Topic 01 -- Abstracts with Biological Entities (English) - 75 Topics / Sub-Topic Model 10 - 15 Topics

cite ad title authors publish year publish time dataset abstract mentions covid pmcid pubmed id doi cord uid topic weight Similarity scispacy Similarity specter
1 Lee_B_2009 Identification of protein functions using a machine-learning approach based on sequence-derived properties Lee, Bum Ju; Shin, Moon Sun; Oh, Young Joon; Oh, Hae Seok; Ryu, Keun Ho 2009 2009-08-09 COMM-USE N PMC2731080 19664241.0 10.1186/1477-5956-7-27 85fqseal 0.930240 Cai_C_2006
2 Hall_2007 Protein microarray technology Hall, David A.; Ptacek, Jason; Snyder, Michael 2007 2007-01-31 None N PMC1828913 17126887.0 10.1016/j.mad.2006.11.021 1ty623bq 0.919645 Ivarsson_2012
3 Bitard‐Feildel_2018 Order in Disorder as Observed by the “Hydrophobic Cluster Analysis” of Protein Sequences Bitard‐Feildel, Tristan; Lamiable, Alexis; Mornon, Jean‐Paul; Callebaut, Isabelle 2018 2018-10-30 PMC N PMC7168002 30299594.0 10.1002/pmic.201800054 9eh8achd 0.918452 Ivarsson_2012, Kinjo_2012
4 Bagowski_2010 The Nature of Protein Domain Evolution: Shaping the Interaction Network Bagowski, Christoph P; Bruins, Wouter; te Velthuis, Aartjan J.W 2010 2010-08-23 COMM-USE N PMC2945003 21286315.0 10.2174/138920210791616725 ampip7od 0.883690 Liu_Z_2008, Ivarsson_2012
5 Zemla_2011 StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase Zemla, Adam T; Lang, Dorothy M; Kostova, Tanya; Andino, Raul; Ecale Zhou, Carol L 2011 2011-06-02 COMM-USE N PMC3121648 21635786.0 10.1186/1471-2105-12-226 s7kzp795 0.881650
6 Shameer_2012 Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome Shameer, Khader; Sowdhamini, Ramanathan 2012 2012-04-03 COMM-USE N PMC3508620 22472218.0 10.1186/2043-9113-2-8 6ld9zqj9 0.881117 Ivarsson_2012, Kinjo_2012, Liu_Z_2008 Abad_2009, Tong_2009, Mascarenhas_2017
7 Liu_X_2009 Donut-shaped fingerprint in homologous polypeptide relationships—A topological feature related to pathogenic structural changes in conformational disease Liu, Xin; Zhao, Ya-Pu 2009 2009-05-21 PMC N PMC7094133 19248793.0 10.1016/j.jtbi.2009.02.009 twmrilk8 0.875909 Ivarsson_2012, Liu_Z_2008 Kumar_2013
8 Liu_Z_2008 Bridging protein local structures and protein functions Liu, Zhi-Ping; Wu, Ling-Yun; Wang, Yong; Zhang, Xiang-Sun; Chen, Luonan 2008 2008-04-18 PMC N PMC7088341 18421562.0 10.1007/s00726-008-0088-8 0oq2n0af 0.871952 Myllykoski_2017, Bagowski_2010
9 Deng_2015 An Overview of Practical Applications of Protein Disorder Prediction and Drive for Faster, More Accurate Predictions Deng, Xin; Gumm, Jordan; Karki, Suman; Eickholt, Jesse; Cheng, Jianlin 2015 2015-07-07 COMM-USE N PMC4519904 26198229.0 10.3390/ijms160715384 ypy56yxr 0.868569 Kirillova_2009, Liu_Z_2008 Uversky_2013, Peng_2013, Wang_2013, Basu_2016
10 Xu_Y_2010 Protein Structure Prediction by Protein Threading Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong 2010 2010-04-29 PMC N PMC7123984 10.1007/978-0-387-68825-1_1 2lia97db 0.863849 Myllykoski_2017, Bielnicki_2005
