| Year |
Citation |
Score |
| 2024 |
Masoudi-Sobhanzadeh Y, Li S, Peng Y, Panchenko AR. Interpretable deep residual network uncovers nucleosome positioning and associated features. Nucleic Acids Research. PMID 39036965 DOI: 10.1093/nar/gkae623 |
0.803 |
|
| 2024 |
Ostroverkhova D, Sheng Y, Panchenko A. Are Next-Generation Pathogenicity Predictors Applicable to Cancer? Journal of Molecular Biology. 436: 168644. PMID 38848867 DOI: 10.1016/j.jmb.2024.168644 |
0.777 |
|
| 2024 |
Peng Y, Song W, Teif VB, Ovcharenko I, Landsman D, Panchenko AR. Detection of new pioneer transcription factors as cell-type-specific nucleosome binders. Elife. 12. PMID 38293962 DOI: 10.7554/eLife.88936 |
0.697 |
|
| 2024 |
Ostroverkhova D, Tyryshkin K, Beach AK, Moore EA, Masoudi-Sobhanzadeh Y, Barbari SR, Rogozin IB, Shaitan KV, Panchenko AR, Shcherbakova PV. DNA polymerase ε and δ variants drive mutagenesis in polypurine tracts in human tumors. Cell Reports. 43: 113655. PMID 38219146 DOI: 10.1016/j.celrep.2023.113655 |
0.774 |
|
| 2023 |
Jensen M, Chandrasekaran V, García-Bonete MJ, Li S, Anindya AL, Andersson K, Erlandsson MC, Oparina NY, Burmann BM, Brath U, Panchenko AR, Bokarewa I M, Katona G. Survivin prevents the polycomb repressor complex 2 from methylating histone 3 lysine 27. Iscience. 26: 106976. PMID 37534134 DOI: 10.1016/j.isci.2023.106976 |
0.642 |
|
| 2023 |
Ostroverkhova D, Espiritu D, Aristizabal MJ, Panchenko AR. Leveraging Gene Redundancy to Find New Histone Drivers in Cancer. Cancers. 15. PMID 37444547 DOI: 10.3390/cancers15133437 |
0.78 |
|
| 2023 |
Peng Y, Song W, Teif VB, Ovcharenko I, Landsman D, Panchenko AR. Detection of new pioneer transcription factors as cell-type specific nucleosome binders. Biorxiv : the Preprint Server For Biology. PMID 37425841 DOI: 10.1101/2023.05.10.540098 |
0.696 |
|
| 2023 |
Ostroverkhova D, Przytycka TM, Panchenko AR. Cancer driver mutations: predictions and reality. Trends in Molecular Medicine. PMID 37076339 DOI: 10.1016/j.molmed.2023.03.007 |
0.789 |
|
| 2023 |
Li S, Wei T, Panchenko AR. Histone variant H2A.Z modulates nucleosome dynamics to promote DNA accessibility. Nature Communications. 14: 769. PMID 36765119 DOI: 10.1038/s41467-023-36465-5 |
0.803 |
|
| 2022 |
Seal RL, Denny P, Bruford EA, Gribkova AK, Landsman D, Marzluff WF, McAndrews M, Panchenko AR, Shaytan AK, Talbert PB. A standardized nomenclature for mammalian histone genes. Epigenetics & Chromatin. 15: 34. PMID 36180920 DOI: 10.1186/s13072-022-00467-2 |
0.67 |
|
| 2022 |
Li S, Peng Y, Panchenko AR. DNA methylation: Precise modulation of chromatin structure and dynamics. Current Opinion in Structural Biology. 75: 102430. PMID 35914496 DOI: 10.1016/j.sbi.2022.102430 |
0.785 |
|
| 2022 |
Li S, Peng Y, Landsman D, Panchenko AR. DNA methylation cues in nucleosome geometry, stability and unwrapping. Nucleic Acids Research. 50: 1864-1874. PMID 35166834 DOI: 10.1093/nar/gkac097 |
0.789 |
|
| 2021 |
Peng Y, Li S, Onufriev A, Landsman D, Panchenko AR. Binding of regulatory proteins to nucleosomes is modulated by dynamic histone tails. Nature Communications. 12: 5280. PMID 34489435 DOI: 10.1038/s41467-021-25568-6 |
0.807 |
|
| 2021 |
Rogozin IB, Roche-Lima A, Tyryshkin K, Carrasquillo-Carrión K, Lada AG, Poliakov LY, Schwartz E, Saura A, Yurchenko V, Cooper DN, Panchenko AR, Pavlov YI. DNA Methylation, Deamination, and Translesion Synthesis Combine to Generate Footprint Mutations in Cancer Driver Genes in B-Cell Derived Lymphomas and Other Cancers. Frontiers in Genetics. 12: 671866. PMID 34093666 DOI: 10.3389/fgene.2021.671866 |
