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David R. Hall - Publications

Affiliations: 
Boston University, Boston, MA, United States 
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40 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
2019 Zhong M, Lynch AJ, Muellers SN, Jehle S, Luo L, Hall DR, Iwase R, Carolan JP, Egbert M, Wakefield A, Streu K, Harvey CM, Ortet PC, Kozakov D, Vajda S, et al. Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-associated Protein 1 (KEAP1) and Nuclear Factor, Erythroid 2 Like 2 (Nrf2). Biochemistry. PMID 31851823 DOI: 10.1021/Acs.Biochem.9B00943  0.768
2019 Yueh C, Rettenmaier J, Xia B, Hall DR, Alekseenko A, Porter KA, Barkovich K, Keseru G, Whitty A, Wells JA, Vajda S, Kozakov D. Kinase Atlas: Druggability Analysis of Potential Allosteric Sites in Kinases. Journal of Medicinal Chemistry. PMID 31274316 DOI: 10.1021/Acs.Jmedchem.9B00089  0.682
2018 Beglov D, Hall DR, Wakefield AE, Luo L, Allen KN, Kozakov D, Whitty A, Vajda S. Exploring the structural origins of cryptic sites on proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 29581267 DOI: 10.1073/Pnas.1711490115  0.737
2017 Padhorny D, Hall DR, Mirzaei H, Mamonov AB, Moghadasi M, Alekseenko A, Beglov D, Kozakov D. Protein-ligand docking using FFT based sampling: D3R case study. Journal of Computer-Aided Molecular Design. PMID 29101520 DOI: 10.1007/S10822-017-0069-7  0.657
2017 Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S. The ClusPro web server for protein-protein docking. Nature Protocols. 12: 255-278. PMID 28079879 DOI: 10.1038/Nprot.2016.169  0.755
2016 Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Kozakov D. New Additions to the ClusPro Server Motivated by CAPRI. Proteins. PMID 27936493 DOI: 10.1002/Prot.25219  0.723
2016 Yueh C, Hall DR, Xia B, Padhorny D, Kozakov D, Vajda S. ClusPro-DC: Dimer Classification by the Cluspro Server for Protein-Protein Docking. Journal of Molecular Biology. PMID 27771482 DOI: 10.1016/J.Jmb.2016.10.019  0.717
2016 Hall DR, Enyedy IJ. The use of fake ligands from computational solvent mapping in ligand and structure-based virtual screening. Future Medicinal Chemistry. PMID 27630057 DOI: 10.4155/Fmc-2016-0115  0.48
2016 Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Hall DR, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.733
2016 Whitty A, Zhong M, Viarengo L, Beglov D, Hall DR, Vajda S. Quantifying the chameleonic properties of macrocycles and other high-molecular-weight drugs. Drug Discovery Today. PMID 26891978 DOI: 10.1016/J.Drudis.2016.02.005  0.509
2015 Hall DR, Kozakov D, Whitty A, Vajda S. Lessons from Hot Spot Analysis for Fragment-Based Drug Discovery. Trends in Pharmacological Sciences. 36: 724-36. PMID 26538314 DOI: 10.1016/J.Tips.2015.08.003  0.747
2015 Kozakov D, Hall DR, Napoleon RL, Yueh C, Whitty A, Vajda S. New Frontiers in Druggability. Journal of Medicinal Chemistry. PMID 26230724 DOI: 10.1021/Acs.Jmedchem.5B00586  0.795
2015 Kozakov D, Hall DR, Jehle S, Luo L, Ochiana SO, Jones EV, Pollastri M, Allen KN, Whitty A, Vajda S. Ligand deconstruction: Why some fragment binding positions are conserved and others are not. Proceedings of the National Academy of Sciences of the United States of America. 112: E2585-94. PMID 25918377 DOI: 10.1073/Pnas.1501567112  0.756
