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Andrew Leaver-Fay - Publications

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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Thieker DF, Maguire JB, Kudlacek ST, Leaver-Fay A, Lyskov S, Kuhlman B. Stabilizing proteins, simplified: A Rosetta-based webtool for predicting favorable mutations. Protein Science : a Publication of the Protein Society. 31: e4428. PMID 36173174 DOI: 10.1002/pro.4428  0.506
2022 Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, et al. Correction to "The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design". Journal of Chemical Theory and Computation. PMID 35667008 DOI: 10.1021/acs.jctc.2c00500  0.776
2022 Albanese KI, Leaver-Fay A, Treacy JW, Park R, Houk KN, Kuhlman B, Waters ML. Comparative Analysis of Sulfonium-π, Ammonium-π, and Sulfur-π Interactions and Relevance to SAM-Dependent Methyltransferases. Journal of the American Chemical Society. PMID 35108000 DOI: 10.1021/jacs.1c09902  0.463
2021 Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, et al. PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Biophysicist (Rockville, Md.). 2: 108-122. PMID 35128343 DOI: 10.35459/tbp.2019.000147  0.735
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, ... ... Leaver-Fay A, 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  0.787
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, ... ... Leaver-Fay A, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.714
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, ... ... Leaver-Fay A, 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  0.78
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, ... ... Leaver-Fay A, et al. Members of the RosettaCommons Consortium. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S009  0.726
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, ... ... Leaver-Fay A, et al. Details of Remaining Collective Challenges. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S008  0.744
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, ... ... Leaver-Fay A, et al. Commercial spin-off companies from the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S007  0.737
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, ... ... Leaver-Fay A, et al. Values Statement: Equality and Inclusion in the RosettaCommons. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S005  0.716
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, ... ... Leaver-Fay A, et al. Descriptions of the Rosetta board positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S004  0.726
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, ... ... Leaver-Fay A, 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, ... ... Leaver-Fay A, et al. Specific tests for Rosetta running on our automated testing framework. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S002  0.737
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, ... ... Leaver-Fay A, et al. Growth in Rosetta PIs and conference attendees. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S001  0.72
2017 Alford RF, Leaver-Fay A, Gonzales L, Dolan EL, Gray JJ. A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design. Plos Computational Biology. 13: e1005837. PMID 29216185 DOI: 10.1371/Journal.Pcbi.1005837  0.487
2017 Froning KJ, Leaver-Fay A, Wu X, Phan S, Gao L, Huang F, Pustilnik A, Bacica M, Houlihan K, Chai Q, Fitchett JR, Hendle J, Kuhlman B, Demarest SJ. Computational Design of a Specific Heavy Chain/κ Light Chain Interface for Expressing Fully IgG Bispecific Antibodies. Protein Science : a Publication of the Protein Society. PMID 28726352 DOI: 10.1002/Pro.3240  0.554
2017 Kleffner R, Flatten J, Leaver-Fay A, Baker D, Siegel JB, Khatib F, Cooper S. Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta. Bioinformatics (Oxford, England). PMID 28481970 DOI: 10.1093/Bioinformatics/Btx283  0.759
2017 Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/Acs.Jctc.7B00125  0.783
2017 Alford RF, Leaver-Fay A, Jeliazkov JR, Pacella MS, Kuhlman B, Kortemme T, Gray JJ. A Deep-Dive into the Rosetta Energy Function for Biological Macromolecules Biophysical Journal. 112: 194a. DOI: 10.1016/J.Bpj.2016.11.1078  0.751
2016 Leaver-Fay A, Froning KJ, Atwell S, Aldaz H, Pustilnik A, Lu F, Huang F, Yuan R, Hassanali S, Chamberlain AK, Fitchett JR, Demarest SJ, Kuhlman B. Computationally Designed Bispecific Antibodies using Negative State Repertoires. Structure (London, England : 1993). PMID 26996964 DOI: 10.1016/J.Str.2016.02.013  0.571