11 Zhang_2007 Estimating residue evolutionary conservation by introducing von Neumann entropy and a novel gap-treating approach Zhang, S.-W.; Zhang, Y.-L.; Pan, Q.; Cheng, Y.-M.; Chou, K.-C. 2007 2007-08-21 PMC N PMC7088136 17710364.0 10.1007/s00726-007-0586-0 7bh8222u 0.851352
12 Xie_X_2012 Protein sequence analysis based on hydropathy profile of amino acids Xie, Xiao-li; Zheng, Li-fei; Yu, Ying; Liang, Li-ping; Guo, Man-cai; Song, John; Yuan, Zhi-fa 2012 2012-01-27 PMC N PMC3274743 22302429.0 10.1631/jzus.b1100052 g1ob16b9 0.845663 Das_J_2017
13 Uversky_2013 A decade and a half of protein intrinsic disorder: Biology still waits for physics Uversky, Vladimir N 2013 2013-04-29 PMC N PMC3690711 23553817.0 10.1002/pro.2261 a7hnuxy5 0.838906 Liu_Z_2008, Kirillova_2009 Uversky_2013, Peng_2013, Basu_2016
14 Kirillova_2009 Protein Domain Boundary Predictions: A Structural Biology Perspective Kirillova, Svetlana; Kumar, Suresh; Carugo, Oliviero 2009 2009-01-21 NONCOMM N PMC2669640 19401756.0 10.2174/1874091x00903010001 qrnhp1ek 0.834304 Liu_Z_2008 RAMAKRISHNA_2015
15 Kinjo_2012 Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins Kinjo, Akira R.; Nakamura, Haruki 2012 2012-02-08 COMM-USE N PMC3275580 22347478.0 10.1371/journal.pone.0031437 hsh2yynq 0.819562 Ivarsson_2012, Liu_Z_2008 Myllykoski_2017
16 Yadav_2017 Homology Modeling and Protein Interaction Map of CHRNA7 Neurogenesis Protein Yadav, Ruchi; Deepshikha, Deepshikha; Srivastava, Prachi 2017 2017-01-01 PMC N PMC5566677 28867899.0 10.1159/000477155 r7o7sxq2 0.783980 Ivarsson_2012, Smith_2003, Choudhury_2017, UNKNOWN_1987 Kumar_2013, Tong_2009
17 Pfab_2020 DeepTracer: Predicting Backbone Atomic Structure from High Resolution Cryo-EM Density Maps of Protein Complexes Jonas Pfab; Dong Si 2020 2020-02-13 BioRxiv N 10.1101/2020.02.12.946772 er6lz09f 0.773770 Zhong_2020, Subramaniam_2016, Yang_2020
18 Vila_2014 (13)C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information Vila, Jorge A.; Arnautova, Yelena A. 2014 2014-01-01 PMC N PMC7121069 10.1007/978-3-642-28554-7_19 jz2mrn4t 0.772495 Liu_Z_2008, Kirillova_2009 Vila_2018
19 Sun_P_2004 Overview of Protein Structural and Functional Folds Sun, Peter D.; Foster, Christine E.; Boyington, Jeffrey C. 2004 2004-05-01 PMC N PMC7162418 18429251.0 10.1002/0471140864.ps1701s35 gl4xk9mg 0.772291 Liu_Z_2008
20 Hung_2006 Alignment using genetic programming with causal trees for identification of protein functions Hung, Chun-Min; Huang, Yueh-Min; Chang, Ming-Shi 2006 2006-09-01 PMC N PMC7117053 10.1016/j.na.2005.09.048 6l688krc 0.768575 Lee_B_2009
21 Conticello_2017 Biomaterials Made from Coiled-Coil Peptides Conticello, Vincent; Hughes, Spencer; Modlin, Charles 2017 2017-01-19 PMC N PMC7121611 28101873.0 10.1007/978-3-319-49674-0_17 6jgao58w 0.758159 Liu_Z_2008 Doll_2015
22 Vila_2018 (13)C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information Vila, Jorge A.; Arnautova, Yelena A. 2018 2018-07-20 PMC N PMC7123919 10.1007/978-3-319-95843-9_20 gytg4iku 0.751275 Liu_Z_2008, Kirillova_2009 Vila_2014
