Year |
Citation |
Score |
2023 |
Höcker B, Lu P, Glasgow A, Marks DS, Chatterjee P, Slusky JSG, Schueler-Furman O, Huang P. How can the protein design community best support biologists who want to harness AI tools for protein structure prediction and design? Cell Systems. 14: 629-632. PMID 37591202 DOI: 10.1016/j.cels.2023.07.005 |
0.737 |
|
2021 |
Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, ... ... Schueler-Furman O, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7 |
0.768 |
|
2020 |
Badaczewska-Dawid AE, Khramushin A, Kolinski A, Schueler-Furman O, Kmiecik S. Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein-Peptide Complex Structures. Methods in Molecular Biology (Clifton, N.J.). 2165: 273-287. PMID 32621231 DOI: 10.1007/978-1-0716-0708-4_16 |
0.305 |
|
2020 |
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Schueler-Furman O, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2 |
0.691 |
|
2020 |
Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, ... Schueler-Furman O, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Computational Biology. 16: e1007507. PMID 32365137 DOI: 10.1371/Journal.Pcbi.1007507 |
0.768 |
|
2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Members of the RosettaCommons Consortium. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S009 |
0.724 |
|
2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Details of Remaining Collective Challenges. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S008 |
0.735 |
|
2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Commercial spin-off companies from the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S007 |
0.735 |
|
2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Values Statement: Equality and Inclusion in the RosettaCommons. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S005 |
0.712 |
|
2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Descriptions of the Rosetta board positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S004 |
0.722 |
|
2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Typical development workflow in the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S003 |
0.756 |
|
2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Specific tests for Rosetta running on our automated testing framework. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S002 |
0.73 |
|
2020 |
Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, et al. Growth in Rosetta PIs and conference attendees. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S001 |
0.714 |
|
2018 |
Ciemny M, Kurcinski M, Kamel K, Kolinski A, Alam N, Schueler-Furman O, Kmiecik S. Protein-peptide docking: opportunities and challenges. Drug Discovery Today. PMID 29733895 DOI: 10.1016/J.Drudis.2018.05.006 |
0.332 |
|
2017 |
Alam N, Goldstein O, Xia B, Porter KA, Kozakov D, Schueler-Furman O. High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. Plos Computational Biology. 13: e1005905. PMID 29281622 DOI: 10.1371/Journal.Pcbi.1005905 |
0.308 |
|
2017 |
Alam N, Schueler-Furman O. Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind. Methods in Molecular Biology (Clifton, N.J.). 1561: 139-169. PMID 28236237 DOI: 10.1007/978-1-4939-6798-8_9 |
0.32 |
|
2016 |
Bohnuud T, Luo L, Wodak SJ, Bonvin AM, Weng Z, Vajda S, Schueler-Furman O, Kozakov D. A benchmark testing ground for integrating homology modeling and protein docking. Proteins. PMID 27172383 DOI: 10.1002/Prot.25063 |
0.39 |
|
2016 |
Sedan Y, Marcu O, Lyskov S, Schueler-Furman O. Peptiderive server: derive peptide inhibitors from protein-protein interactions. Nucleic Acids Research. PMID 27141963 DOI: 10.1093/Nar/Gkw385 |
0.318 |
|
2015 |
Dodson EJ, Fishbain-Yoskovitz V, Rotem-Bamberger S, Schueler-Furman O. Versatile communication strategies among tandem WW domain repeats. Experimental Biology and Medicine (Maywood, N.J.). 240: 351-60. PMID 25710931 DOI: 10.1177/1535370214566558 |
0.326 |
|
2013 |
London N, Raveh B, Schueler-Furman O. Druggable protein-protein interactions--from hot spots to hot segments. Current Opinion in Chemical Biology. 17: 952-9. PMID 24183815 DOI: 10.1016/J.Cbpa.2013.10.011 |
0.304 |
|
2013 |
London N, Raveh B, Schueler-Furman O. Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how. Current Opinion in Structural Biology. 23: 894-902. PMID 24138780 DOI: 10.1016/J.Sbi.2013.07.006 |
0.315 |
|
2013 |
Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ. Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27. Proteins. 81: 2201-9. PMID 24123494 DOI: 10.1002/Prot.24425 |
