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Richard D. Smith - Publications

Affiliations: 
2010 University of Michigan, Ann Arbor, Ann Arbor, MI 
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21 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
2023 Wagle S, Smith RD, Dominic AJ, DasGupta D, Tripathi SK, Carlson HA. Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools. Scientific Reports. 13: 3008. PMID 36810894 DOI: 10.1038/s41598-023-29996-w  0.669
2022 Siebenaler RF, Chugh S, Waninger JJ, Dommeti VL, Kenum C, Mody M, Gautam A, Patel N, Chu A, Bawa P, Hon J, Smith RD, Carlson H, Cao X, Tesmer JJG, et al. Argonaute 2 modulates EGFR-RAS signaling to promote mutant and driven malignancies. Pnas Nexus. 1: pgac084. PMID 35923912 DOI: 10.1093/pnasnexus/pgac084  0.488
2021 Smith RD, Carlson HA. Identification of Cryptic Binding Sites Using MixMD with Standard and Accelerated Molecular Dynamics. Journal of Chemical Information and Modeling. PMID 33599485 DOI: 10.1021/acs.jcim.0c01002  0.617
2019 Smith RD, Clark JJ, Ahmed A, Orban ZJ, Dunbar JB, Carlson HA. Updates to Binding MOAD (Mother of All Databases): Polypharmacology Tools and Their Utility in Drug Repurposing. Journal of Molecular Biology. PMID 31125569 DOI: 10.1016/J.Jmb.2019.05.024  0.809
2019 Clark JJ, Benson ML, Smith RD, Carlson HA. Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures. Plos Computational Biology. 15: e1006705. PMID 30699115 DOI: 10.1371/Journal.Pcbi.1006705  0.795
2017 Graham S, Smith RD, Carlson HA. Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics. Journal of Chemical Information and Modeling. PMID 29286658 DOI: 10.1021/Acs.Jcim.7B00268  0.646
2017 Smith RD, Lu J, Carlson HA. Are there physicochemical differences between allosteric and competitive ligands? Plos Computational Biology. 13: e1005813. PMID 29125840 DOI: 10.1371/Journal.Pcbi.1005813  0.658
2016 Carlson HA, Smith RD, Damm-Ganamet KL, Stuckey JA, Ahmed A, Convery MA, Somers DO, Kranz M, Elkins PA, Cui G, Peishoff CE, Lambert MH, Dunbar JB. CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma. Journal of Chemical Information and Modeling. PMID 27149958 DOI: 10.1021/Acs.Jcim.5B00523  0.669
2015 Smith RD, Damm-Ganamet KL, Dunbar JB, Ahmed A, Chinnaswamy K, Delproposto JE, Kubish GM, Tinberg CE, Khare SD, Dou J, Doyle L, Stuckey JA, Baker D, Carlson HA. CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge. Journal of Chemical Information and Modeling. PMID 26419257 DOI: 10.1021/Acs.Jcim.5B00387  0.667
2015 Ahmed A, Smith RD, Clark JJ, Dunbar JB, Carlson HA. Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures. Nucleic Acids Research. 43: D465-9. PMID 25378330 DOI: 10.1093/Nar/Gku1088  0.802
2013 Dunbar JB, Smith RD, Damm-Ganamet KL, Ahmed A, Esposito EX, Delproposto J, Chinnaswamy K, Kang YN, Kubish G, Gestwicki JE, Stuckey JA, Carlson HA. CSAR data set release 2012: ligands, affinities, complexes, and docking decoys. Journal of Chemical Information and Modeling. 53: 1842-52. PMID 23617227 DOI: 10.1021/Ci4000486  0.663
2013 Damm-Ganamet KL, Smith RD, Dunbar JB, Stuckey JA, Carlson HA. CSAR benchmark exercise 2011-2012: evaluation of results from docking and relative ranking of blinded congeneric series. Journal of Chemical Information and Modeling. 53: 1853-70. PMID 23548044 DOI: 10.1021/Ci400025F  0.671
2012 Smith RD, Engdahl AL, Dunbar JB, Carlson HA. Biophysical limits of protein-ligand binding. Journal of Chemical Information and Modeling. 52: 2098-106. PMID 22713103 DOI: 10.1021/Ci200612F  0.701
2011 Smith RD, Dunbar JB, Ung PM, Esposito EX, Yang CY, Wang S, Carlson HA. CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions. Journal of Chemical Information and Modeling. 51: 2115-31. PMID 21809884 DOI: 10.1021/Ci200269Q  0.644
2011 Dunbar JB, Smith RD, Yang CY, Ung PM, Lexa KW, Khazanov NA, Stuckey JA, Wang S, Carlson HA. CSAR benchmark exercise of 2010: selection of the protein-ligand complexes. Journal of Chemical Information and Modeling. 51: 2036-46. PMID 21728306 DOI: 10.1021/Ci200082T  0.768
2011 Dunbar JB, Smith RD, Yang C, Ung PM, Lexa KW, Khazanov NA, Stuckey JA, Wang S, Carlson HA. Correction to CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes Journal of Chemical Information and Modeling. 51: 2146-2146. DOI: 10.1021/Ci200363Q  0.711
2008 Carlson HA, Smith RD, Khazanov NA, Kirchhoff PD, Dunbar JB, Benson ML. Differences between high- and low-affinity complexes of enzymes and nonenzymes. Journal of Medicinal Chemistry. 51: 6432-41. PMID 18826206 DOI: 10.1021/Jm8006504  0.786
2008 Benson ML, Smith RD, Khazanov NA, Dimcheff B, Beaver J, Dresslar P, Nerothin J, Carlson HA. Binding MOAD, a high-quality protein-ligand database. Nucleic Acids Research. 36: D674-8. PMID 18055497 DOI: 10.1093/Nar/Gkm911  0.808
2006 Smith RD, Hu L, Falkner JA, Benson ML, Nerothin JP, Carlson HA. Exploring protein-ligand recognition with Binding MOAD. Journal of Molecular Graphics & Modelling. 24: 414-25. PMID 16168689 DOI: 10.1016/J.Jmgm.2005.08.002  0.78
2005 Silverman J, Liu Q, Lu Q, Bakker A, To W, Duguay A, Alba BM, Smith R, Rivas A, Li P, Le H, Whitehorn E, Moore KW, Swimmer C, Perlroth V, et al. Multivalent avimer proteins evolved by exon shuffling of a family of human receptor domains. Nature Biotechnology. 23: 1556-61. PMID 16299519 DOI: 10.1038/Nbt1166  0.313
2005 Hu L, Benson ML, Smith RD, Lerner MG, Carlson HA. Binding MOAD (Mother Of All Databases). Proteins. 60: 333-40. PMID 15971202 DOI: 10.1002/Prot.20512  0.818
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