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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:

Year:

2018

Language:

english

File:

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

Year:

2020

File:

PDF, 1.26 MB

2020

3

PatchDock and SymmDock: servers for rigid and symmetric docking

Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., Wolfson, H. J.

Journal:

Nucleic Acids Research

Year:

2005

Language:

english

File:

PDF, 1.47 MB

english, 2005

4

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

Year:

2013

Language:

english

File:

PDF, 4.01 MB

english, 2013

5

FireDock: a web server for fast interaction refinement in molecular docking

Mashiach, E., Schneidman-Duhovny, D., Andrusier, N., Nussinov, R., Wolfson, H. J.

Journal:

Nucleic Acids Research

Year:

2008

Language:

english

File:

PDF, 1.40 MB

english, 2008

6

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

Year:

2020

File:

PDF, 4.36 MB

2020

7

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

Year:

2020

File:

PDF, 3.34 MB

2020

8

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:

Year:

2020

File:

PDF, 2.77 MB

2020

9

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

Year:

2008

Language:

english

File:

PDF, 1.02 MB

english, 2008

10

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

Year:

2003

Language:

english

File:

PDF, 253 KB

english, 2003

11

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

Year:

2005

Language:

english

File:

PDF, 280 KB

english, 2005

12

Geometry-based flexible and symmetric protein docking

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2005

Language:

english

File:

PDF, 803 KB

english, 2005

13

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

Year:

2008

Language:

english

File:

PDF, 326 KB

english, 2008

14

Automatic prediction of protein interactions with large scale motion

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 496 KB

english, 2007

15

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

Year:

2010

Language:

english

File:

PDF, 214 KB

english, 2010

16

Mechanism of Two Classes of Cancer Mutations in the Phosphoinositide 3-Kinase Catalytic Subunit

Miled, N., Yan, Y., Hon, W.-C., Perisic, O., Zvelebil, M., Inbar, Y., Schneidman-Duhovny, D., Wolfson, H. J., Backer, J. M., Williams, R. L.

Journal:

Year:

2007

Language:

english

File:

PDF, 366 KB

english, 2007

17

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

Year:

2009

Language:

english

File:

PDF, 941 KB

english, 2009

18

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

Year:

2008

Language:

english

File:

PDF, 546 KB

english, 2008

19

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

Dina Schneidman-Duhovny, Michal Hammel, Andrej Sali

Journal:

Journal of Structural Biology

Year:

2011

Language:

english

File:

PDF, 1.93 MB

english, 2011

20

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

Year:

2011

Language:

english

File:

PDF, 3.36 MB

english, 2011

21

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

Year:

2012

Language:

english

File:

PDF, 2.50 MB

english, 2012

22

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

Year:

2009

Language:

english

File:

PDF, 4.59 MB

english, 2009

23

Integrative structural modeling with small angle X-ray scattering profiles

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

Journal:

BMC Structural Biology

Year:

2012

Language:

english

File:

PDF, 1.10 MB

english, 2012

24

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

Year:

2008

Language:

english

File:

PDF, 611 KB

english, 2008

25

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

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

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 2.37 MB

english, 2013

26

Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data

Lasker, K., Phillips, J. L., Russel, D., Velazquez-Muriel, J., Schneidman-Duhovny, D., Tjioe, E., Webb, B., Schlessinger, A., Sali, A.

Journal:

Molecular & Cellular Proteomics

Year:

2010

Language:

english

File:

PDF, 485 KB

english, 2010

27

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

Year:

2014

Language:

english

File:

PDF, 1.81 MB

english, 2014

28

Uncertainty in integrative structural modeling

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

Journal:

Current Opinion in Structural Biology

Year:

2014

Language:

english

File:

PDF, 886 KB

english, 2014

29

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

Year:

2014

Language:

english

File:

PDF, 2.99 MB

english, 2014

30

FoXS: a web server for rapid computation and fitting of SAXS profiles

Schneidman-Duhovny, D., Hammel, M., Sali, A.