0.321 |
|
| 2021 |
Espiritu D, Gribkova AK, Gupta S, Shaytan AK, Panchenko AR. Molecular Mechanisms of Oncogenesis through the Lens of Nucleosomes and Histones. The Journal of Physical Chemistry. B. PMID 33769808 DOI: 10.1021/acs.jpcb.1c00694 |
0.795 |
|
| 2020 |
Peng Y, Markov Y, Goncearenco A, Landsman D, Panchenko AR. Data sets on human histone interaction networks. Data in Brief. 33: 106555. PMID 33299912 DOI: 10.1016/j.dib.2020.106555 |
0.808 |
|
| 2020 |
Peng Y, Li S, Landsman D, Panchenko AR. Histone tails as signaling antennas of chromatin. Current Opinion in Structural Biology. 67: 153-160. PMID 33279866 DOI: 10.1016/j.sbi.2020.10.018 |
0.789 |
|
| 2020 |
Zhou BR, Feng H, Kale S, Fox T, Khant H, de Val N, Ghirlando R, Panchenko AR, Bai Y. Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. Molecular Cell. PMID 33238161 DOI: 10.1016/j.molcel.2020.10.038 |
0.56 |
|
| 2020 |
Peng Y, Markov Y, Goncearenco A, Landsman D, Panchenko AR. Human histone interaction networks: an old concept, new trends. Journal of Molecular Biology. PMID 33098859 DOI: 10.1016/j.jmb.2020.10.018 |
0.817 |
|
| 2020 |
Zhang N, Chen Y, Lu H, Zhao F, Alvarez RV, Goncearenco A, Panchenko AR, Li M. MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions. Iscience. 23: 100939. PMID 32169820 DOI: 10.1016/J.Isci.2020.100939 |
0.754 |
|
| 2020 |
Armeev G, Panchenko A, Feofanov A, Shaytan AK. Integrative Modeling of Nucleosomes and Supranucleosomal Structures Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.527 |
0.637 |
|
| 2019 |
Fuxreiter M, Panchenko A. Editorial overview: Dynamic protein interactions - from complexes to molecular machines. Current Opinion in Structural Biology. 56: vi-viii. PMID 31337468 DOI: 10.1016/J.Sbi.2019.06.006 |
0.33 |
|
| 2019 |
Hada A, Hota SK, Luo J, Lin YC, Kale S, Shaytan AK, Bhardwaj SK, Persinger J, Ranish J, Panchenko AR, Bartholomew B. Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling. Cell Reports. 28: 282-294.e6. PMID 31269447 DOI: 10.1016/J.Celrep.2019.05.106 |
0.746 |
|
| 2019 |
Brown AL, Li M, Goncearenco A, Panchenko AR. Finding driver mutations in cancer: Elucidating the role of background mutational processes. Plos Computational Biology. 15: e1006981. PMID 31034466 DOI: 10.1371/Journal.Pcbi.1006981 |
0.716 |
|
| 2019 |
Kale S, Goncearenco A, Markov Y, Landsman D, Panchenko AR. Molecular recognition of nucleosomes by binding partners. Current Opinion in Structural Biology. 56: 164-170. PMID 30991239 DOI: 10.1016/J.Sbi.2019.03.010 |
0.782 |
|
| 2019 |
Roper N, Gao S, Maity TK, Banday AR, Zhang X, Venugopalan A, Cultraro CM, Patidar R, Sindiri S, Brown AL, Goncearenco A, Panchenko AR, Biswas R, Thomas A, Rajan A, et al. APOBEC Mutagenesis and Copy-Number Alterations Are Drivers of Proteogenomic Tumor Evolution and Heterogeneity in Metastatic Thoracic Tumors. Cell Reports. 26: 2651-2666.e6. PMID 30840888 DOI: 10.1016/J.Celrep.2019.02.028 |
0.663 |
|
| 2019 |
Armeev G, Panchenko A, Shaytan A. Abstract OR-19: Integrative Approach on Nucleosome Complexes Modeling International Journal of Biomedicine. 9. DOI: 10.21103/Ijbm.9.Suppl_1.Or19 |
0.624 |
|
| 2018 |
Shaytan AK, Xiao H, Armeev GA, Gaykalova DA, Komarova GA, Wu C, Studitsky VM, Landsman D, Panchenko AR. Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID. Nature Protocols. PMID 30341436 DOI: 10.1038/S41596-018-0048-Z |
0.653 |
|
| 2018 |
Zhao F, Zheng L, Goncearenco A, Panchenko AR, Li M. Computational Approaches to Prioritize Cancer Driver Missense Mutations. International Journal of Molecular Sciences. 19. PMID 30037003 DOI: 10.3390/Ijms19072113 |
