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Wei Wang - Publications

Affiliations: 
2004 University of Pennsylvania, Philadelphia, PA, United States 
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36 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 Zhang Y, Chen M, Lu J, Li W, Wolynes PG, Wang W. Frustration and the Kinetic Repartitioning Mechanism of Substrate Inhibition in Enzyme Catalysis. The Journal of Physical Chemistry. B. PMID 36044985 DOI: 10.1021/acs.jpcb.2c03832  0.345
2020 Wang M, Wang D, Zhang K, Ngo V, Fan S, Wang W. Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss. Genetics. PMID 32816922 DOI: 10.1534/Genetics.120.303597  0.304
2020 Parkinson J, Hard R, Ainsworth RI, Li N, Wang W. Engineering a Histone Reader Protein by Combining Directed Evolution, Sequencing, and Neural Network Based Ordinal Regression. Journal of Chemical Information and Modeling. PMID 32786513 DOI: 10.1021/Acs.Jcim.0C00441  0.343
2018 Hard R, Li N, He W, Ross B, Mo GCH, Peng Q, Stein RSL, Komives E, Wang Y, Zhang J, Wang W. Deciphering and engineering chromodomain-methyllysine peptide recognition. Science Advances. 4: eaau1447. PMID 30417094 DOI: 10.1126/Sciadv.Aau1447  0.303
2015 Li N, Ainsworth RI, Wu M, Ding B, Ainsworth RI, Wang W. MIEC-SVM: Automated Pipeline for Protein Peptide/ligand Interaction Prediction. Bioinformatics (Oxford, England). PMID 26568623 DOI: 10.1093/Bioinformatics/Btv666  0.315
2013 Li N, Stein RS, He W, Komives E, Wang W. Identification of methyllysine peptides binding to chromobox protein homolog 6 chromodomain in the human proteome. Molecular & Cellular Proteomics : McP. 12: 2750-60. PMID 23842000 DOI: 10.1074/Mcp.O112.025015  0.344
2013 Stein RS, Li N, He W, Komives E, Wang W. Recognition of methylated peptides by Drosophila melanogaster polycomb chromodomain. Journal of Proteome Research. 12: 1467-77. PMID 23320494 DOI: 10.1021/Pr3011205  0.316
2013 Ding B, Wang J, Li N, Wang W. Characterization of small molecule binding. I. Accurate identification of strong inhibitors in virtual screening. Journal of Chemical Information and Modeling. 53: 114-22. PMID 23259763 DOI: 10.1021/Ci300508M  0.318
2013 Whitaker JW, Chen Z, Wang W. Interplay between DNA sequence motifs and the human epigenome Embnet.Journal. 19: 32-33. DOI: 10.14806/Ej.19.A.615  0.316
2012 Won KJ, Xu Z, Zhang X, Whitaker JW, Shoemaker R, Ren B, Xu Y, Wang W. Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells Nucleic Acids Research. 40: 8199-8209. PMID 22730289 DOI: 10.1093/Nar/Gks584  0.302
2012 Hou T, Li N, Li Y, Wang W. Characterization of domain-peptide interaction interface: prediction of SH3 domain-mediated protein-protein interaction network in yeast by generic structure-based models. Journal of Proteome Research. 11: 2982-95. PMID 22468754 DOI: 10.1021/Pr3000688  0.326
2012 Cui T, Mowrey D, Bondarenko V, Tillman T, Ma D, Landrum E, Perez-Aguilar JM, He J, Wang W, Saven JG, Eckenhoff RG, Tang P, Xu Y. NMR structure and dynamics of a designed water-soluble transmembrane domain of nicotinic acetylcholine receptor. Biochimica Et Biophysica Acta. 1818: 617-26. PMID 22155685 DOI: 10.1016/J.Bbamem.2011.11.021  0.577
2011 Xu Z, Hou T, Li N, Xu Y, Wang W. Proteome-wide detection of Abl1 SH3-binding peptides by integrating computational prediction and peptide microarray. Molecular & Cellular Proteomics : McP. 11: O111.010389. PMID 22023807 DOI: 10.1074/Mcp.O111.010389  0.34
2011 Li N, Hou T, Ding B, Wang W. Characterization of PDZ domain-peptide interaction interface based on energetic patterns. Proteins. 79: 3208-20. PMID 21928318 DOI: 10.1002/Prot.23157  0.315
2011 Stein RS, Wang W. The recognition specificity of the CHD1 chromodomain with modified histone H3 peptides. Journal of Molecular Biology. 406: 527-41. PMID 21195088 DOI: 10.1016/J.Jmb.2010.12.030  0.337
2011 McLaughlin WA, Hou T, Taylor SS, Wang W. The identification of novel cyclic AMP-dependent protein kinase anchoring proteins using bioinformatic filters and peptide arrays. Protein Engineering, Design & Selection : Peds. 24: 333-9. PMID 21115539 DOI: 10.1093/Protein/Gzq106  0.311
2008 Chang CE, McLaughlin WA, Baron R, Wang W, McCammon JA. Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association. Proceedings of the National Academy of Sciences of the United States of America. 105: 7456-61. PMID 18495919 DOI: 10.1073/Pnas.0800452105  0.329
