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1

Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition

Schneidman-Duhovny, Dina, Khuri, Natalia, Dong, Guang Qiang, Winter, Michael B., Shifrut, Eric, Friedman, Nir, Craik, Charles S., Pratt, Kathleen P., Paz, Pedro, Aswad, Fred, Sali, Andrej, Ansari, Aft

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 3.97 MB

english, 2018

2

Moving analytical ultracentrifugation software to a good manufacturing practices (GMP) environment

Savelyev, Alexey, Gorbet, Gary E., Henrickson, Amy, Demeler, Borries, Schneidman-Duhovny, Dina

Journal:

PLoS Computational Biology

Année:

2020

Fichier:

PDF, 1.26 MB

2020

3

Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data

Berlin, Konstantin, Castañeda, Carlos A., Schneidman-Duhovny, Dina, Sali, Andrej, Nava-Tudela, Alfredo, Fushman, David

Journal:

Journal of the American Chemical Society

Année:

2013

Langue:

english

Fichier:

PDF, 4.01 MB

english, 2013

4

Mindboggling morphometry of human brains

Klein, Arno, Ghosh, Satrajit S., Bao, Forrest S., Giard, Joachim, Häme, Yrjö, Stavsky, Eliezer, Lee, Noah, Rossa, Brian, Reuter, Martin, Chaibub Neto, Elias, Keshavan, Anisha, Schneidman, Dina

Journal:

PLoS Computational Biology

Année:

2017

Langue:

english

Fichier:

PDF, 8.88 MB

english, 2017

5

Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC

Wright, Eric, Ferrato, Mauricio, Bryer, Alexander J., Searles, Robert, Perilla, Juan R., Chandrasekaran, Sunita, Schneidman-Duhovny, Dina

Journal:

PLoS Computational Biology

Année:

2020

Fichier:

PDF, 4.36 MB

2020

6

Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion

Korfhage, Nikolaus, MÃ¼hling, Markus, Ringshandl, Stephan, Becker, Anke, Schmeck, Bernd, Freisleben, Bernd, Schneidman-Duhovny, Dina

Journal:

PLoS Computational Biology

Année:

2020

Fichier:

PDF, 3.34 MB

2020

7

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

Xiang, Yufei, Nambulli, Sham, Xiao, Zhengyun, Liu, Heng, Sang, Zhe, Duprex, W. Paul, Schneidman-Duhovny, Dina, Zhang, Cheng, Shi, Yi

Journal:

Année:

2020

Fichier:

PDF, 2.77 MB

2020

8

Metabolic stereoselectivity of cytochrome P450 3A4 towards deoxypodophyllotoxin: In silico predictions and experimental validation

Mattijs K. Julsing, Nikolay P. Vasilev, Dina Schneidman-Duhovny, Remco Muntendam, Herman J. Woerdenbag, Wim J. Quax, Haim J. Wolfson, Iliana Ionkova, Oliver Kayser

Journal:

European Journal of Medicinal Chemistry

Année:

2008

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2008

9

Taking geometry to its edge: Fast unbound rigid (and hinge-bent) docking

Dina Schneidman-Duhovny, Yuval Inbar, Vladimir Polak, Maxim Shatsky, Inbal Halperin, Hadar Benyamini, Adi Barzilai, Oranit Dror, Nurit Haspel, Ruth Nussinov, Haim J. Wolfson

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2003

Langue:

english

Fichier:

PDF, 253 KB

english, 2003

10

Approaching the CAPRI challenge with an efficient geometry-based docking

Yuval Inbar, Dina Schneidman-Duhovny, Inbal Halperin, Assaf Oron, Ruth Nussinov, Haim J. Wolfson

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2005

Langue:

english

Fichier:

PDF, 280 KB

english, 2005

11

Geometry-based flexible and symmetric protein docking

Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2005

Langue:

english

Fichier:

PDF, 803 KB

english, 2005

12

HingeProt: Automated prediction of hinges in protein structures

Ugur Emekli, Dina Schneidman-Duhovny, Haim J. Wolfson, Ruth Nussinov, Turkan Haliloglu

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2008

Langue:

english

Fichier:

PDF, 326 KB

english, 2008

13

Automatic prediction of protein interactions with large scale motion

Dina Schneidman-Duhovny, Ruth Nussinov, Haim J. Wolfson

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2007

Langue:

english

Fichier:

PDF, 496 KB

english, 2007

14

An integrated suite of fast docking algorithms

Efrat Mashiach, Dina Schneidman-Duhovny, Aviyah Peri, Yoli Shavit, Ruth Nussinov, Haim J. Wolfson

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2010

Langue:

english

Fichier:

PDF, 214 KB

english, 2010

15

The structural dynamics of macromolecular processes

Daniel Russel, Keren Lasker, Jeremy Phillips, Dina Schneidman-Duhovny, Javier A. Velázquez-Muriel, Andrej Sali

Journal:

Current Opinion in Cell Biology

Année:

2009

Langue:

english

Fichier:

PDF, 941 KB

english, 2009

16

Structural similarity of genetically interacting proteins

Oranit Dror, Dina Schneidman-Duhovny, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J Wolfson, Roded Sharan

Journal:

BMC Systems Biology

Année:

2008

Langue:

english

Fichier:

PDF, 546 KB

english, 2008

17

Macromolecular docking restrained by a small angle X-ray scattering profile

Dina Schneidman-Duhovny, Michal Hammel, Andrej Sali

Journal:

Journal of Structural Biology

Année:

2011

Langue:

english

Fichier:

PDF, 1.93 MB

english, 2011

18

Statistical Potential for Modeling and Ranking of Protein–Ligand Interactions

Fan, Hao, Schneidman-Duhovny, Dina, Irwin, John J., Dong, Guangqiang, Shoichet, Brian K., Sali, Andrej

Journal:

Journal of Chemical Information and Modeling

Année:

2011

Langue:

english

Fichier:

PDF, 3.36 MB

english, 2011

19

UCSF Chimera, MODELLER, and IMP: An integrated modeling system

Zheng Yang, Keren Lasker, Dina Schneidman-Duhovny, Ben Webb, Conrad C. Huang, Eric F. Pettersen, Thomas D. Goddard, Elaine C. Meng, Andrej Sali, Thomas E. Ferrin

Journal:

Journal of Structural Biology

Année:

2012

Langue:

english

Fichier:

PDF, 2.50 MB

english, 2012

20

Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications

Dror, Oranit, Schneidman-Duhovny, Dina, Inbar, Yuval, Nussinov, Ruth, Wolfson, Haim J.

Journal:

Journal of Chemical Information and Modeling

Année:

2009

Langue:

english

Fichier:

PDF, 4.59 MB

english, 2009

21

Integrative structural modeling with small angle X-ray scattering profiles

Schneidman-Duhovny, Dina, Kim, Seung, Sali, Andrej

Journal:

BMC Structural Biology

Année:

2012

Langue:

english

Fichier:

PDF, 1.10 MB

english, 2012

22

Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules

Schneidman-Duhovny, Dina, Dror, Oranit, Inbar, Yuval, Nussinov, Ruth, Wolfson, Haim J.

Journal:

Journal of Computational Biology

Année:

2008

Langue:

english

Fichier:

PDF, 611 KB

english, 2008

23

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

Schneidman-Duhovny, Dina, Hammel, Michal, Tainer, John A., Sali, Andrej

Journal:

Biophysical Journal

Année:

2013

Langue:

english

Fichier:

PDF, 2.37 MB

english, 2013

24

Integrative Structure Determination of the Components of the Nuclear Pore Complex by X-Ray Crystallography, Small Angle X-Ray Scattering, Electron Microscopy, NMR, and Comparative Modeling

Joong Kim, Seung, Sampathkumar, Parthasarathy, Fernandez-Martinez, Javier, Phillips, Jeremy, Schneidman, Dina, Matsui, Tsutomu, Tsuruta, Hiro, Sauder, Michael, Burley, Stephen K., Rout, Michael, Sali,

Journal:

Biophysical Journal

Année:

2012

Langue:

english

Fichier:

PDF, 37 KB

english, 2012

25

Determination of the Pseudo-Atomic Structure of Nuclear Pore Complex (NPC) Components by Small Angle X-Ray Scattering (SAXS) and Computational Modeling

Kim, Seung Joong, Phillips, Jeremy, Martel, Anne, Schneidman, Dina, Sauder, Michael, Rout, Michael P., Tsuruta, Hiro, Sali, Andrej

Journal:

Biophysical Journal

Année:

2010

Langue:

english

Fichier:

PDF, 40 KB

english, 2010

26

Molecular Architecture of Photoreceptor Phosphodiesterase Elucidated by Chemical Cross-Linking and Integrative Modeling

Zeng-Elmore, Xiaohui, Gao, Xiong-Zhuo, Pellarin, Riccardo, Schneidman-Duhovny, Dina, Zhang, Xiu-Jun, Kozacka, Katie A., Tang, Yang, Sali, Andrej, Chalkley, Robert J., Cote, Rick H., Chu, Feixia

Journal:

Journal of Molecular Biology

Année:

2014

Langue:

english

Fichier:

PDF, 1.81 MB

english, 2014

27

Uncertainty in integrative structural modeling

Schneidman-Duhovny, Dina, Pellarin, Riccardo, Sali, Andrej

Journal:

Current Opinion in Structural Biology

Année:

2014

Langue:

english

Fichier:

PDF, 886 KB

english, 2014

28

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex

Shi, Yi, Fernandez-Martinez, Javier, Tjioe, Elina, Pellarin, Riccardo, Kim, Seung Joong, Williams, Rosemary, Schneidman-Duhovny, Dina, Sali, Andrej, Rout, Michael P., Chait, Brian T.