23 Shen_2006 Probabilistic analysis of the frequencies of amino acid pairs within characterized protein sequences Shen, Shiyi; Kai, Bo; Ruan, Jishou; Torin Huzil, J.; Carpenter, Eric; Tuszynski, Jack A. 2006 2006-10-15 PMC N PMC7127678 10.1016/j.physa.2006.03.004 hjo78o1q 0.749245
24 Peng_2013 A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome Peng, Zhenling; Oldfield, Christopher J.; Xue, Bin; Mizianty, Marcin J.; Dunker, A. Keith; Kurgan, Lukasz; Uversky, Vladimir N. 2013 2013-08-13 None N PMC7079807 23942625.0 10.1007/s00018-013-1446-6 8a3o5lmo 0.745883 Ivarsson_2012, Choudhury_2017 Uversky_2013, Basu_2016
25 Anthonsen_1994 The blind watchmaker and rational protein engineering Anthonsen, Henrik W.; Baptista, António; Drabløs, Finn; Martel, Paulo; Petersen, Steffen B. 1994 1994-08-31 PMC N 7765263.0 10.1016/0168-1656(94)90152-x 8lnpujip 0.737322 Liu_Z_2008, Ivarsson_2012
26 Lomonossoff_1996 Use of macromolecular assemblies as expression systems for peptides and synthetic vaccines Lomonossoff, George P; Johnson, John E 1996 1996-04-30 PMC N 8728650.0 10.1016/s0959-440x(96)80072-8 0jarr7hj 0.725894 Kirillova_2009, Liu_Z_2008 Doll_2015
27 CAO_S_2012 Statistical mechanical modeling of RNA folding: from free energy landscape to tertiary structural prediction CAO, Song; CHEN, Shi-Jie 2012 2012-01-01 PMC N PMC4902161 27293312.0 10.1007/978-3-642-25740-7_10 ywd88kmq 0.716443 DiMaio_2016
28 Wang_2014 Advantages of mRNA display selections over other selection techniques for investigation of protein–protein interactions Wang, Hui; Liu, Rihe 2014 2014-01-09 PMC N PMC7103729 21679115.0 10.1586/epr.11.15 3o6mdx3e 0.713146
29 Punjani_2019 Non-uniform refinement: Adaptive regularization improves single particle cryo-EM reconstruction Ali Punjani; Haowei Zhang; David J. Fleet 2019 2019-12-16 BioRxiv N 10.1101/2019.12.15.877092 bqwmx5dy 0.708518 DiMaio_2016 Punjani_2020, Zhong_2020, Jonić_2016
30 Uversky_2013 The alphabet of intrinsic disorder: II. Various roles of glutamic acid in ordered and intrinsically disordered proteins Uversky, Vladimir N 2013 2013-04-01 NONCOMM N PMC5424795 28516010.0 10.4161/idp.24684 63gh2tg4 0.702237 Ivarsson_2012 Myllykoski_2017, Peng_2013
31 Farhadi_2018 Computer-aided design of amino acid-based therapeutics: a review Farhadi, Tayebeh; Hashemian, Seyed MohammadReza 2018 2018-05-14 NONCOMM N PMC5958949 29795978.0 10.2147/dddt.s159767 q69f57el 0.701110 Liu_Z_2008 Robinson_2013, Wang_2013
32 Sanchez-Weatherby_2016 Crystal Dehydration in Membrane Protein Crystallography Sanchez-Weatherby, Juan; Moraes, Isabel 2016 2016-04-28 COMM-USE N PMC6126552 27553236.0 10.1007/978-3-319-35072-1_6 ssp499fe 0.689361 Liu_Z_2008
33 Liu_H_2008 A new approach to the prediction of transmembrane structures Liu, HongDe; Wang, Rui; Lu, XiaoQuan; Chen, Jing; Liu, Xiuhui; Ding, Lan 2008 2008-05-23 PMC N PMC7088861 10.1007/s11434-008-0055-5 n10ia3j3 0.681841 UNKNOWN_1987 Wang_2013, Cai_C_2006, RAMAKRISHNA_2015
