Haim Wolfson Wolfson

2023

Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study

Schweke, H., Xu, Q., Tauriello, G., Pantolini, L., Schwede, T., Cazals, F., Lhéritier, A., Fernandez-Recio, J., Rodríguez-Lumbreras, L. A., Schueler-Furman, O., Varga, J. K., Jiménez-García, B., Réau, M. F., Bonvin, A. M. J. J., Savojardo, C., Martelli, P. L., Casadio, R., Tubiana, J., Wolfson, H. J. & Oliva, R. & 26 others, Barradas-Bautista, D., Ricciardelli, T., Cavallo, L., Venclovas, Č., Olechnovič, K., Guerois, R., Andreani, J., Martin, J., Wang, X., Terashi, G., Sarkar, D., Christoffer, C., Aderinwale, T., Verburgt, J., Kihara, D., Marchand, A., Correia, B. E., Duan, R., Qiu, L., Xu, X., Zhang, S., Zou, X., Dey, S., Dunbrack, R. L., Levy, E. D. & Wodak, S. J., Sep 2023, In: Proteomics. 23, 17, 2200323.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

EvoRator2: Predicting Site-specific Amino Acid Substitutions Based on Protein Structural Information Using Deep Learning

Nagar, N., Tubiana, J., Loewenthal, G., Wolfson, H. J., Ben Tal, N. & Pupko, T., 15 Jul 2023, In: Journal of Molecular Biology. 435, 14, 168155.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions

Tubiana, J., Adriana-Lifshits, L., Nissan, M., Gabay, M., Sher, I., Sova, M., Wolfson, H. J. & Gal, M., Feb 2023, In: PLoS Computational Biology. 19, 2, e1010874.

Research output: Contribution to journal › Article › peer-review

Open Access

5 Scopus citations

SegmA: Residue Segmentation of cryo-EM density maps

Rozanov, M. & Wolfson, H. J., 2023, Proceedings - 2023 2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023. Jiang, X., Wang, H., Alhajj, R., Hu, X., Engel, F., Mahmud, M., Pisanti, N., Cui, X. & Song, H. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 2191-2196 6 p. (Proceedings - 2023 2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Open Access

2022

Pep–Whisperer: Inhibitory peptide design

Hurwitz, N., Zaidman, D. & Wolfson, H. J., Nov 2022, In: Proteins: Structure, Function and Bioinformatics. 90, 11, p. 1886-1895 10 p.

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Reduced B cell antigenicity of Omicron lowers host serologic response

Tubiana, J., Xiang, Y., Fan, L., Wolfson, H. J., Chen, K., Schneidman-Duhovny, D. & Shi, Y., 18 Oct 2022, In: Cell Reports. 41, 3, 111512.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction

Tubiana, J., Schneidman-Duhovny, D. & Wolfson, H. J., Jun 2022, In: Nature Methods. 19, 6, p. 730-739 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

99 Scopus citations

ScanNet: A Web Server for Structure-based Prediction of Protein Binding Sites with Geometric Deep Learning

Tubiana, J., Schneidman-Duhovny, D. & Wolfson, H. J., 15 Oct 2022, In: Journal of Molecular Biology. 434, 19, 167758.

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

2021

Memdock: An α-Helical Membrane Protein Docking Algorithm

Hurwitz, N. & Wolfson, H. J., 2021, Methods in Molecular Biology. Humana Press Inc., p. 111-117 7 p. (Methods in Molecular Biology; vol. 2315).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

4 Scopus citations

2020

Design of disruptors of the Hsp90–Cdc37 interface

D’Annessa, I., Hurwitz, N., Pirota, V., Beretta, G. L., Tinelli, S., Woodford, M., Freccero, M., Mollapour, M., Zaffaroni, N., Wolfson, H. & Colombo, G., 15 Jan 2020, In: Molecules. 25, 2, 25.