0.693 |
|
2012 |
London N, Gullá S, Keating AE, Schueler-Furman O. In silico and in vitro elucidation of BH3 binding specificity toward Bcl-2. Biochemistry. 51: 5841-50. PMID 22702834 DOI: 10.1021/Bi3003567 |
0.304 |
|
2012 |
London N, Raveh B, Schueler-Furman O. Modeling peptide-protein interactions. Methods in Molecular Biology (Clifton, N.J.). 857: 375-98. PMID 22323231 DOI: 10.1007/978-1-61779-588-6_17 |
0.317 |
|
2012 |
Schueler-Furman O. Structure-Based Characterization of Peptide-Mediated Protein Interactions Biophysical Journal. 102: 4-9. DOI: 10.1016/J.Bpj.2011.11.2402 |
0.325 |
|
2011 |
Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Schueler-Furman O, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031 |
0.795 |
|
2010 |
London N, Raveh B, Movshovitz-Attias D, Schueler-Furman O. Can self-inhibitory peptides be derived from the interfaces of globular protein-protein interactions? Proteins. 78: 3140-9. PMID 20607702 DOI: 10.1002/Prot.22785 |
0.309 |
|
2010 |
Raveh B, London N, Schueler-Furman O. Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins. 78: 2029-40. PMID 20455260 DOI: 10.1002/Prot.22716 |
0.303 |
|
2010 |
Movshovitz-Attias D, London N, Schueler-Furman O. On the use of structural templates for high-resolution docking. Proteins. 78: 1939-49. PMID 20408170 DOI: 10.1002/Prot.22710 |
0.346 |
|
2008 |
London N, Schueler-Furman O. FunHunt: model selection based on energy landscape characteristics. Biochemical Society Transactions. 36: 1418-21. PMID 19021567 DOI: 10.1042/Bst0361418 |
0.307 |
|
2007 |
Goobes G, Goobes R, Shaw WJ, Gibson JM, Long JR, Raghunathan V, Schueler-Furman O, Popham JM, Baker D, Campbell CT, Stayton PS, Drobny GP. The structure, dynamics, and energetics of protein adsorption-lessons learned from adsorption of statherin to hydroxyapatite. Magnetic Resonance in Chemistry : Mrc. 45: S32-47. PMID 18172904 DOI: 10.1002/Mrc.2123 |
0.381 |
|
2007 |
London N, Schueler-Furman O. Assessing the energy landscape of CAPRI targets by FunHunt. Proteins. 69: 809-15. PMID 17803233 DOI: 10.1002/Prot.21736 |
0.314 |
|
2007 |
Wang C, Schueler-Furman O, Andre I, London N, Fleishman SJ, Bradley P, Qian B, Baker D. RosettaDock in CAPRI rounds 6-12. Proteins. 69: 758-63. PMID 17671979 DOI: 10.1002/Prot.21684 |
0.759 |
|
2006 |
Goobes G, Goobes R, Schueler-Furman O, Baker D, Stayton PS, Drobny GP. Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proceedings of the National Academy of Sciences of the United States of America. 103: 16083-8. PMID 17060618 DOI: 10.1073/Pnas.0607193103 |
0.374 |
|
2005 |
Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science (New York, N.Y.). 310: 638-42. PMID 16254179 DOI: 10.1126/Science.1112160 |
0.789 |
|
2005 |
Lacy DB, Lin HC, Melnyk RA, Schueler-Furman O, Reither L, Cunningham K, Baker D, Collier RJ. A model of anthrax toxin lethal factor bound to protective antigen. Proceedings of the National Academy of Sciences of the United States of America. 102: 16409-14. PMID 16251269 DOI: 10.1073/Pnas.0508259102 |
0.41 |
|
2005 |
Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins. 60: 187-94. PMID 15981249 DOI: 10.1002/Prot.20556 |
0.526 |
|
2005 |
Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Science : a Publication of the Protein Society. 14: 1328-39. PMID 15802647 DOI: 10.1110/Ps.041222905 |
0.533 |
|
2003 |
Bradley P, Chivian D, Meiler J, Misura KM, Rohl CA, Schief WR, Wedemeyer WJ, Schueler-Furman O, Murphy P, Schonbrun J, Strauss CE, Baker D. Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins. 53: 457-68. PMID 14579334 DOI: 10.1002/Prot.10552 |
0.742 |
|
2003 |
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of Molecular Biology. 331: 281-99. PMID 12875852 DOI: 10.1016/S0022-2836(03)00670-3 |
0.785 |
|
2003 |
Schueler-Furman O, Baker D. Conserved residue clustering and protein structure prediction. Proteins. 52: 225-35. PMID 12833546 DOI: 10.1002/Prot.10365 |
0.42 |
|
2003 |
Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D. Protein-protein docking predictions for the CAPRI experiment. Proteins. 52: 118-22. PMID 12784377 DOI: 10.1002/Prot.10384 |
0.773 |
|
2001 |
Convery M, Dennis C, Rowsell S, Kortemme T, Schueler-Furman O, Watters A, Engel A, Fiser A, Parkinson G, Copley R, Gilardi G, Newman R, Sinning I, Flitsch SL, Lowden PA, et al. Paper alert: Structural biology Current Opinion in Structural Biology. 11: 501-510. DOI: 10.1016/S0959-440X(00)00240-2 |
0.56 |
|
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