0.756 |
|
| 2018 |
Roper N, Gao J, Banday R, Maity T, Zhang X, Venugopalan A, Patidar R, Sindiri S, Cultraro C, Goncearenco A, Panchenko A, Biswas R, Wang J, Hewitt S, Kleiner D, et al. Abstract A182: Apobec-mutagenesis drives mutational heterogeneity while copy number alterations drive transcriptomic and proteogenomic heterogeneity in metastatic lung adenocarcinoma and thymic carcinoma Molecular Cancer Therapeutics. 17. DOI: 10.1158/1535-7163.Targ-17-A182 |
0.688 |
|
| 2017 |
Rogozin IB, Goncearenco A, Lada AG, De S, Nudelman G, Panchenko AR, Cooper DN, Pavlov YI. DNA polymerase η mutational signatures are found in a variety of different types of cancer. Cell Cycle (Georgetown, Tex.). 1-31. PMID 29139326 DOI: 10.1080/15384101.2017.1404208 |
0.713 |
|
| 2017 |
Xiao H, Wang F, Wisniewski J, Shaytan AK, Ghirlando R, FitzGerald PC, Huang Y, Wei D, Li S, Landsman D, Panchenko AR, Wu C. Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres. Genes & Development. PMID 29074736 DOI: 10.1101/Gad.304782.117 |
0.703 |
|
| 2017 |
Shaytan AK, Xiao H, Armeev GA, Wu C, Landsman D, Panchenko AR. Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning. Nucleic Acids Research. 45: 9229-9243. PMID 28934480 DOI: 10.1093/Nar/Gkx616 |
0.674 |
|
| 2017 |
Goncearenco A, Li M, Simonetti FL, Shoemaker BA, Panchenko AR. Exploring Protein-Protein Interactions as Drug Targets for Anti-cancer Therapy with In Silico Workflows. Methods in Molecular Biology (Clifton, N.J.). 1647: 221-236. PMID 28809006 DOI: 10.1007/978-1-4939-7201-2_15 |
0.798 |
|
| 2017 |
Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN. Mutational signatures and mutable motifs in cancer genomes. Briefings in Bioinformatics. PMID 28498882 DOI: 10.1093/Bib/Bbx049 |
0.703 |
|
| 2017 |
Goncearenco A, Rager SL, Li M, Sang QX, Rogozin IB, Panchenko AR. Exploring background mutational processes to decipher cancer genetic heterogeneity. Nucleic Acids Research. PMID 28472504 DOI: 10.1093/Nar/Gkx367 |
0.74 |
|
| 2017 |
Li M, Goncearenco A, Panchenko AR. Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols. Methods in Molecular Biology (Clifton, N.J.). 1550: 235-260. PMID 28188534 DOI: 10.1007/978-1-4939-6747-6_17 |
0.753 |
|
| 2017 |
El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, Landsman D, Pflieger D, Govin J. MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones. Epigenetics & Chromatin. 10: 2. PMID 28096900 DOI: 10.1186/S13072-016-0109-X |
0.665 |
|
| 2016 |
Rogozin IB, Lada AG, Goncearenco A, Green MR, De S, Nudelman G, Panchenko AR, Koonin EV, Pavlov YI. Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers. Scientific Reports. 6: 38133. PMID 27924834 DOI: 10.1038/Srep38133 |
0.7 |
|
| 2016 |
Biswas R, Gao S, Cultraro CM, Maity TK, Venugopalan A, Abdullaev Z, Shaytan AK, Carter CA, Thomas A, Rajan A, Song Y, Pitts S, Chen K, Bass S, Boland J, ... ... Panchenko AR, et al. Genomic profiling of multiple sequentially acquired tumor metastatic sites from an "exceptional responder" lung adenocarcinoma patient reveals extensive genomic heterogeneity and novel somatic variants driving treatment response. Cold Spring Harbor Molecular Case Studies. 2: a001263. PMID 27900369 DOI: 10.1101/mcs.a001263 |
0.62 |
|
| 2016 |
Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles. Data in Brief. 7: 1678-81. PMID 27222871 DOI: 10.1016/J.Dib.2016.04.073 |
0.763 |
|
| 2016 |
Li M, Simonetti FL, Goncearenco A, Panchenko AR. MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions. Nucleic Acids Research. 44: W494-501. PMID 27150810 DOI: 10.1093/Nar/Gkw374 |