Research output: Contribution to journal › Article › peer-review

Open Access

15 Scopus citations

Modeling of Multimolecular Complexes

Schneidman-Duhovny, D. & Wolfson, H. J., 2020, Methods in Molecular Biology. Humana Press Inc., p. 163-174 12 p. (Methods in Molecular Biology; vol. 2112).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

6 Scopus citations

2019

AAnchor: CNN guided detection of anchor amino acids in high resolution cryo-EM density maps

Rozanov, M. & Wolfson, H. J., 21 Jan 2019, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Schmidt, H., Griol, D., Wang, H., Baumbach, J., Zheng, H., Callejas, Z., Hu, X., Dickerson, J. & Zhang, L. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 88-91 4 p. 8621288. (Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

5 Scopus citations

2017

Accelerating protein-protein complex validation by GPU based funnel generation

Zabejansky, M. & Wolfson, H. J., 17 Jan 2017, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Burrage, K., Zhu, Q., Liu, Y., Tian, T., Wang, Y., Hu, X. T., Jiang, Q., Song, J., Morishita, S., Burrage, K. & Wang, G. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 150-155 6 p. 7822510. (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Protein-peptide interaction design: Pepcrawler and pinacolada

Zaidman, D. & Wolfson, H. J., 2017, Methods in Molecular Biology. Humana Press Inc., p. 279-290 12 p. (Methods in Molecular Biology; vol. 1561).

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

3 Scopus citations

SnapDock-template-based docking by Geometric Hashing

Estrin, M. & Wolfson, H. J., 15 Jul 2017, In: Bioinformatics. 33, 14, p. i30-i36

Research output: Contribution to journal › Article › peer-review

Open Access

12 Scopus citations

2016

Memdock: An α-helical membrane protein docking algorithm

Hurwitz, N., Schneidman-Duhovny, D. & Wolfson, H. J., 15 Aug 2016, In: Bioinformatics. 32, 16, p. 2444-2450 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

36 Scopus citations

PinaColada: Peptide-inhibitor ant colony ad-hoc design algorithm

Zaidman, D. & Wolfson, H. J., 1 Aug 2016, In: Bioinformatics. 32, 15, p. 2289-2296 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

26 Scopus citations

2015

Dockstar: A novel ILP based integrative method for structural modelling of multimolecular protein complexes (extended abstract)

Amir, N., Cohen, D. & Wolfson, H. J., 2015, Research in Computational Molecular Biology - 19th Annual International Conference, RECOMB 2015, Proceedings. Przytycka, T. M. (ed.). Springer Verlag, p. 13-15 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9029).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

DockStar: A novel ILP-based integrative method for structural modeling of multimolecular protein complexes

Amir, N., Cohen, D. & Wolfson, H. J., 6 Feb 2015, In: Bioinformatics. 31, 17, p. 2801-2807 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

11 Scopus citations

2014

Blind prediction of interfacial water positions in CAPRI

Lensink, M. F., Moal, I. H., Bates, P. A., Kastritis, P. L., Melquiond, A. S. J., Karaca, E., Schmitz, C., van Dijk, M., Bonvin, A. M. J. J., Eisenstein, M., Jiménez-García, B., Grosdidier, S., Solernou, A., Pérez-Cano, L., Pallara, C., Fernández-Recio, J., Xu, J., Muthu, P., Praneeth Kilambi, K. & Gray, J. J. & 38 others, Grudinin, S., Derevyanko, G., Mitchell, J. C., Wieting, J., Kanamori, E., Tsuchiya, Y., Murakami, Y., Sarmiento, J., Standley, D. M., Shirota, M., Kinoshita, K., Nakamura, H., Chavent, M., Ritchie, D. W., Park, H., Ko, J., Lee, H., Seok, C., Shen, Y., Kozakov, D., Vajda, S., Kundrotas, P. J., Vakser, I. A., Pierce, B. G., Hwang, H., Vreven, T., Weng, Z., Buch, I., Farkash, E., Wolfson, H. J., Zacharias, M., Qin, S., Zhou, H. X., Huang, S. Y., Zou, X., Wojdyla, J. A., Kleanthous, C. & Wodak, S. J., Apr 2014, In: Proteins: Structure, Function and Bioinformatics. 82, 4, p. 620-632 13 p.

Research output: Contribution to journal › Article › peer-review

Open Access

42 Scopus citations

Novel LIMK2 inhibitor blocks Panc-1 tumor growth in a mouse xenograft model

Rak, R., Haklai, R., Elad-Tzfadia, G., Wolfson, H. J., Carmeli, S. & Kloog, Y., 2014, In: Oncoscience. 1, 1, p. 39-48 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

30 Scopus citations

2013

Conformational transitions in human translin enable nucleic acid binding

Pérez-Cano, L., Eliahoo, E., Lasker, K., Wolfson, H. J., Glaser, F., Manor, H., Bernadó, P. & Fernández-Recio, J., Nov 2013, In: Nucleic Acids Research. 41, 21, p. 9956-9966 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

12 Scopus citations

Diameter-selective dispersion of carbon nanotubes by β-lactoglobulin whey protein

Karchemsky, F., Drug, E., Mashiach-Farkash, E., Fadeev, L., Wolfson, H. J., Gozin, M. & Regev, O., 1 Dec 2013, In: Colloids and Surfaces B: Biointerfaces. 112, p. 16-22 7 p.

