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Items: 20

1.

Structure of the Human Core Centromeric Nucleosome Complex.

Allu PK, Dawicki-McKenna JM, Van Eeuwen T, Slavin M, Braitbard M, Xu C, Kalisman N, Murakami K, Black BE.

Curr Biol. 2019 Aug 19;29(16):2625-2639.e5. doi: 10.1016/j.cub.2019.06.062. Epub 2019 Jul 25.

PMID:
31353180
2.

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.

Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A.

Anal Chem. 2019 Jun 4;91(11):6953-6961. doi: 10.1021/acs.analchem.9b00658. Epub 2019 May 22.

3.

Integrative Structure Modeling: Overview and Assessment.

Braitbard M, Schneidman-Duhovny D, Kalisman N.

Annu Rev Biochem. 2019 Jun 20;88:113-135. doi: 10.1146/annurev-biochem-013118-111429. Epub 2019 Mar 4.

PMID:
30830798
4.

Automatic Inference of Sequence from Low-Resolution Crystallographic Data.

Ben-Aharon Z, Levitt M, Kalisman N.

Structure. 2018 Nov 6;26(11):1546-1554.e2. doi: 10.1016/j.str.2018.08.011. Epub 2018 Oct 4.

5.

Structural Analysis of Protein Complexes by Cross-Linking and Mass Spectrometry.

Slavin M, Kalisman N.

Methods Mol Biol. 2018;1764:173-183. doi: 10.1007/978-1-4939-7759-8_11.

PMID:
29605915
6.

Def1 interacts with TFIIH and modulates RNA polymerase II transcription.

Damodaren N, Van Eeuwen T, Zamel J, Lin-Shiao E, Kalisman N, Murakami K.

Proc Natl Acad Sci U S A. 2017 Dec 12;114(50):13230-13235. doi: 10.1073/pnas.1707955114. Epub 2017 Nov 27.

7.

Archaeal flagellin combines a bacterial type IV pilin domain with an Ig-like domain.

Braun T, Vos MR, Kalisman N, Sherman NE, Rachel R, Wirth R, Schröder GF, Egelman EH.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10352-7. doi: 10.1073/pnas.1607756113. Epub 2016 Aug 30.

8.

Structure of an RNA polymerase II preinitiation complex.

Murakami K, Tsai KL, Kalisman N, Bushnell DA, Asturias FJ, Kornberg RD.

Proc Natl Acad Sci U S A. 2015 Nov 3;112(44):13543-8. doi: 10.1073/pnas.1518255112. Epub 2015 Oct 19.

9.

Architecture of an RNA polymerase II transcription pre-initiation complex.

Murakami K, Elmlund H, Kalisman N, Bushnell DA, Adams CM, Azubel M, Elmlund D, Levi-Kalisman Y, Liu X, Gibbons BJ, Levitt M, Kornberg RD.

Science. 2013 Nov 8;342(6159):1238724. doi: 10.1126/science.1238724. Epub 2013 Sep 26.

10.

The crystal structures of the eukaryotic chaperonin CCT reveal its functional partitioning.

Kalisman N, Schröder GF, Levitt M.

Structure. 2013 Apr 2;21(4):540-9. doi: 10.1016/j.str.2013.01.017. Epub 2013 Mar 7.

11.

Subunit order of eukaryotic TRiC/CCT chaperonin by cross-linking, mass spectrometry, and combinatorial homology modeling.

Kalisman N, Adams CM, Levitt M.

Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):2884-9. doi: 10.1073/pnas.1119472109. Epub 2012 Feb 1.

12.

Structure-based identification of catalytic residues.

Yahalom R, Reshef D, Wiener A, Frankel S, Kalisman N, Lerner B, Keasar C.

Proteins. 2011 Jun;79(6):1952-63. doi: 10.1002/prot.23020. Epub 2011 Apr 12.

13.

Synthesis and characterization of Au102(p-MBA)44 nanoparticles.

Levi-Kalisman Y, Jadzinsky PD, Kalisman N, Tsunoyama H, Tsukuda T, Bushnell DA, Kornberg RD.

J Am Chem Soc. 2011 Mar 9;133(9):2976-82. doi: 10.1021/ja109131w. Epub 2011 Feb 14.

PMID:
21319754
14.

Consistent refinement of submitted models at CASP using a knowledge-based potential.

Chopra G, Kalisman N, Levitt M.

Proteins. 2010 Sep;78(12):2668-78. doi: 10.1002/prot.22781.

15.
16.

Prediction of structural stability of short beta-hairpin peptides by molecular dynamics and knowledge-based potentials.

Noy K, Kalisman N, Keasar C.

BMC Struct Biol. 2008 May 29;8:27. doi: 10.1186/1472-6807-8-27.

17.

Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities.

Amir ED, Kalisman N, Keasar C.

Proteins. 2008 Jul;72(1):62-73. doi: 10.1002/prot.21896.

PMID:
18186478
18.

MESHI: a new library of Java classes for molecular modeling.

Kalisman N, Levi A, Maximova T, Reshef D, Zafriri-Lynn S, Gleyzer Y, Keasar C.

Bioinformatics. 2005 Oct 15;21(20):3931-2. Epub 2005 Aug 16.

PMID:
16105898
19.

The neocortical microcircuit as a tabula rasa.

Kalisman N, Silberberg G, Markram H.

Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):880-5. Epub 2005 Jan 3.

20.

Deriving physical connectivity from neuronal morphology.

Kalisman N, Silberberg G, Markram H.

Biol Cybern. 2003 Mar;88(3):210-8.

PMID:
12647228

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