2015 Kozakov D, Grove LE, Hall DR, Bohnuud T, Mottarella SE, Luo L, Xia B, Beglov D, Vajda S. The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins. Nature Protocols. 10: 733-55. PMID 25855957 DOI: 10.1038/Nprot.2015.043  0.794
2015 Hall DR, Enyedy IJ. Computational solvent mapping in structure-based drug design. Future Medicinal Chemistry. 7: 337-53. PMID 25826363 DOI: 10.4155/Fmc.14.155  0.448
2014 Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, Schueler-Furman O, Paschalidis ICh, Clore GM, Vajda S. Encounter complexes and dimensionality reduction in protein-protein association. Elife. 3: e01370. PMID 24714491 DOI: 10.7554/Elife.01370  0.747
2014 Shin U, Williams DE, Kozakov D, Hall DR, Beglov D, Vajda S, Andersen RJ, Pelletier J. Stimulators of translation identified during a small molecule screening campaign. Analytical Biochemistry. 447: 6-14. PMID 24513115 DOI: 10.1016/J.Ab.2013.10.026  0.697
2014 Kozakov D, Li K, Hall DR, Beglov D, Zheng J, Vakili P, Schueler-Furman O, Paschalidis IC, Clore GM, Vajda S. Author response: Encounter complexes and dimensionality reduction in protein–protein association Elife. DOI: 10.7554/Elife.01370.021  0.461
2013 Kozakov D, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Vajda S. How good is automated protein docking? Proteins. 81: 2159-66. PMID 23996272 DOI: 10.1002/Prot.24403  0.718
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Hall DR, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356  0.718
2013 Vajda S, Hall DR, Kozakov D. Sampling and scoring: a marriage made in heaven. Proteins. 81: 1874-84. PMID 23775627 DOI: 10.1002/Prot.24343  0.736
2013 Grove LE, Hall DR, Beglov D, Vajda S, Kozakov D. FTFlex: accounting for binding site flexibility to improve fragment-based identification of druggable hot spots. Bioinformatics (Oxford, England). 29: 1218-9. PMID 23476022 DOI: 10.1093/Bioinformatics/Btt102  0.734
2013 Bohnuud T, Beglov D, Ngan C, Zerbe B, Hall D, Brenke R, Vajda S, Frank-Kamenetskii M, Kozakov D. 89 Computational mapping reveals effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde Journal of Biomolecular Structure and Dynamics. 31: 57-57. DOI: 10.1080/07391102.2013.786523  0.738
2012 Brenke R, Hall DR, Chuang GY, Comeau SR, Bohnuud T, Beglov D, Schueler-Furman O, Vajda S, Kozakov D. Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics (Oxford, England). 28: 2608-14. PMID 23053206 DOI: 10.1093/Bioinformatics/Bts493  0.762
2012 Hingtgen S, Kasmieh R, Elbayly E, Nesterenko I, Figueiredo JL, Dash R, Sarkar D, Hall D, Kozakov D, Vajda S, Fisher PB, Shah K. A first-generation multi-functional cytokine for simultaneous optical tracking and tumor therapy. Plos One. 7: e40234. PMID 22808125 DOI: 10.1371/Journal.Pone.0040234  0.657
2012 Zerbe BS, Hall DR, Vajda S, Whitty A, Kozakov D. Relationship between hot spot residues and ligand binding hot spots in protein-protein interfaces. Journal of Chemical Information and Modeling. 52: 2236-44. PMID 22770357 DOI: 10.1021/Ci300175U  0.833
2012 Bohnuud T, Beglov D, Ngan CH, Zerbe B, Hall DR, Brenke R, Vajda S, Frank-Kamenetskii MD, Kozakov D. Computational mapping reveals dramatic effect of Hoogsteen breathing on duplex DNA reactivity with formaldehyde. Nucleic Acids Research. 40: 7644-52. PMID 22705795 DOI: 10.1093/Nar/Gks519  0.736
