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Items: 16

1.

Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins.

Devaurs D, Antunes DA, Hall-Swan S, Mitchell N, Moll M, Lizée G, Kavraki LE.

BMC Mol Cell Biol. 2019 Sep 5;20(1):42. doi: 10.1186/s12860-019-0218-z.

2.

APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations.

Abella JR, Antunes DA, Clementi C, Kavraki LE.

Molecules. 2019 Mar 2;24(5). pii: E881. doi: 10.3390/molecules24050881.

3.

Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling.

Devaurs D, Papanastasiou M, Antunes DA, Abella JR, Moll M, Ricklin D, Lambris JD, Kavraki LE.

Int J Comput Biol Drug Des. 2018;11(1-2):90-113. doi: 10.1504/IJCBDD.2018.090834. Epub 2018 Mar 24.

4.

Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes.

Antunes DA, Abella JR, Devaurs D, Rigo MM, Kavraki LE.

Curr Top Med Chem. 2018;18(26):2239-2255. doi: 10.2174/1568026619666181224101744. Review.

5.

Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data.

Devaurs D, Antunes DA, Kavraki LE.

Int J Mol Sci. 2018 Oct 31;19(11). pii: E3406. doi: 10.3390/ijms19113406.

6.

General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept.

Antunes DA, Devaurs D, Moll M, Lizée G, Kavraki LE.

Sci Rep. 2018 Mar 12;8(1):4327. doi: 10.1038/s41598-018-22173-4.

7.

DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach.

Antunes DA, Moll M, Devaurs D, Jackson KR, Lizée G, Kavraki LE.

Cancer Res. 2017 Nov 1;77(21):e55-e57. doi: 10.1158/0008-5472.CAN-17-0511.

8.

Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy.

Antunes DA, Rigo MM, Freitas MV, Mendes MFA, Sinigaglia M, Lizée G, Kavraki LE, Selin LK, Cornberg M, Vieira GF.

Front Immunol. 2017 Oct 4;8:1210. doi: 10.3389/fimmu.2017.01210. eCollection 2017.

9.

Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.

Devaurs D, Antunes DA, Papanastasiou M, Moll M, Ricklin D, Lambris JD, Kavraki LE.

Front Mol Biosci. 2017 Mar 10;4:13. doi: 10.3389/fmolb.2017.00013. eCollection 2017.

10.

Understanding the challenges of protein flexibility in drug design.

Antunes DA, Devaurs D, Kavraki LE.

Expert Opin Drug Discov. 2015 Dec;10(12):1301-13. doi: 10.1517/17460441.2015.1094458. Epub 2015 Sep 28. Review.

PMID:
26414598
11.

Improved structural method for T-cell cross-reactivity prediction.

Mendes MF, Antunes DA, Rigo MM, Sinigaglia M, Vieira GF.

Mol Immunol. 2015 Oct;67(2 Pt B):303-10. doi: 10.1016/j.molimm.2015.06.017. Epub 2015 Jul 2.

PMID:
26141239
12.

Frequency, Private Specificity, and Cross-Reactivity of Preexisting Hepatitis C Virus (HCV)-Specific CD8+ T Cells in HCV-Seronegative Individuals: Implications for Vaccine Responses.

Zhang S, Bakshi RK, Suneetha PV, Fytili P, Antunes DA, Vieira GF, Jacobs R, Klade CS, Manns MP, Kraft AR, Wedemeyer H, Schlaphoff V, Cornberg M.

J Virol. 2015 Aug;89(16):8304-17. doi: 10.1128/JVI.00539-15. Epub 2015 Jun 3.

13.

Lessons from molecular modeling human α-L-iduronidase.

Figueiredo DF, Antunes DA, Rigo MM, Mendes MF, Silva JP, Mayer FQ, Matte U, Giugliani R, Vieira GF, Sinigaglia M.

J Mol Graph Model. 2014 Nov;54:107-13. doi: 10.1016/j.jmgm.2014.10.004. Epub 2014 Oct 18.

PMID:
25459762
14.

New insights into the in silico prediction of HIV protease resistance to nelfinavir.

Antunes DA, Rigo MM, Sinigaglia M, de Medeiros RM, Junqueira DM, Almeida SE, Vieira GF.

PLoS One. 2014 Jan 31;9(1):e87520. doi: 10.1371/journal.pone.0087520. eCollection 2014.

15.

Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A*02:01 allele.

Antunes DA, Rigo MM, Silva JP, Cibulski SP, Sinigaglia M, Chies JA, Vieira GF.

Mol Immunol. 2011 Jul;48(12-13):1461-7. doi: 10.1016/j.molimm.2011.03.019. Epub 2011 Apr 21.

PMID:
21513985
16.

Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment.

Antunes DA, Vieira GF, Rigo MM, Cibulski SP, Sinigaglia M, Chies JA.

PLoS One. 2010 Apr 26;5(4):e10353. doi: 10.1371/journal.pone.0010353.

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