34 Yang_2009 Peptide Bioinformatics- Peptide Classification Using Peptide Machines Yang, Zheng Rong 2009 2009-01-01 PMC N PMC7122642 19065810.0 10.1007/978-1-60327-101-1_9 hkvll3xh 0.680529 Liu_Z_2008 Cai_C_2006, Lee_B_2009
35 Dolinnaya_2017 Structure, properties, and biological relevance of the DNA and RNA G-quadruplexes: Overview 50 years after their discovery Dolinnaya, N. G.; Ogloblina, A. M.; Yakubovskaya, M. G. 2017 2017-01-06 PMC N PMC7087716 28260487.0 10.1134/s0006297916130034 dhml7rlz 0.671931 Ivarsson_2012, Liu_Z_2008
36 Shulman-Peleg_2004 Recognition of Functional Sites in Protein Structures Shulman-Peleg, Alexandra; Nussinov, Ruth; Wolfson, Haim J. 2004 2004-06-04 PMC N PMC7126412 15147845.0 10.1016/j.jmb.2004.04.012 66qoykl1 0.670873 Liu_Z_2008 Kuhn_2006, Myllykoski_2017, Ziółkowska_2006
37 Zhong_2020 CryoDRGN: Reconstruction of heterogeneous structures from cryo-electron micrographs using neural networks Ellen D. Zhong; Tristan Bepler; Bonnie Berger; Joseph H Davis 2020 2020-03-29 BioRxiv N 10.1101/2020.03.27.003871 oohx14kl 0.634781 Liu_Z_2008 Jonić_2016, Punjani_2020, Pfab_2020, DiMaio_2016
38 Ritchie_2015 Probing the structural dynamics of proteins and nucleic acids with optical tweezers Ritchie, Dustin B; Woodside, Michael T 2015 2015-10-31 PMC N PMC7126019 26189090.0 10.1016/j.sbi.2015.06.006 tj3knwxi 0.619343 Ivarsson_2012, Chan_2016 Chan_2016, Myllykoski_2017, Shengjuler_2017, Moulaei_2010
39 Rahaman_2016 Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses Rahaman, Jordon; Siltberg-Liberles, Jessica 2016 2016-11-09 NONCOMM N PMC5203785 27797946.0 10.1093/gbe/evw246 pygykil7 0.612614
40 Bungard_2017 Foldability of a natural de novo evolved protein Bungard, Dixie; Copple, Jacob S.; Yan, Jing; Chhun, Jimmy J.; Kumirov, Vlad K.; Foy, Scott G.; Masel, Joanna; Wysocki, Vicki H.; Cordes, Matthew H. J. 2017 2017-11-01 PMC N PMC5677532 29033289.0 10.1016/j.str.2017.09.006 leeiuknr 0.611481
41 Uversky_2013 Under‐folded proteins: Conformational ensembles and their roles in protein folding, function, and pathogenesis Uversky, Vladimir N. 2013 2013-08-28 PMC N PMC7161862 23754493.0 10.1002/bip.22298 licb2qhi 0.588590 Ivarsson_2012, UNKNOWN_1987
42 Subramaniam_2016 Resolution advances in cryo-EM enable application to drug discovery Subramaniam, Sriram; Earl, Lesley A.; Falconieri, Veronica; Milne, Jacqueline L. S.; Egelman, Edward H. 2016 2016-12-01 PMC N PMC5154827 27552081.0 10.1016/j.sbi.2016.07.009 n6ett8uo 0.586560 Liu_Z_2008, DiMaio_2016 Jonić_2016, Robinson_2013, Effantin_2016, Wang_2013
43 Neuman_2014 Atlas of coronavirus replicase structure Neuman, Benjamin W.; Chamberlain, Peter; Bowden, Fern; Joseph, Jeremiah 2014 2014-12-19 PMC N PMC7114488 24355834.0 10.1016/j.virusres.2013.12.004 q5332l0s 0.578050 Liu_Z_2008 Sutton_2004
44 Heal_2018 Applying graph theory to protein structures: an Atlas of coiled coils Heal, Jack W; Bartlett, Gail J; Wood, Christopher W; Thomson, Andrew R; Woolfson, Derek N 2018 2018-10-01 COMM-USE N PMC6157074 29722888.0 10.1093/bioinformatics/bty347 pq1vaknj 0.574054 Apgar_2008
