AC, Julien JP, Wilson IA, Burton DR, Crotty S, Schief WR.

Science. 2016 Mar 25;351(6280):1458-63. doi: 10.1126/science.aad9195.

10.

HIV-1 VACCINES. Priming a broadly neutralizing antibody response to HIV-1 using a germline-targeting immunogen.

Jardine JG, Ota T, Sok D, Pauthner M, Kulp DW, Kalyuzhniy O, Skog PD, Thinnes TC, Bhullar D, Briney B, Menis S, Jones M, Kubitz M, Spencer S, Adachi Y, Burton DR, Schief WR, Nemazee D.

Science. 2015 Jul 10;349(6244):156-61. doi: 10.1126/science.aac5894. Epub 2015 Jun 18.

11.

Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design.

Neshich IA, Nishimura L, de Moraes FR, Salim JA, Villalta-Romero F, Borro L, Yano IH, Mazoni I, Tasic L, Jardine JG, Neshich G.

Curr Protein Pept Sci. 2015;16(8):701-17.

PMID:
25961402
12.

Proof of principle for epitope-focused vaccine design.

Correia BE, Bates JT, Loomis RJ, Baneyx G, Carrico C, Jardine JG, Rupert P, Correnti C, Kalyuzhniy O, Vittal V, Connell MJ, Stevens E, Schroeter A, Chen M, Macpherson S, Serra AM, Adachi Y, Holmes MA, Li Y, Klevit RE, Graham BS, Wyatt RT, Baker D, Strong RK, Crowe JE Jr, Johnson PR, Schief WR.

Nature. 2014 Mar 13;507(7491):201-6. doi: 10.1038/nature12966. Epub 2014 Feb 5.

13.

Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages.

de Moraes FR, Neshich IA, Mazoni I, Yano IH, Pereira JG, Salim JA, Jardine JG, Neshich G.

PLoS One. 2014 Jan 28;9(1):e87107. doi: 10.1371/journal.pone.0087107. eCollection 2014.

14.

Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases in silico docked to different inhibitors.

Ribeiro C, Togawa RC, Neshich IA, Mazoni I, Mancini AL, Minardi RC, da Silveira CH, Jardine JG, Santoro MM, Neshich G.

BMC Struct Biol. 2010 Oct 20;10:36. doi: 10.1186/1472-6807-10-36.

15.

Sting_RDB: a relational database of structural parameters for protein analysis with support for data warehousing and data mining.

Oliveira SR, Almeida GV, Souza KR, Rodrigues DN, Kuser-Falcão PR, Yamagishi ME, Santos EH, Vieira FD, Jardine JG, Neshich G.

Genet Mol Res. 2007 Oct 5;6(4):911-22.

16.

The Star STING server: a multiplatform environment for protein structure analysis.

Neshich G, Mazoni I, Oliveira SR, Yamagishi ME, Kuser-Falcão PR, Borro LC, Morita DU, Souza KR, Almeida GV, Rodrigues DN, Jardine JG, Togawa RC, Mancini AL, Higa RH, Cruz SA, Vieira FD, Santos EH, Melo RC, Santoro MM.

Genet Mol Res. 2006 Dec 1;5(4):717-22.

17.

Predicting enzyme class from protein structure using Bayesian classification.

Borro LC, Oliveira SR, Yamagishi ME, Mancini AL, Jardine JG, Mazoni I, Santos EH, Higa RH, Kuser PR, Neshich G.

Genet Mol Res. 2006 Mar 31;5(1):193-202.

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