☰

Ryan H. Lilien, Ph.D. - Publications

Affiliations: 
2004 Dartmouth College, Hanover, NH, United States 
Area:
Computer Science, Biochemistry, Molecular Biology
Tree Info Similar researchers PubMed Report error

24 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
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
Show low-probability matches.