Research output: Contribution to journal › Article › peer-review

14 Scopus citations

Protein-protein interaction modeling and inhibition: The TAU Bioinfo3D perspective

Wolfson, H. J., Apr 2013, In: Israel Journal of Chemistry. 53, 3-4, p. 180-184 5 p.

Research output: Contribution to journal › Review article › peer-review

Structure-based in silico identification of ubiquitin-binding domains provides insights into the ALIX-V:ubiquitin complex and retrovirus budding

Keren-Kaplan, T., Attali, I., Estrin, M., Kuo, L. S., Farkash, E., Jerabek-Willemsen, M., Blutraich, N., Artzi, S., Peri, A., Freed, E. O., Wolfson, H. J. & Prag, G., 20 Feb 2013, In: EMBO Journal. 32, 4, p. 538-551 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

57 Scopus citations

2012

Computer-Based identification of a novel LIMK1/2 inhibitor that synergizes with salirasib to destabilize the actin cytoskeleton

Mashiach-Farkash, E., Rak, R., Elad-Sfadia, G., Haklai, R., Carmeli, S., Kloog, Y. & Wolfson, H. J., Jun 2012, In: Oncotarget. 3, 6, p. 629-639 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

42 Scopus citations

2011

GOSSIP: A method for fast and accurate global alignment of protein structures

Kifer, I., Nussinov, R. & Wolfson, H. J., Apr 2011, In: Bioinformatics. 27, 7, p. 925-932 8 p., btr044.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

Inexact graph matching by "geodesic hashing" for the alignment of pseudoknoted RNA secondary structures

Abraham, M. & Wolfson, H. J., 2011, Proceedings of the Prague Stringology Conference 2011. p. 45-58 14 p. (Proceedings of the Prague Stringology Conference 2011).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

2 Scopus citations

MultiFit: A web server for fitting multiple protein structures into their electron microscopy density map

Tjioe, E., Lasker, K., Webb, B., Wolfson, H. J. & Sali, A., 1 Jul 2011, In: Nucleic Acids Research. 39, SUPPL. 2, p. W167-W170

Research output: Contribution to journal › Article › peer-review

Open Access

27 Scopus citations

ParaDock: A flexible non-specific DNA - Rigid protein docking algorithm

Banitt, I. & Wolfson, H. J., Nov 2011, In: Nucleic Acids Research. 39, 20

Research output: Contribution to journal › Article › peer-review

Open Access

28 Scopus citations

PepCrawler: A fast RRT-based algorithm for high-resolution refinement and binding affinity estimation of peptide inhibitors

Donsky, E. & Wolfson, H. J., Oct 2011, In: Bioinformatics. 27, 20, p. 2836-2842 7 p., btr498.

Research output: Contribution to journal › Article › peer-review

85 Scopus citations

PepCrawler: A fast RRT-like algorithm for high-resolution refinement and binding-affinity estimation of peptide inhibitors

Donsky, E. & Wolfson, H. J., 2011, Algorithms in Bioinformatics - 11th International Workshop, WABI 2011, Proceedings. p. 73-75 3 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6833 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

1 Scopus citations

Protein structure prediction using a docking-based hierarchical folding scheme

Kifer, I., Nussinov, R. & Wolfson, H. J., Jun 2011, In: Proteins: Structure, Function and Bioinformatics. 79, 6, p. 1759-1773 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

Symmetry-based self-assembled nanotubes constructed using native protein structures: The key role of flexible linkers

Buch, I., Tsai, C. J., Wolfson, H. J. & Nussinov, R., Apr 2011, In: Protein and Peptide Letters. 18, 4, p. 362-372 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

SymmRef: A flexible refinement method for symmetric multimers

Mashiach-Farkash, E., Nussinov, R. & Wolfson, H. J., Sep 2011, In: Proteins: Structure, Function and Bioinformatics. 79, 9, p. 2607-2623 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

13 Scopus citations

2010

Allosteric regulation of glycogen synthase kinase 3β: A theoretical study

Buch, I., Fishelovitch, D., London, N., Raveh, B., Wolfson, H. J. & Nussinov, R., 28 Dec 2010, In: Biochemistry. 49, 51, p. 10890-10901 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

