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Items: 1 to 20 of 44

1.

Data-driven supervised learning of a viral protease specificity landscape from deep sequencing and molecular simulations.

Pethe MA, Rubenstein AB, Khare SD.

Proc Natl Acad Sci U S A. 2019 Jan 2;116(1):168-176. doi: 10.1073/pnas.1805256116. Epub 2018 Dec 26.

PMID:
30587591
2.

Systematic Comparison of Amber and Rosetta Energy Functions for Protein Structure Evaluation.

Rubenstein AB, Blacklock K, Nguyen H, Case DA, Khare SD.

J Chem Theory Comput. 2018 Nov 13;14(11):6015-6025. doi: 10.1021/acs.jctc.8b00303. Epub 2018 Oct 12.

PMID:
30240210
3.

Multi-Pronged Interactions Underlie Inhibition of α-Synuclein Aggregation by β-Synuclein.

Williams JK, Yang X, Atieh TB, Olson MP, Khare SD, Baum J.

J Mol Biol. 2018 Aug 3;430(16):2360-2371. doi: 10.1016/j.jmb.2018.05.024. Epub 2018 May 18.

PMID:
29782835
4.

Computational assessment of thioether isosteres.

Barrows RD, Blacklock KM, Rablen PR, Khare SD, Knapp S.

J Mol Graph Model. 2018 Mar;80:282-292. doi: 10.1016/j.jmgm.2018.01.018. Epub 2018 Feb 1.

PMID:
29414047
5.

Computational Design of a Photocontrolled Cytosine Deaminase.

Blacklock KM, Yachnin BJ, Woolley GA, Khare SD.

J Am Chem Soc. 2018 Jan 10;140(1):14-17. doi: 10.1021/jacs.7b08709. Epub 2017 Dec 28.

PMID:
29251923
6.

A computational method for the design of nested proteins by loop-directed domain insertion.

Blacklock KM, Yang L, Mulligan VK, Khare SD.

Proteins. 2018 Mar;86(3):354-369. doi: 10.1002/prot.25445. Epub 2018 Jan 24.

PMID:
29250820
7.

Enzyme stabilization via computationally guided protein stapling.

Moore EJ, Zorine D, Hansen WA, Khare SD, Fasan R.

Proc Natl Acad Sci U S A. 2017 Nov 21;114(47):12472-12477. doi: 10.1073/pnas.1708907114. Epub 2017 Nov 6.

8.

Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition.

Davis KM, Schramma KR, Hansen WA, Bacik JP, Khare SD, Seyedsayamdost MR, Ando N.

Proc Natl Acad Sci U S A. 2017 Sep 26;114(39):10420-10425. doi: 10.1073/pnas.1703663114. Epub 2017 Sep 11.

9.

Computation-Guided Design of a Stimulus-Responsive Multienzyme Supramolecular Assembly.

Yang L, Dolan EM, Tan SK, Lin T, Sontag ED, Khare SD.

Chembiochem. 2017 Oct 18;18(20):2000-2006. doi: 10.1002/cbic.201700425. Epub 2017 Sep 1.

PMID:
28799209
10.

Design and Evolution of a Macrocyclic Peptide Inhibitor of the Sonic Hedgehog/Patched Interaction.

Owens AE, de Paola I, Hansen WA, Liu YW, Khare SD, Fasan R.

J Am Chem Soc. 2017 Sep 13;139(36):12559-12568. doi: 10.1021/jacs.7b06087. Epub 2017 Aug 30.

11.

A pH-dependent switch promotes β-synuclein fibril formation via glutamate residues.

Moriarty GM, Olson MP, Atieh TB, Janowska MK, Khare SD, Baum J.

J Biol Chem. 2017 Sep 29;292(39):16368-16379. doi: 10.1074/jbc.M117.780528. Epub 2017 Jul 14.

12.

MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory.

Rubenstein AB, Pethe MA, Khare SD.

PLoS Comput Biol. 2017 Jun 26;13(6):e1005614. doi: 10.1371/journal.pcbi.1005614. eCollection 2017 Jun.

13.

Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces.

Hansen WA, Khare SD.

Protein Sci. 2017 Aug;26(8):1584-1594. doi: 10.1002/pro.3194. Epub 2017 May 31.

14.

Engineering carboxypeptidase G2 circular permutations for the design of an autoinhibited enzyme.

Yachnin BJ, Khare SD.

Protein Eng Des Sel. 2017 Apr 1;30(4):321-331. doi: 10.1093/protein/gzx005.

15.

Large-Scale Structure-Based Prediction and Identification of Novel Protease Substrates Using Computational Protein Design.

Pethe MA, Rubenstein AB, Khare SD.

J Mol Biol. 2017 Jan 20;429(2):220-236. doi: 10.1016/j.jmb.2016.11.031. Epub 2016 Dec 6.

PMID:
27932294
16.

Computational Design of Ligand Binding Proteins.

Tinberg CE, Khare SD.

Methods Mol Biol. 2017;1529:363-373.

PMID:
27914062
17.

Computational Design of Multinuclear Metalloproteins Using Unnatural Amino Acids.

Hansen WA, Mills JH, Khare SD.

Methods Mol Biol. 2016;1414:173-85. doi: 10.1007/978-1-4939-3569-7_10.

PMID:
27094291
18.

Improving Binding Affinity and Selectivity of Computationally Designed Ligand-Binding Proteins Using Experiments.

Tinberg CE, Khare SD.

Methods Mol Biol. 2016;1414:155-71. doi: 10.1007/978-1-4939-3569-7_9.

PMID:
27094290
19.

Introduction to the Rosetta Special Collection.

Khare SD, Whitehead TA.

PLoS One. 2015 Dec 29;10(12):e0144326. doi: 10.1371/journal.pone.0144326. eCollection 2015.

20.

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.

Bednar D, Beerens K, Sebestova E, Bendl J, Khare S, Chaloupkova R, Prokop Z, Brezovsky J, Baker D, Damborsky J.

PLoS Comput Biol. 2015 Nov 3;11(11):e1004556. doi: 10.1371/journal.pcbi.1004556. eCollection 2015 Nov.

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