2012 Ngan CH, Bohnuud T, Mottarella SE, Beglov D, Villar EA, Hall DR, Kozakov D, Vajda S. FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Research. 40: W271-5. PMID 22589414 DOI: 10.1093/Nar/Gks441  0.813
2012 Hall DR, Kozakov D, Vajda S. Analysis of protein binding sites by computational solvent mapping. Methods in Molecular Biology (Clifton, N.J.). 819: 13-27. PMID 22183527 DOI: 10.1007/978-1-61779-465-0_2  0.794
2012 Hall DR, Ngan CH, Zerbe BS, Kozakov D, Vajda S. Hot spot analysis for driving the development of hits into leads in fragment-based drug discovery. Journal of Chemical Information and Modeling. 52: 199-209. PMID 22145575 DOI: 10.1021/Ci200468P  0.794
2012 Ngan CH, Hall DR, Zerbe B, Grove LE, Kozakov D, Vajda S. FTSite: high accuracy detection of ligand binding sites on unbound protein structures. Bioinformatics (Oxford, England). 28: 286-7. PMID 22113084 DOI: 10.1093/Bioinformatics/Btr651  0.792
2012 Beglov D, Hall DR, Brenke R, Shapovalov MV, Dunbrack RL, Kozakov D, Vajda S. Minimal ensembles of side chain conformers for modeling protein-protein interactions. Proteins. 80: 591-601. PMID 22105850 DOI: 10.1002/Prot.23222  0.796
2011 Kozakov D, Hall DR, Chuang GY, Cencic R, Brenke R, Grove LE, Beglov D, Pelletier J, Whitty A, Vajda S. Structural conservation of druggable hot spots in protein-protein interfaces. Proceedings of the National Academy of Sciences of the United States of America. 108: 13528-33. PMID 21808046 DOI: 10.1073/Pnas.1101835108  0.826
2011 Cencic R, Desforges M, Hall DR, Kozakov D, Du Y, Min J, Dingledine R, Fu H, Vajda S, Talbot PJ, Pelletier J. Blocking eIF4E-eIF4G interaction as a strategy to impair coronavirus replication. Journal of Virology. 85: 6381-9. PMID 21507972 DOI: 10.1128/Jvi.00078-11  0.706
2011 Cencic R, Hall DR, Robert F, Du Y, Min J, Li L, Qui M, Lewis I, Kurtkaya S, Dingledine R, Fu H, Kozakov D, Vajda S, Pelletier J. Reversing chemoresistance by small molecule inhibition of the translation initiation complex eIF4F. Proceedings of the National Academy of Sciences of the United States of America. 108: 1046-51. PMID 21191102 DOI: 10.1073/Pnas.1011477108  0.707
2010 Kozakov D, Hall DR, Beglov D, Brenke R, Comeau SR, Shen Y, Li K, Zheng J, Vakili P, Paschalidis ICh, Vajda S. Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19. Proteins. 78: 3124-30. PMID 20818657 DOI: 10.1002/Prot.22835  0.791
2009 Brenke R, Kozakov D, Chuang GY, Beglov D, Hall D, Landon MR, Mattos C, Vajda S. Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques. Bioinformatics (Oxford, England). 25: 621-7. PMID 19176554 DOI: 10.1093/Bioinformatics/Btp036  0.814
2007 Natrajan G, Hall DR, Thompson AC, Gutsche I, Terradot L. Structural similarity between the DnaA-binding proteins HobA (HP1230) from Helicobacter pylori and DiaA from Escherichia coli. Molecular Microbiology. 65: 995-1005. PMID 17683397 DOI: 10.1111/j.1365-2958.2007.05843.x  0.31
2005 Leiros I, Timmins J, Hall DR, McSweeney S. Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans. The Embo Journal. 24: 906-18. PMID 15719017 DOI: 10.1038/sj.emboj.7600582  0.338
2001 McIlwraith MJ, Hall DR, Stasiak AZ, Stasiak A, Wigley DB, West SC. RadA protein from Archaeoglobus fulgidus forms rings, nucleoprotein filaments and catalyses homologous recombination. Nucleic Acids Research. 29: 4509-17. PMID 11713300 DOI: 10.1093/Nar/29.22.4509  0.309
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