0.76 |
|
| 2016 |
Draizen EJ, Shaytan AK, Mariño-Ramírez L, Talbert PB, Landsman D, Panchenko AR. HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants. Database : the Journal of Biological Databases and Curation. 2016. PMID 26989147 DOI: 10.1093/Database/Baw014 |
0.691 |
|
| 2016 |
Draizen EJ, Shaytan AK, Mariño-Ramírez L, Talbert PB, Landsman D, Panchenko AR. HistoneDB 2.0: A histone database with variants - An integrated resource to explore histones and their variants Database. 2016. DOI: 10.1093/database/baw014 |
0.691 |
|
| 2016 |
Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Trajectories of microsecond molecular dynamics simulations of nucleosomes and nucleosome core particles Data in Brief. 7: 1678-1681. DOI: 10.1016/j.dib.2016.04.073 |
0.763 |
|
| 2016 |
Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Nucleosome Dynamics at Microsecond Timescale: DNA-Protein Interactions, Water-Mediated Interactions and Nucleosome Formation Biophysical Journal. 110: 405. DOI: 10.1016/J.Bpj.2015.11.2189 |
0.815 |
|
| 2015 |
Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Coupling between histone conformations and DNA geometry in nucleosomes on a microsecond timescale: atomistic insights into nucleosome functions. Journal of Molecular Biology. PMID 26699921 DOI: 10.1016/J.Jmb.2015.12.004 |
0.812 |
|
| 2015 |
Li M, Kales SC, Ma K, Shoemaker B, Crespo-Barreto J, Cangelosi A, Lipkowitz S, Panchenko A. Balancing protein stability and activity in cancer: a new approach for identifying driver mutations affecting CBL ubiquitin ligase activation. Cancer Research. PMID 26676746 DOI: 10.1158/0008-5472.Can-14-3812 |
0.733 |
|
| 2015 |
Goncearenco A, Shaytan AK, Shoemaker BA, Panchenko AR. Structural Perspectives on the Evolutionary Expansion of Unique Protein-Protein Binding Sites. Biophysical Journal. 109: 1295-306. PMID 26213149 DOI: 10.1016/J.Bpj.2015.06.056 |
0.801 |
|
| 2015 |
Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. 6 Combined influence of linker DNA and histone tails on nucleosome dynamics as revealed by microsecond molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics. 33: 3. PMID 26103217 DOI: 10.1080/07391102.2015.1032630 |
0.783 |
|
| 2015 |
Shaytan AK, Landsman D, Panchenko AR. Nucleosome adaptability conferred by sequence and structural variations in histone H2A-H2B dimers. Current Opinion in Structural Biology. 32: 48-57. PMID 25731851 DOI: 10.1016/J.Sbi.2015.02.004 |
0.683 |
|
| 2015 |
Nishi H, Demir E, Panchenko AR. Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites. Journal of Molecular Biology. 427: 511-20. PMID 25451034 DOI: 10.1016/J.Jmb.2014.11.001 |
0.69 |
|
| 2015 |
Petukh M, Morrison J, Li M, Panchenko A, Alexov E. SAMBE: The New Webserver for Predicting the Effect of nssNP on the Protein-Protein Binding Free Energy Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.867 |
0.523 |
|
| 2015 |
Shaytan AK, Armeev GA, Zhurkin VB, Landsman D, Panchenko AR. Polymorphism of Histone Tail Interactions in Nucleosome Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.431 |
0.702 |
|
| 2014 |
Nishi H, Shaytan A, Panchenko AR. Physicochemical mechanisms of protein regulation by phosphorylation. Frontiers in Genetics. 5: 270. PMID 25147561 DOI: 10.3389/Fgene.2014.00270 |
0.803 |
|
| 2014 |
Goncearenco A, Shoemaker BA, Zhang D, Sarychev A, Panchenko AR. Coverage of protein domain families with structural protein-protein interactions: current progress and future trends. Progress in Biophysics and Molecular Biology. 116: 187-93. PMID 24931138 DOI: 10.1016/J.Pbiomolbio.2014.05.005 |