32 Scopus citations

An integrated suite of fast docking algorithms

Mashiach, E., Schneidman-Duhovny, D., Peri, A., Shavit, Y., Nussinov, R. & Wolfson, H. J., 15 Nov 2010, In: Proteins: Structure, Function and Bioinformatics. 78, 15, p. 3197-3204 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

94 Scopus citations

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map

Lasker, K., Sali, A. & Wolfson, H. J., 15 Nov 2010, In: Proteins: Structure, Function and Bioinformatics. 78, 15, p. 3205-3211 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

58 Scopus citations

FiberDock: A web server for flexible induced-fit backbone refinement in molecular docking

Mashiach, E., Nussinov, R. & Wolfson, H. J., 11 May 2010, In: Nucleic Acids Research. 38, SUPPL. 2, p. W457-W461 gkq373.

Research output: Contribution to journal › Article › peer-review

Open Access

81 Scopus citations

FiberDock: Flexible induced-fit backbone refinement in molecular docking

Mashiach, E., Nussinov, R. & Wolfson, H. J., 2010, In: Proteins: Structure, Function and Bioinformatics. 78, 6, p. 1503-1519 17 p.

Research output: Contribution to journal › Article › peer-review

Open Access

168 Scopus citations

How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel?

Fishelovitch, D., Shaik, S., Wolfson, H. J. & Nussinov, R., 6 May 2010, In: Journal of Physical Chemistry B. 114, 17, p. 5964-5970 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

54 Scopus citations

2009

Computational validation of protein nanotubes

Buch, I., Brooks, B. R., Wolfson, H. J. & Nussinov, R., 11 Mar 2009, In: Nano Letters. 9, 3, p. 1096-1102 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

Inferential Optimization for Simultaneous Fitting of Multiple Components into a CryoEM Map of Their Assembly

Lasker, K., Topf, M., Sali, A. & Wolfson, H. J., 24 Apr 2009, In: Journal of Molecular Biology. 388, 1, p. 180-194 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

102 Scopus citations

Novel approach for efficient pharmacophore-based virtual screening: Method and applications

Dror, O., Schneidman-Duhovny, D., Inbar, Y., Nussinov, R. & Wolfson, H. J., 26 Oct 2009, In: Journal of Chemical Information and Modeling. 49, 10, p. 2333-2343 11 p.

Research output: Contribution to journal › Article › peer-review

Open Access

122 Scopus citations

RsiteDB: A database of protein binding pockets that interact with RNA nucleotide bases

Shulman-Peleg, A., Nussinov, R. & Wolfson, H. J., 2009, In: Nucleic Acids Research. 37, SUPPL. 1, p. D369-D373

Research output: Contribution to journal › Article › peer-review

Open Access

28 Scopus citations

Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism

Fishelovitch, D., Shaik, S., Wolfson, H. J. & Nussinov, R., 1 Oct 2009, In: Journal of Physical Chemistry B. 113, 39, p. 13018-13025 8 p.

Research output: Contribution to journal › Article › peer-review

Open Access

109 Scopus citations

2008

Analysis and classification of RNA tertiary structures

Abraham, M., Dror, O., Nussinov, R. & Wolfson, H. J., Nov 2008, In: RNA. 14, 11, p. 2274-2289 16 p.

Research output: Contribution to journal › Article › peer-review

Open Access

43 Scopus citations

Computational Approaches and Tools for Establishing Structural Models for Short Amyloid-forming Peptides

Haspel, N., Zanuy, D., Tsai, H. H., Ma, B., Wolfson, H. & Nussinov, R., 23 Jan 2008, Amyloid Proteins: The Beta Sheet Conformation and Disease. Wiley-VCH Verlag GmbH, Vol. 1. p. 301-315 15 p.

Research output: Chapter in Book/Report/Conference proceeding › Chapter › peer-review

Constructing templates for protein structure prediction by simulation of protein folding pathways

Kifer, I., Nussinov, R. & Wolfson, H. J., 1 Nov 2008, In: Proteins: Structure, Function and Genetics. 73, 2, p. 380-394 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules

Schneidman-Duhovny, D., Dror, O., Inbar, Y., Nussinov, R. & Wolfson, H. J., 1 Sep 2008, In: Journal of Computational Biology. 15, 7, p. 737-754 18 p.

Research output: Contribution to journal › Article › peer-review

Open Access

71 Scopus citations

Haim Wolfson Wolfson

Research output

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