Journal:

Molecular & Cellular Proteomics

Année:

2014

Langue:

english

Fichier:

PDF, 2.99 MB

english, 2014

29

CRB2 Mutations Produce a Phenotype Resembling Congenital Nephrosis, Finnish Type, with Cerebral Ventriculomegaly and Raised Alpha-Fetoprotein

Slavotinek, Anne, Kaylor, Julie, Pierce, Heather, Cahr, Michelle, DeWard, Stephanie J., Schneidman-Duhovny, Dina, Alsadah, Adnan, Salem, Fadi, Schmajuk, Gabriela, Mehta, Lakshmi

Journal:

The American Journal of Human Genetics

Année:

2015

Langue:

english

Fichier:

PDF, 960 KB

english, 2015

30

From Structure to Function: Methods and Applications

Wolfson, Haim, Shatsky, Maxim, Schneidman-Duhovny, Dina, Dror, Oranit, Shulman-Peleg, Alexandra, Ma, Buyong, Nussinov, Ruth

Journal:

Current Protein & Peptide Science

Année:

2005

Langue:

english

Fichier:

PDF, 304 KB

english, 2005

31

Prion Protein—Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering

Carter, Lester, Kim, Seung Joong, Schneidman-Duhovny, Dina, Stöhr, Jan, Poncet-Montange, Guillaume, Weiss, Thomas M., Tsuruta, Hiro, Prusiner, Stanley B., Sali, Andrej

Journal:

Biophysical Journal

Année:

2015

Langue:

english

Fichier:

PDF, 2.93 MB

english, 2015

32

DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes Sequence Insertion 1

Parshin, Andrey, Shiver, Anthony L., Lee, Jookyung, Ozerova, Maria, Schneidman-Duhovny, Dina, Gross, Carol A., Borukhov, Sergei

Journal:

Proceedings of the National Academy of Sciences

Année:

2015

Langue:

english

Fichier:

PDF, 2.38 MB

english, 2015

33

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites

Cimermancic, Peter, Weinkam, Patrick, Rettenmaier, T. Justin, Bichmann, Leon, Keedy, Daniel A., Woldeyes, Rahel A., Schneidman-Duhovny, Dina, Demerdash, Omar N., Mitchell, Julie C., Wells, James A., F

Journal:

Journal of Molecular Biology

Année:

2016

Langue:

english

Fichier:

PDF, 1.57 MB

english, 2016

34

Expansion of phenotype and genotypic data in CRB2-related syndrome

Lamont, Ryan E, Tan, Wen-Hann, Innes, A Micheil, Parboosingh, Jillian S, Schneidman-Duhovny, Dina, Rajkovic, Aleksandar, Pappas, John, Altschwager, Pablo, DeWard, Stephanie, Fulton, Anne, Gray, Kathry

Journal:

European Journal of Human Genetics

Année:

2016

Fichier:

PDF, 682 KB

2016

35

Expansion of phenotype and genotypic data in CRB2-related syndrome

Lamont, Ryan E, Tan, Wen-Hann, Innes, A Micheil, Parboosingh, Jillian S, Schneidman-Duhovny, Dina, Rajkovic, Aleksandar, Pappas, John, Altschwager, Pablo, DeWard, Stephanie, Fulton, Anne, Gray, Kathry

Journal:

European Journal of Human Genetics

Année:

2016

Langue:

english

Fichier:

PDF, 682 KB

english, 2016

36

Memdock: An α-helical membrane protein docking algorithm

Hurwitz, Naama, Schneidman-Duhovny, Dina, Wolfson, Haim J.

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 463 KB

english, 2016

37

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

Schneidman-Duhovny, Dina, Hammel, Michal, Tainer, John A., Sali, Andrej

Journal:

Nucleic Acids Research

Année:

2016

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2016

38

Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment

Lensink, Marc F., Velankar, Sameer, Kryshtafovych, Andriy, Huang, Shen-You, Schneidman-Duhovny, Dina, Sali, Andrej, Segura, Joan, Fernandez-Fuentes, Narcis, Viswanath, Shruthi, Elber, Ron, Grudinin, S

Journal:

Proteins: Structure, Function, and Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2016

39

DRES-11. A CROSS-ACTIVATING c-Met/β1 INTEGRIN COMPLEX DRIVES THERAPEUTIC RESISTANCE IN GLIOBLASTOMA

Jahangiri, Arman, Sidorov, Maxim, Han, Sung Won, Chen, William, Rick, Jonathan, Schneidman-Duhovny, Dina, Mascharak, Smita, De Lay, Michael, Wagner, Jeffrey, Castro, Brandyn, Imber, Brandon, Flanigan,

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 64 KB

english, 2016

40

Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1

Michael, Alicia K., Fribourgh, Jennifer L., Chelliah, Yogarany, Sandate, Colby R., Hura, Greg L., Schneidman-Duhovny, Dina, Tripathi, Sarvind M., Takahashi, Joseph S., Partch, Carrie L.