0.804 |
|
| 2014 |
Li M, Petukh M, Alexov E, Panchenko AR. Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity. Journal of Chemical Theory and Computation. 10: 1770-1780. PMID 24803870 DOI: 10.1021/Ct401022C |
0.48 |
|
| 2013 |
Shoemaker B, Wuchty S, Panchenko AR. Computational large-scale mapping of protein-protein interactions using structural complexes. Current Protocols in Protein Science / Editorial Board, John E. Coligan ... [Et Al.]. 73: Unit 3.9. PMID 24510594 DOI: 10.1002/0471140864.ps0309s73 |
0.693 |
|
| 2013 |
Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E. Molecular mechanisms of disease-causing missense mutations. Journal of Molecular Biology. 425: 3919-36. PMID 23871686 DOI: 10.1016/J.Jmb.2013.07.014 |
0.724 |
|
| 2013 |
Nishi H, Tyagi M, Teng S, Shoemaker BA, Hashimoto K, Alexov E, Wuchty S, Panchenko AR. Cancer missense mutations alter binding properties of proteins and their interaction networks. Plos One. 8: e66273. PMID 23799087 DOI: 10.1371/Journal.Pone.0066273 |
0.81 |
|
| 2013 |
Li M, Shoemaker BA, Thangudu RR, Ferraris JD, Burg MB, Panchenko AR. Mutations in DNA-binding loop of NFAT5 transcription factor produce unique outcomes on protein-DNA binding and dynamics. The Journal of Physical Chemistry. B. 117: 13226-34. PMID 23734591 DOI: 10.1021/Jp403310A |
0.735 |
|
| 2013 |
Nishi H, Hashimoto K, Madej T, Panchenko AR. Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization. Progress in Molecular Biology and Translational Science. 117: 3-24. PMID 23663963 DOI: 10.1016/B978-0-12-386931-9.00001-5 |
0.781 |
|
| 2013 |
Nishi H, Fong JH, Chang C, Teichmann SA, Panchenko AR. Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes. Molecular Biosystems. 9: 1620-6. PMID 23364837 DOI: 10.1039/C3Mb25514J |
0.72 |
|
| 2013 |
Panchenko A. Protein Interaction Networks: Impact of Disease Mutations F1000research. 4. DOI: 10.7490/F1000Research.1093570.1 |
0.372 |
|
| 2013 |
Nishi H, Demir E, Panchenko AR. 1P271 Crosstalk between signaling pathways revealed by database analysis of human phosphorylation sites(22B. Bioinformatics: Functional genomics,Poster) Seibutsu Butsuri. 53. DOI: 10.2142/Biophys.53.S150_6 |
0.664 |
|
| 2013 |
Panchenko A. 179 Impact of cancer mutations on protein binding and activity Journal of Biomolecular Structure & Dynamics. 31: 115-116. DOI: 10.1080/07391102.2013.786421 |
0.448 |
|
| 2013 |
Panchenko A. Regulation of Protein-Protein Binding through the Coupling Between Phosphorylation and Intrinsic Disorder Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.1070 |
0.35 |
|
| 2012 |
Hashimoto K, Rogozin IB, Panchenko AR. Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases. Human Mutation. 33: 1566-75. PMID 22753356 DOI: 10.1002/Humu.22145 |
0.582 |
|
| 2012 |
Tyagi M, Thangudu RR, Zhang D, Bryant SH, Madej T, Panchenko AR. Homology inference of protein-protein interactions via conserved binding sites. Plos One. 7: e28896. PMID 22303436 DOI: 10.1371/Journal.Pone.0028896 |
0.67 |
|
| 2012 |
Tyagi M, Hashimoto K, Shoemaker BA, Wuchty S, Panchenko AR. Large-scale mapping of human protein interactome using structural complexes. Embo Reports. 13: 266-71. PMID 22261719 DOI: 10.1038/Embor.2011.261 |
0.792 |
|
| 2012 |
Shoemaker BA, Zhang D, Tyagi M, Thangudu RR, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR. IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins. Nucleic Acids Research. 40: D834-40. PMID 22102591 DOI: 10.1093/Nar/Gkr997 |
0.788 |
|
| 2012 |
Fong JH, Shoemaker BA, Panchenko AR. Intrinsic protein disorder in human pathways. Molecular Biosystems. 8: 320-6. PMID 22012032 DOI: 10.1039/c1mb05274h |