2008 Yu RX, Liu J, True N, Wang W. Identification of direct target genes using joint sequence and expression likelihood with application to DAF-16. Plos One. 3. PMID 18350157 DOI: 10.1371/Journal.Pone.0001821  0.301
2008 Hou T, Zhang W, Case DA, Wang W. Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain. Journal of Molecular Biology. 376: 1201-14. PMID 18206907 DOI: 10.1016/J.Jmb.2007.12.054  0.312
2007 Philibert P, Stoessel A, Wang W, Sibler AP, Bec N, Larroque C, Saven JG, Courtête J, Weiss E, Martineau P. A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm. Bmc Biotechnology. 7: 81. PMID 18034894 DOI: 10.1186/1472-6750-7-81  0.551
2007 Daly NL, Chen Y, Rosengren KJ, Marx U, Phillips M, Waring A, Wang W, Lehrer R, Craik DJ. Retrocyclin-2: structural analysis of a potent anti-HIV theta-defensin. Biochemistry. 46: 9920-9928. PMID 17685559 DOI: 10.1021/Bi700720E  0.305
2007 Chung JL, Wang W, Bourne PE. High-throughput identification of interacting protein-protein binding sites. Bmc Bioinformatics. 8: 223. PMID 17594507 DOI: 10.1186/1471-2105-8-223  0.32
2007 Chowdhury P, Wang W, Lavender S, Bunagan MR, Klemke JW, Tang J, Saven JG, Cooperman BS, Gai F. Fluorescence correlation spectroscopic study of serpin depolymerization by computationally designed peptides. Journal of Molecular Biology. 369: 462-73. PMID 17442346 DOI: 10.1016/J.Jmb.2007.03.042  0.556
2007 Kono H, Wang W, Saven JG. Combinatorial protein design strategies using computational methods. Methods in Molecular Biology (Clifton, N.J.). 352: 3-22. PMID 17041256 DOI: 10.1385/1-59745-187-8:3  0.621
2006 McLaughlin WA, Hou T, Wang W. Prediction of binding sites of peptide recognition domains: an application on Grb2 and SAP SH2 domains. Journal of Molecular Biology. 357: 1322-34. PMID 16476443 DOI: 10.1016/J.Jmb.2006.01.005  0.332
2006 Hou T, Chen K, McLaughlin WA, Lu B, Wang W. Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain. Plos Computational Biology. 2: e1. PMID 16446784 DOI: 10.1371/Journal.Pcbi.0020001  0.331
2006 Hou T, McLaughlin W, Lu B, Chen K, Wang W. Prediction of binding affinities between the human amphiphysin-1 SH3 domain and its peptide ligands using homology modeling, molecular dynamics and molecular field analysis. Journal of Proteome Research. 5: 32-43. PMID 16396493 DOI: 10.1021/Pr0502267  0.314
2006 Chung JL, Wang W, Bourne PE. Exploiting sequence and structure homologs to identify protein-protein binding sites. Proteins. 62: 630-40. PMID 16329107 DOI: 10.1002/Prot.20741  0.332
2006 Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien aMJ, DeGrado WF. Computational De Novo Design and Characterization of a Four-Helix Bundle Protein that Selectively Binds a Nonbiological Cofactor [J. Am. Chem. Soc. 2005, 127, 1346−1347]. Journal of the American Chemical Society. 128: 663-663. DOI: 10.1021/Ja059923Q  0.591
2005 Cochran FV, Wu SP, Wang W, Nanda V, Saven JG, Therien MJ, DeGrado WF. Computational de novo design and characterization of a four-helix bundle protein that selectively binds a nonbiological cofactor. Journal of the American Chemical Society. 127: 1346-7. PMID 15686346 DOI: 10.1021/Ja044129A  0.601
2005 Park S, Kono H, Wang W, Boder ET, Saven JG. Progress in the development and application of computational methods for probabilistic protein design Computers and Chemical Engineering. 29: 407-421. DOI: 10.1016/J.Compchemeng.2004.07.037  0.634
2004 Cole AM, Wang W, Waring AJ, Lehrer RI. Retrocyclins: Using past as prologue Current Protein and Peptide Science. 5: 373-381. PMID 15544532 DOI: 10.2174/1389203043379657  0.318
2004 Park S, Stowell XF, Wang W, Yang X, Saven JG. Computational protein design and discovery Annual Reports On the Progress of Chemistry - Section C. 100: 195-236. DOI: 10.1039/B313669H  0.641
2003 Calhoun JR, Kono H, Lahr S, Wang W, DeGrado WF, Saven JG. Computational design and characterization of a monomeric helical dinuclear metalloprotein. Journal of Molecular Biology. 334: 1101-15. PMID 14643669 DOI: 10.1016/J.Jmb.2003.10.004  0.618
2002 Wang W, Saven JG. Designing gene libraries from protein profiles for combinatorial protein experiments. Nucleic Acids Research. 30: e120. PMID 12409479 DOI: 10.1093/Nar/Gnf119  0.664
2001 Wang W, Lim WA, Jakalian A, Wang J, Wang J, Luo R, Bayly CI, Kollman PA. An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. Journal of the American Chemical Society. 123: 3986-94. PMID 11457149 DOI: 10.1021/Ja003164O  0.315
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