Journal:

Nucleic Acids Research

Year:

2010

Language:

english

File:

PDF, 2.04 MB

english, 2010

31

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

Year:

2015

Language:

english

File:

PDF, 960 KB

english, 2015

32

Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images

Velazquez-Muriel, J., Lasker, K., Russel, D., Phillips, J., Webb, B. M., Schneidman-Duhovny, D., Sali, A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2012

Language:

english

File:

PDF, 1.67 MB

english, 2012

33

Identification of the N-terminal Peptide Binding Site of Glucose-regulated Protein 94

Gidalevitz, T., Biswas, C., Ding, H., Schneidman-Duhovny, D., Wolfson, H. J., Stevens, F., Radford, S., Argon, Y.

Journal:

Journal of Biological Chemistry

Year:

2004

Language:

english

File:

PDF, 1.06 MB

english, 2004

34

Optimized atomic statistical potentials: assessment of protein interfaces and loops

Dong, G. Q., Fan, H., Schneidman-Duhovny, D., Webb, B., Sali, A.

Journal:

Year:

2013

Language:

english

File:

PDF, 864 KB

english, 2013

35

PharmaGist: a webserver for ligand-based pharmacophore detection

Schneidman-Duhovny, D., Dror, O., Inbar, Y., Nussinov, R., Wolfson, H. J.

Journal:

Nucleic Acids Research

Year:

2008

Language:

english

File:

PDF, 3.71 MB

english, 2008

36

ModBase, a database of annotated comparative protein structure models and associated resources

Pieper, U., Webb, B. M., Dong, G. Q., Schneidman-Duhovny, D., Fan, H., Kim, S. J., Khuri, N., Spill, Y. G., Weinkam, P., Hammel, M., Tainer, J. A., Nilges, M., Sali, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 6.22 MB

english, 2014

37

ModBase, a database of annotated comparative protein structure models, and associated resources

Pieper, U., Webb, B. M., Barkan, D. T., Schneidman-Duhovny, D., Schlessinger, A., Braberg, H., Yang, Z., Meng, E. C., Pettersen, E. F., Huang, C. C., Datta, R. S., Sampathkumar, P., Madhusudhan, M. S.

Journal:

Nucleic Acids Research

Year:

2011

Language:

english

File:

PDF, 6.17 MB

english, 2011

38

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

Year:

2005

Language:

english

File:

PDF, 304 KB

english, 2005

39

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

Year:

2015

Language:

english

File:

PDF, 2.93 MB

english, 2015

40

Predicting Molecular Interactions in silico: II. Protein-Protein and Protein- Drug Docking

D. Schneidman-Duhovny, Bentham Science Publisher, R. Nussinov, Bentham Science Publisher, H. J. Wolfson, Bentham Science Publisher

Journal:

Current Medicinal Chemistry

Year:

2004

Language:

english

File:

PDF, 224 KB

english, 2004

41

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

Year:

2015

Language:

english

File:

PDF, 2.38 MB

english, 2015

42

BioInfo3D: a suite of tools for structural bioinformatics

Shatsky, M., Dror, O., Schneidman-Duhovny, D., Nussinov, R., Wolfson, H. J.

Journal:

Nucleic Acids Research

Year:

2004

Language:

english

File:

PDF, 313 KB

english, 2004

43

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

Year:

2016

Language:

english

File:

PDF, 1.57 MB

english, 2016

44

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

Year:

2016

File:

PDF, 682 KB

2016

45

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

Year:

2016

Language:

english

File:

PDF, 682 KB

english, 2016

46

Memdock: An α-helical membrane protein docking algorithm

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

Journal:

Year:

2016

Language:

english

File:

PDF, 463 KB

english, 2016

47

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

Year:

2016

Language:

english

File:

PDF, 1.06 MB

english, 2016

48

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

Year:

2016

Language:

english

File:

PDF, 1.18 MB

english, 2016

49

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:

Year:

2016

Language:

english

File:

PDF, 64 KB

english, 2016

50

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

Year:

2017

Language:

english

File:

PDF, 1.70 MB

english, 2017