0.677 |
|
| 2011 |
Nishi H, Hashimoto K, Panchenko AR. Phosphorylation in protein-protein binding: effect on stability and function. Structure (London, England : 1993). 19: 1807-15. PMID 22153503 DOI: 10.1016/J.Str.2011.09.021 |
0.779 |
|
| 2011 |
Hashimoto K, Nishi H, Bryant S, Panchenko AR. Caught in self-interaction: evolutionary and functional mechanisms of protein homooligomerization. Physical Biology. 8: 035007. PMID 21572178 DOI: 10.1088/1478-3975/8/3/035007 |
0.783 |
|
| 2010 |
Hashimoto K, Panchenko AR. Mechanisms of protein oligomerization, the critical role of insertions and deletions in maintaining different oligomeric states. Proceedings of the National Academy of Sciences of the United States of America. 107: 20352-7. PMID 21048085 DOI: 10.1073/Pnas.1012999107 |
0.628 |
|
| 2010 |
Thangudu RR, Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR, Madej T. Knowledge-based annotation of small molecule binding sites in proteins. Bmc Bioinformatics. 11: 365. PMID 20594344 DOI: 10.1186/1471-2105-11-365 |
0.777 |
|
| 2010 |
Hashimoto K, Madej T, Bryant SH, Panchenko AR. Functional states of homooligomers: insights from the evolution of glycosyltransferases. Journal of Molecular Biology. 399: 196-206. PMID 20381499 DOI: 10.1016/J.Jmb.2010.03.059 |
0.609 |
|
| 2010 |
Lobanov MY, Shoemaker BA, Garbuzynskiy SO, Fong JH, Panchenko AR, Galzitskaya OV. ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder. Nucleic Acids Research. 38: D283-7. PMID 19906708 DOI: 10.1093/nar/gkp963 |
0.681 |
|
| 2010 |
Dayhoff JE, Shoemaker BA, Bryant SH, Panchenko AR. Evolution of protein binding modes in homooligomers. Journal of Molecular Biology. 395: 860-70. PMID 19879880 DOI: 10.1016/j.jmb.2009.10.052 |
0.656 |
|
| 2010 |
Shoemaker BA, Zhang D, Thangudu RR, Tyagi M, Fong JH, Marchler-Bauer A, Bryant SH, Madej T, Panchenko AR. Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites. Nucleic Acids Research. 38: D518-24. PMID 19843613 DOI: 10.1093/Nar/Gkp842 |
0.787 |
|
| 2010 |
Tyagi M, Thangudu RR, Shoemaker BA, Bryant SH, Madej T, Panchenko AR. Inferring protein-protein interactions based on conservation of interfaces in homologs F1000research. 1. DOI: 10.7490/F1000Research.254.1 |
0.65 |
|
| 2009 |
Tyagi M, Shoemaker BA, Bryant SH, Panchenko AR. Exploring functional roles of multibinding protein interfaces. Protein Science : a Publication of the Protein Society. 18: 1674-83. PMID 19591200 DOI: 10.1002/Pro.181 |
0.784 |
|
| 2009 |
Teng S, Madej T, Panchenko A, Alexov E. Modeling effects of human single nucleotide polymorphisms on protein-protein interactions. Biophysical Journal. 96: 2178-88. PMID 19289044 DOI: 10.1016/J.Bpj.2008.12.3904 |
0.362 |
|
| 2009 |
Fong JH, Shoemaker BA, Garbuzynskiy SO, Lobanov MY, Galzitskaya OV, Panchenko AR. Intrinsic disorder in protein interactions: insights from a comprehensive structural analysis. Plos Computational Biology. 5: e1000316. PMID 19282967 DOI: 10.1371/journal.pcbi.1000316 |
0.665 |
|
| 2009 |
Kann MG, Shoemaker BA, Panchenko AR, Przytycka TM. Correlated evolution of interacting proteins: looking behind the mirrortree. Journal of Molecular Biology. 385: 91-8. PMID 18930732 DOI: 10.1016/J.Jmb.2008.09.078 |
0.693 |
|
| 2007 |
Shoemaker BA, Panchenko AR. Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. Plos Computational Biology. 3: e43. PMID 17465672 DOI: 10.1371/journal.pcbi.0030043 |
0.684 |
|
| 2007 |
