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Items: 1 to 20 of 54

1.

A Robotics-Inspired Screening Algorithm for Molecular Caging Prediction.

Kravchenko O, Varava A, Pokorny FT, Devaurs D, Kavraki LE, Kragic D.

J Chem Inf Model. 2020 Mar 23;60(3):1302-1316. doi: 10.1021/acs.jcim.9b00945. Epub 2020 Mar 13.

PMID:
32130862
2.

Improving the organization and interactivity of metabolic pathfinding with precomputed pathways.

Kim SM, Peña MI, Moll M, Bennett GN, Kavraki LE.

BMC Bioinformatics. 2020 Jan 10;21(1):13. doi: 10.1186/s12859-019-3328-x.

3.

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.

4.

Learning Feasibility for Task and Motion Planning in Tabletop Environments.

Wells AM, Dantam NT, Shrivastava A, Kavraki LE.

IEEE Robot Autom Lett. 2019 Apr;4(2):1255-1262. doi: 10.1109/LRA.2019.2894861. Epub 2019 Jan 23.

PMID:
31058229
5.

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.

6.

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.

7.

Quantitative comparison of adaptive sampling methods for protein dynamics.

Hruska E, Abella JR, Nüske F, Kavraki LE, Clementi C.

J Chem Phys. 2018 Dec 28;149(24):244119. doi: 10.1063/1.5053582.

PMID:
30599712
8.

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.

9.

Machine Learning Guided Atom Mapping of Metabolic Reactions.

Litsa EE, Peña MI, Moll M, Giannakopoulos G, Bennett GN, Kavraki LE.

J Chem Inf Model. 2019 Mar 25;59(3):1121-1135. doi: 10.1021/acs.jcim.8b00434. Epub 2018 Dec 14.

PMID:
30500191
10.

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.

11.

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.

12.

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.

13.

A review of parameters and heuristics for guiding metabolic pathfinding.

Kim SM, Peña MI, Moll M, Bennett GN, Kavraki LE.

J Cheminform. 2017 Sep 15;9(1):51. doi: 10.1186/s13321-017-0239-6. Review.

14.

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.

15.

Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.

Abella JR, Moll M, Kavraki LE.

J Comput Biol. 2018 Jan;25(1):3-20. doi: 10.1089/cmb.2017.0164. Epub 2017 Oct 16.

16.

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.

17.

Big Data on Robotics.

Bohg J, Ciocarlie M, Civera J, Kavraki LE.

Big Data. 2016 Dec;4(4):195-196. No abstract available.

PMID:
27992266
18.

Defining Low-Dimensional Projections to Guide Protein Conformational Sampling.

Novinskaya A, Devaurs D, Moll M, Kavraki LE.

J Comput Biol. 2017 Jan;24(1):79-89. doi: 10.1089/cmb.2016.0144. Epub 2016 Nov 28.

PMID:
27892695
19.

Structure-guided selection of specificity determining positions in the human Kinome.

Moll M, Finn PW, Kavraki LE.

BMC Genomics. 2016 Aug 18;17 Suppl 4:431. doi: 10.1186/s12864-016-2790-3.

20.

Call for Papers: Special Issue on Big Data in Robotics.

Bohg J, Ciocarlie M, Civera J, Kavraki LE.

Big Data. 2016 Jun;4(2):69-70. doi: 10.1089/big.2016.29008.cfp. No abstract available.

PMID:
27441709

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