2015 O'Meara MJ, Leaver-Fay A, Tyka M, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B. A Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta. Journal of Chemical Theory and Computation. 11: 609-622. PMID 25866491 DOI: 10.1021/Ct500864R  0.752
2015 Jacobs TM, Yumerefendi H, Kuhlman B, Leaver-Fay A. SwiftLib: rapid degenerate-codon-library optimization through dynamic programming. Nucleic Acids Research. 43: e34. PMID 25539925 DOI: 10.1093/nar/gku1323  0.49
2014 Lewis SM, Wu X, Pustilnik A, Sereno A, Huang F, Rick HL, Guntas G, Leaver-Fay A, Smith EM, Ho C, Hansen-Estruch C, Chamberlain AK, Truhlar SM, Conner EM, Atwell S, et al. Generation of bispecific IgG antibodies by structure-based design of an orthogonal Fab interface. Nature Biotechnology. 32: 191-8. PMID 24463572 DOI: 10.1038/Nbt.2797  0.535
2013 Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, et al. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. Plos One. 8: e67051. PMID 23869206 DOI: 10.1371/Journal.Pone.0067051  0.807
2013 Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, et al. Scientific benchmarks for guiding macromolecular energy function improvement. Methods in Enzymology. 523: 109-43. PMID 23422428 DOI: 10.1016/B978-0-12-394292-0.00006-0  0.761
2012 Jacak R, Leaver-Fay A, Kuhlman B. Computational protein design with explicit consideration of surface hydrophobic patches. Proteins. 80: 825-38. PMID 22223219 DOI: 10.1002/Prot.23241  0.557
2011 Leaver-Fay A, Jacak R, Stranges PB, Kuhlman B. A generic program for multistate protein design. Plos One. 6: e20937. PMID 21754981 DOI: 10.1371/journal.pone.0020937  0.552
2011 DiMaio F, Leaver-Fay A, Bradley P, Baker D, André I. Modeling symmetric macromolecular structures in Rosetta3. Plos One. 6: e20450. PMID 21731614 DOI: 10.1371/Journal.Pone.0020450  0.742
2011 Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, Koga N, Ashworth J, Murphy P, Richter F, Lemmon G, Meiler J, Baker D. RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. Plos One. 6: e20161. PMID 21731610 DOI: 10.1371/Journal.Pone.0020161  0.778
2011 Richter F, Leaver-Fay A, Khare SD, Bjelic S, Baker D. De novo enzyme design using Rosetta3. Plos One. 6: e19230. PMID 21603656 DOI: 10.1371/Journal.Pone.0019230  0.667
2011 Song Y, Tyka M, Leaver-Fay A, Thompson J, Baker D. Structure-guided forcefield optimization. Proteins. 79: 1898-909. PMID 21488100 DOI: 10.1002/Prot.23013  0.634
2011 Kellogg EH, Leaver-Fay A, Baker D. Role of conformational sampling in computing mutation-induced changes in protein structure and stability. Proteins. 79: 830-8. PMID 21287615 DOI: 10.1002/Prot.22921  0.689
2011 Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology. 487: 545-74. PMID 21187238 DOI: 10.1016/B978-0-12-381270-4.00019-6  0.753
2010 Cooper S, Khatib F, Treuille A, Barbero J, Lee J, Beenen M, Leaver-Fay A, Baker D, Popovi? Z, Players F. Predicting protein structures with a multiplayer online game. Nature. 466: 756-60. PMID 20686574 DOI: 10.1038/Nature09304  0.691
2010 Jha RK, Leaver-Fay A, Yin S, Wu Y, Butterfoss GL, Szyperski T, Dokholyan NV, Kuhlman B. Computational design of a PAK1 binding protein. Journal of Molecular Biology. 400: 257-70. PMID 20460129 DOI: 10.1016/J.Jmb.2010.05.006  0.537
2010 Cooper S, Treuille A, Barbero J, Leaver-Fay A, Tuite K, Khatib F, Snyder AC, Beenen M, Salesin D, Baker D, Popović Z. The challenge of designing scientific discovery games Fdg 2010 - Proceedings of the 5th International Conference On the Foundations of Digital Games. 40-47. DOI: 10.1145/1822348.1822354  0.651
2008 Leaver-Fay A, Snoeyink J, Kuhlman B. On-the-fly rotamer pair energy evaluation in protein design Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4983: 343-354. DOI: 10.1007/978-3-540-79450-9_32  0.514
2007 Davis IW, Leaver-Fay A, Chen VB, Block JN, Kapral GJ, Wang X, Murray LW, Arendall WB, Snoeyink J, Richardson JS, Richardson DC. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research. 35: W375-83. PMID 17452350 DOI: 10.1093/Nar/Gkm216  0.485
2007 Leaver-Fay A, Butterfoss GL, Snoeyink J, Kuhlman B. Maintaining solvent accessible surface area under rotamer substitution for protein design. Journal of Computational Chemistry. 28: 1336-41. PMID 17285560 DOI: 10.1002/Jcc.20626  0.568
2005 Leaver-Fay A, Kuhlman B, Snoeyink J. An adaptive dynamic programming algorithm for the side chain placement problem. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 16-27. PMID 15759610  0.464
2005 Leaver-Fay A, Kuhlman B, Snoeyink J. Rotamer-pair energy calculations using a trie data structure Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3692: 389-400. DOI: 10.1007/11557067_32  0.48
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