Shoemaker BA, Panchenko AR. Deciphering protein-protein interactions. Part I. Experimental techniques and databases. Plos Computational Biology. 3: e42. PMID 17397251 DOI: 10.1371/journal.pcbi.0030042 |
0.676 |
|
| 2007 |
Wolf Y, Madej T, Babenko V, Shoemaker B, Panchenko AR. Long-term trends in evolution of indels in protein sequences. Bmc Evolutionary Biology. 7: 19. PMID 17298668 DOI: 10.1186/1471-2148-7-19 |
0.659 |
|
| 2006 |
Shoemaker BA, Panchenko AR, Bryant SH. Finding biologically relevant protein domain interactions: conserved binding mode analysis. Protein Science : a Publication of the Protein Society. 15: 352-61. PMID 16385001 DOI: 10.1110/ps.051760806 |
0.679 |
|
| 2003 |
Chen J, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler-Bauer A, Marchler GH, ... ... Panchenko AR, et al. MMDB: Entrez's 3D-structure database. Nucleic Acids Research. 31: 474-7. PMID 12520055 DOI: 10.1093/nar/gkg086 |
0.648 |
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| 2003 |
Marchler-Bauer A, Anderson JB, DeWeese-Scott C, Fedorova ND, Geer LY, He S, Hurwitz DI, Jackson JD, Jacobs AR, Lanczycki CJ, Liebert CA, Liu C, Madej T, Marchler GH, Mazumder R, ... ... Panchenko AR, et al. CDD: a curated Entrez database of conserved domain alignments. Nucleic Acids Research. 31: 383-7. PMID 12520028 DOI: 10.1093/Nar/Gkg087 |
0.66 |
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| 2002 |
Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH. CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Research. 30: 281-3. PMID 11752315 |
0.672 |
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| 2002 |
Wang Y, Anderson JB, Chen J, Geer LY, He S, Hurwitz DI, Liebert CA, Madej T, Marchler GH, Marchler-Bauer A, Panchenko AR, Shoemaker BA, Song JS, Thiessen PA, Yamashita RA, et al. MMDB: Entrez's 3D-structure database. Nucleic Acids Research. 30: 249-52. PMID 11752307 |
0.636 |
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| 1999 |
Panchenko A, Marchler-Bauer A, Bryant SH. Threading with explicit models for evolutionary conservation of structure and sequence. Proteins. 37: 133-140. DOI: 10.1002/(Sici)1097-0134(1999)37:3+<133::Aid-Prot18>3.0.Co;2-D |
0.307 |
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| 1997 |
Panchenko AR, Luthey-Schulten Z, Cole R, Wolynes PG. The foldon universe: a survey of structural similarity and self-recognition of independently folding units. Journal of Molecular Biology. 272: 95-105. PMID 9299340 DOI: 10.1006/Jmbi.1997.1205 |
0.449 |
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| 1997 |
Panchenko AR, Luthey-Schulten Z, Wolynes PG. Foldons as independently folding units of proteins Physica D: Nonlinear Phenomena. 107: 312-315. DOI: 10.1016/S0167-2789(97)00098-5 |
0.474 |
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| 1996 |
Panchenko AR, Luthey-Schulten Z, Wolynes PG. Foldons, protein structural modules, and exons. Proceedings of the National Academy of Sciences of the United States of America. 93: 2008-13. PMID 8700876 DOI: 10.1073/Pnas.93.5.2008 |
0.454 |
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| 1995 |
Panchenko AR, Wang J, Nienhaus GU, Wolynes PG. Analysis of Ligand Binding to Heme Proteins Using a Fluctuating Path Description The Journal of Physical Chemistry. 99: 9278-9282. DOI: 10.1021/J100022A049 |
0.444 |
|
| 1990 |
Kurinov IV, Krupyanskii YF, Panchenko AR, Suzdalev IP, Uporov IV, Shaitan KV, Rubin AB, Goldanskii VI. Intramolecular dynamics of hydrated DNA studied by Rayleigh scattering of Mössbauer radiation (RSMR) Hyperfine Interactions. 58: 2355-2357. DOI: 10.1007/BF02398343 |
0.484 |
|
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