Adam T. Zemla - Search Results

Year	Number of Results
2005	1
2006	1
2008	1
2011	1
2012	1
2013	1
2016	1
2019	1
2020	1
2022	2
2023	2
2024	0

1

Large-scale application of free energy perturbation calculations for antibody design.

Zhu F, Bourguet FA, Bennett WFD, Lau EY, Arrildt KT, Segelke BW, Zemla AT, Desautels TA, Faissol DM. Zhu F, et al. Among authors: zemla at. Sci Rep. 2022 Jul 21;12(1):12489. doi: 10.1038/s41598-022-14443-z. Sci Rep. 2022. PMID: 35864134 Free PMC article.

2

PDBspheres: a method for finding 3D similarities in local regions in proteins.

Zemla AT, Allen JE, Kirshner D, Lightstone FC. Zemla AT, et al. NAR Genom Bioinform. 2022 Oct 10;4(4):lqac078. doi: 10.1093/nargab/lqac078. eCollection 2022 Dec. NAR Genom Bioinform. 2022. PMID: 36225529 Free PMC article.

3

Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants.

Desautels TA, Arrildt KT, Zemla AT, Lau EY, Zhu F, Ricci D, Cronin S, Zost SJ, Binshtein E, Scheaffer SM, Dadonaite B, Petersen BK, Engdahl TB, Chen E, Handal LS, Hall L, Goforth JW, Vashchenko D, Nguyen S, Weilhammer DR, Lo JK, Rubinfeld B, Saada EA, Weisenberger T, Lee TH, Whitener B, Case JB, Ladd A, Silva MS, Haluska RM, Grzesiak EA, Earnhart CG, Hopkins S, Bates TW, Thackray LB, Segelke BW, Lillo AM, Sundaram S, Bloom J, Diamond MS, Crowe JE Jr, Carnahan RH, Faissol DM. Desautels TA, et al. Among authors: zemla at. bioRxiv [Preprint]. 2023 Apr 24:2022.10.21.513237. doi: 10.1101/2022.10.21.513237. bioRxiv. 2023. PMID: 36324800 Free PMC article. Preprint.

4

A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2.

Sandholtz SH, Drocco JA, Zemla AT, Torres MW, Silva MS, Allen JE. Sandholtz SH, et al. Among authors: zemla at. ACS Omega. 2023 Jun 6;8(24):21871-21884. doi: 10.1021/acsomega.3c01621. eCollection 2023 Jun 20. ACS Omega. 2023. PMID: 37309388 Free PMC article.

5

Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo.

Collette NM, Lao VHI, Weilhammer DR, Zingg B, Cohen SD, Hwang M, Coffey LL, Grady SL, Zemla AT, Borucki MK. Collette NM, et al. Among authors: zemla at. Viruses. 2020 Nov 12;12(11):1295. doi: 10.3390/v12111295. Viruses. 2020. PMID: 33198111 Free PMC article.

6

Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence.

Borucki MK, Collette NM, Coffey LL, Van Rompay KKA, Hwang MH, Thissen JB, Allen JE, Zemla AT. Borucki MK, et al. Among authors: zemla at. PLoS One. 2019 Dec 6;14(12):e0225699. doi: 10.1371/journal.pone.0225699. eCollection 2019. PLoS One. 2019. PMID: 31809512 Free PMC article.

7

Sendai virus intra-host population dynamics and host immunocompetence influence viral virulence during in vivo passage.

Peña J, Chen-Harris H, Allen JE, Hwang M, Elsheikh M, Mabery S, Bielefeldt-Ohmann H, Zemla AT, Bowen RA, Borucki MK. Peña J, et al. Among authors: zemla at. Virus Evol. 2016 Apr 9;2(1):vew008. doi: 10.1093/ve/vew008. eCollection 2016 Jan. Virus Evol. 2016. PMID: 27774301 Free PMC article.

8

Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin.

Zhou CL, Zemla AT, Roe D, Young M, Lam M, Schoeniger JS, Balhorn R. Zhou CL, et al. Among authors: zemla at. Bioinformatics. 2005 Jul 15;21(14):3089-96. doi: 10.1093/bioinformatics/bti498. Epub 2005 May 19. Bioinformatics. 2005. PMID: 15905278

9

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

Zemla AT, Lang DM, Kostova T, Andino R, Ecale Zhou CL. Zemla AT, et al. BMC Bioinformatics. 2011 Jun 2;12:226. doi: 10.1186/1471-2105-12-226. BMC Bioinformatics. 2011. PMID: 21635786 Free PMC article.

10

Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction.

Chaudhury S, Abdulhameed MD, Singh N, Tawa GJ, D'haeseleer PM, Zemla AT, Navid A, Zhou CE, Franklin MC, Cheung J, Rudolph MJ, Love J, Graf JF, Rozak DA, Dankmeyer JL, Amemiya K, Daefler S, Wallqvist A. Chaudhury S, et al. Among authors: zemla at. PLoS One. 2013 May 21;8(5):e63369. doi: 10.1371/journal.pone.0063369. Print 2013. PLoS One. 2013. PMID: 23704901 Free PMC article.

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