Journal:

Proceedings of the National Academy of Sciences

Année:

2017

Langue:

english

Fichier:

PDF, 1.70 MB

english, 2017

41

Cross-activating c-Met/β1 integrin complex drives metastasis and invasive resistance in cancer

Jahangiri, Arman, Nguyen, Alan, Chandra, Ankush, Sidorov, Maxim K., Yagnik, Garima, Rick, Jonathan, Han, Sung Won, Chen, William, Flanigan, Patrick M., Schneidman-Duhovny, Dina, Mascharak, Smita, De L

Journal:

Proceedings of the National Academy of Sciences

Année:

2017

Langue:

english

Fichier:

PDF, 2.18 MB

english, 2017

42

De novo, deleterious sequence variants that alter the transcriptional activity of the homeoprotein PBX1 are associated with intellectual disability and pleiotropic developmental defects

Slavotinek, Anne, Risolino, Maurizio, Losa, Marta, Cho, Megan T., Monaghan, Kristin G., Schneidman-Duhovny, Dina, Parisotto, Sarah, Herkert, Johanna C., Stegmann, Alexander P.A., Miller, Kathryn, Shur

Journal:

Human Molecular Genetics

Année:

2017

Langue:

english

Fichier:

PDF, 21.19 MB

english, 2017

43

PCSF: An R-package for network-based interpretation of high-throughput data

Akhmedov, Murodzhon, Kedaigle, Amanda, Chong, Renan Escalante, Montemanni, Roberto, Bertoni, Francesco, Fraenkel, Ernest, Kwee, Ivo, Schneidman, Dina

Journal:

PLoS Computational Biology

Année:

2017

Langue:

english

Fichier:

PDF, 1.48 MB

english, 2017

44

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

Russel, Daniel, Lasker, Keren, Webb, Ben, Velázquez-Muriel, Javier, Tjioe, Elina, Schneidman-Duhovny, Dina, Peterson, Bret, Sali, Andrej

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 248 KB

english, 2012

45

An open source tool for automatic spatiotemporal assessment of calcium transients and local ‘signal-close-to-noise’ activity in calcium imaging data

Prada, Juan, Sasi, Manju, Martin, Corinna, Jablonka, Sibylle, Dandekar, Thomas, Blum, Robert, Schneidman, Dina

Journal:

PLoS Computational Biology

Année:

2018

Langue:

english

Fichier:

PDF, 16.96 MB

english, 2018

46

MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures

Bradley, Anthony R., Rose, Alexander S., Pavelka, Antonín, Valasatava, Yana, Duarte, Jose M., Prlić, Andreas, Rose, Peter W., Schneidman, Dina

Journal:

PLoS Computational Biology

Année:

2017

Langue:

english

Fichier:

PDF, 5.80 MB

english, 2017

47

speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification

Beirnaert, Charlie, Meysman, Pieter, Vu, Trung Nghia, Hermans, Nina, Apers, Sandra, Pieters, Luc, Covaci, Adrian, Laukens, Kris, Schneidman, Dina

Journal:

PLoS Computational Biology

Année:

2018

Langue:

english

Fichier:

PDF, 9.09 MB

english, 2018

48

Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages

Chen, Qi, Vieth, Michal, Timm, David E., Humblet, Christine, Schneidman-Duhovny, Dina, Chemmama, Ilan E., Sali, Andrej, Zeng, Wei, Lu, Jirong, Liu, Ling, Srinivasan, Narayanaswamy

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 2.61 MB

english, 2017

49

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

Zappia, Luke, Phipson, Belinda, Oshlack, Alicia, Schneidman, Dina

Journal:

PLoS Computational Biology

Année:

2018

Langue:

english

Fichier:

PDF, 1.96 MB

english, 2018

50

NFTsim: Theory and Simulation of Multiscale Neural Field Dynamics

Sanz-Leon, Paula, Robinson, Peter A., Knock, Stuart A., Drysdale, Peter M., Abeysuriya, Romesh G., Fung, Felix K., Rennie, Chris J., Zhao, Xuelong, Schneidman, Dina

Journal:

PLoS Computational Biology

Année:

2018

Langue:

english

Fichier:

PDF, 10.47 MB

english, 2018