Year |
Citation |
Score |
2013 |
Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR. OSPREY: protein design with ensembles, flexibility, and provable algorithms. Methods in Enzymology. 523: 87-107. PMID 23422427 DOI: 10.1016/B978-0-12-394292-0.00005-9 |
0.761 |
|
2011 |
Wallach I, Lilien R. Virtual decoy sets for molecular docking benchmarks. Journal of Chemical Information and Modeling. 51: 196-202. PMID 21207928 DOI: 10.1021/Ci100374F |
0.351 |
|
2010 |
Wallach I, Jaitly N, Lilien R. A structure-based approach for mapping adverse drug reactions to the perturbation of underlying biological pathways. Plos One. 5: e12063. PMID 20808786 DOI: 10.1371/Journal.Pone.0012063 |
0.336 |
|
2010 |
Heifets A, Lilien RH. LigAlign: flexible ligand-based active site alignment and analysis. Journal of Molecular Graphics & Modelling. 29: 93-101. PMID 20713281 DOI: 10.1016/J.Jmgm.2010.05.005 |
0.355 |
|
2010 |
Safi M, Lilien RH. Restricted dead-end elimination: protein redesign with a bounded number of residue mutations. Journal of Computational Chemistry. 31: 1207-15. PMID 19885869 DOI: 10.1002/Jcc.21407 |
0.448 |
|
2009 |
Wallach I, Lilien R. Predicting multiple ligand binding modes using self-consistent pharmacophore hypotheses. Journal of Chemical Information and Modeling. 49: 2116-28. PMID 19711952 DOI: 10.1021/Ci900199E |
0.454 |
|
2009 |
Wallach I, Lilien RH. Prediction of sub-cavity binding preferences using an adaptive physicochemical structure representation. Bioinformatics (Oxford, England). 25: i296-304. PMID 19478002 DOI: 10.1093/Bioinformatics/Btp204 |
0.519 |
|
2009 |
Wallach I, Lilien R. The protein-small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding. Bioinformatics (Oxford, England). 25: 615-20. PMID 19153135 DOI: 10.1093/Bioinformatics/Btp035 |
0.482 |
|
2008 |
Georgiev I, Lilien RH, Donald BR. The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. Journal of Computational Chemistry. 29: 1527-42. PMID 18293294 DOI: 10.1002/Jcc.20909 |
0.754 |
|
2007 |
Gorczynski MJ, Grembecka J, Zhou Y, Kong Y, Roudaia L, Douvas MG, Newman M, Bielnicka I, Baber G, Corpora T, Shi J, Sridharan M, Lilien R, Donald BR, Speck NA, et al. Allosteric inhibition of the protein-protein interaction between the leukemia-associated proteins Runx1 and CBFbeta. Chemistry & Biology. 14: 1186-97. PMID 17961830 DOI: 10.1016/J.Chembiol.2007.09.006 |
0.626 |
|
2006 |
Stevens BW, Lilien RH, Georgiev I, Donald BR, Anderson AC. Redesigning the PheA domain of gramicidin synthetase leads to a new understanding of the enzyme's mechanism and selectivity. Biochemistry. 45: 15495-504. PMID 17176071 DOI: 10.1021/Bi061788M |
0.685 |
|
2006 |
Georgiev I, Lilien RH, Donald BR. Improved Pruning algorithms and Divide-and-Conquer strategies for Dead-End Elimination, with application to protein design. Bioinformatics (Oxford, England). 22: e174-83. PMID 16873469 DOI: 10.1093/Bioinformatics/Btl220 |
0.764 |
|
2006 |
Georgiev I, Lilien RH, Donald BR. A novel minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 530-545. DOI: 10.1007/11732990_44 |
0.761 |
|
2005 |
Lilien RH, Stevens BW, Anderson AC, Donald BR. A novel ensemble-based scoring and search algorithm for protein redesign and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 740-61. PMID 16108714 DOI: 10.1089/Cmb.2005.12.740 |
0.713 |
|
2005 |
Mettu RR, Lilien RH, Donald BR. High-throughput inference of protein-protein interfaces from unassigned NMR data. Bioinformatics (Oxford, England). 21: i292-301. PMID 15961470 DOI: 10.1093/Bioinformatics/Bti1005 |
0.693 |
|
2004 |
Langmead CJ, Yan A, Lilien R, Wang L, Donald BR. A polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 277-98. PMID 15285893 DOI: 10.1089/1066527041410436 |
0.705 |
|
2004 |
Gillilan RE, Lilien RH. Optimization and dynamics of protein-protein complexes using B-splines. Journal of Computational Chemistry. 25: 1630-46. PMID 15264257 DOI: 10.1002/Jcc.20088 |
0.445 |
|
2004 |
Lilien RH, Bailey-Kellogg C, Anderson AC, Donald BR. A subgroup algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry. Acta Crystallographica. Section D, Biological Crystallography. 60: 1057-67. PMID 15159565 DOI: 10.1107/S090744490400695X |
0.616 |
|
2004 |
Lilien RH, Stevens BW, Andersen AC, Donald BR. A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase a phenylalanine adenylation enzyme Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 8: 46-57. |
0.692 |
|
2003 |
Lilien RH, Farid H, Donald BR. Probabilistic disease classification of expression-dependent proteomic data from mass spectrometry of human serum. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 925-46. PMID 14980018 DOI: 10.1089/106652703322756159 |
0.608 |
|
2003 |
O'Neil RH, Lilien RH, Donald BR, Stroud RM, Anderson AC. The crystal structure of dihydrofolate reductase-thymidylate synthase from Cryptosporidium hominis reveals a novel architecture for the bifunctional enzyme. The Journal of Eukaryotic Microbiology. 50: 555-6. PMID 14736160 DOI: 10.1111/J.1550-7408.2003.Tb00627.X |
0.575 |
|
2003 |
O'Neil RH, Lilien RH, Donald BR, Stroud RM, Anderson AC. Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase. The Journal of Biological Chemistry. 278: 52980-7. PMID 14555647 DOI: 10.1074/Jbc.M310328200 |
0.58 |
|
2003 |
Wang L, Mettu RR, Lilien R, Donald BR. An exact algorithm for determining protein backbone structure from NH residual dipolar couplings Proceedings of the 2003 Ieee Bioinformatics Conference, Csb 2003. 611-612. DOI: 10.1109/CSB.2003.1227422 |
0.647 |
|
2001 |
Bailey-Kellogg C, Kelley JJ, Lilien R, Donald BR. Physical geometric algorithms for structural molecular biology Proceedings - Ieee International Conference On Robotics and Automation. 1: 940-947. DOI: 10.1109/ROBOT.2001.932671 |
0.682 |
|
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