45 Zhang_2005 Putative structure and function of ORF3 in SARS coronavirus Zhang, Xue Wu; Yap, Yee Leng 2005 2005-02-28 PMC N PMC7113666 10.1016/j.theochem.2004.10.073 fzkxvr2e 0.571382 Liu_Z_2008 Nelson_2005
46 Kuhn_2006 From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase Kuhn, Daniel; Weskamp, Nils; Schmitt, Stefan; Hüllermeier, Eyke; Klebe, Gerhard 2006 2006-06-16 PMC N PMC7094329 16697007.0 10.1016/j.jmb.2006.04.024 h7leow0q 0.570409 Ivarsson_2012, Liu_Z_2008, Kinjo_2012 Myllykoski_2017, Ziółkowska_2006
47 DiMaio_2016 Chapter Ten Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps DiMaio, F.; Chiu, W. 2016 2016-12-31 None N PMC5103630 27572730.0 10.1016/bs.mie.2016.06.003 1voq7zxz 0.560633 Jonić_2016, Subramaniam_2016
48 Aouacheria_2015 Redefining the BH3 Death Domain as a ‘Short Linear Motif’ Aouacheria, Abdel; Combet, Christophe; Tompa, Peter; Hardwick, J. Marie 2015 2015-12-31 None N PMC5056427 26541461.0 10.1016/j.tibs.2015.09.007 gyon6hsj 0.555601 Ivarsson_2012, Choudhury_2017
49 Cai_C_2006 Prediction of Transmembrane Proteins from Their Primary Sequence by Support Vector Machine Approach Cai, C. Z.; Yuan, Q. F.; Xiao, H. G.; Liu, X. H.; Han, L. Y.; Chen, Y. Z. 2006 2006-01-01 PMC N PMC7121931 10.1007/11816102_56 rktwtqtq 0.545985 Lee_B_2009, Wang_2013
50 Nagae_2018 Biophysical Analyses for Probing Glycan-Protein Interactions Nagae, Masamichi; Yamaguchi, Yoshiki 2018 2018-11-28 PMC N PMC7153041 30484247.0 10.1007/978-981-13-2158-0_7 rzlfxfn7 0.541759 Liu_Z_2008 Voß_D_2009
51 Pandey_2016 Current strategies for protein production and purification enabling membrane protein structural biology Pandey, Aditya; Shin, Kyungsoo; Patterson, Robin E.; Liu, Xiang-Qin; Rainey, Jan K. 2016 2016-12-01 PMC N PMC5752365 27010607.0 10.1139/bcb-2015-0143 9k2z7xri 0.541421 Liu_Z_2008, Ivarsson_2012 Chen_2009
52 Loschwitz_2020 Chapter Seven Computer simulations of protein–membrane systems Loschwitz, Jennifer; Olubiyi, Olujide O.; Hub, Jochen S.; Strodel, Birgit; Poojari, Chetan S. 2020 2020-12-31 PMC N PMC7109768 32145948.0 10.1016/bs.pmbts.2020.01.001 h1kuzit7 0.538617 Liu_Z_2008 OuYang_2018
53 Clarkson_2009 Mesodynamics in the SARS nucleocapsid measured by NMR field cycling Clarkson, Michael W.; Lei, Ming; Eisenmesser, Elan Z.; Labeikovsky, Wladimir; Redfield, Alfred; Kern, Dorothee 2009 2009-07-30 NONCOMM N PMC2728245 19641854.0 10.1007/s10858-009-9347-6 zso72hho 0.535847 CAO_S_2012 Luo_H_2004, Vicente_2015, Ramírez-Sarmiento_2015
54 Azoitei_2012 Computational Design of High-Affinity Epitope Scaffolds by Backbone Grafting of a Linear Epitope Azoitei, Mihai L.; Ban, Yih-En Andrew; Julien, Jean-Philippe; Bryson, Steve; Schroeter, Alexandria; Kalyuzhniy, Oleksandr; Porter, Justin R.; Adachi, Yumiko; Baker, David; Pai, Emil F.; Schief, William R. 2012 2012-01-06 PMC N PMC7105911 22061265.0 10.1016/j.jmb.2011.10.003 eti90wxk 0.533406 Ivarsson_2012, Wang_2014, Kinjo_2012 Azoitei_2014, Irving_2010, Robinson_2013
55 Hänel_2005 Solution structure of the X4 protein coded by the SARS related coronavirus reveals an immunoglobulin like fold and suggests a binding activity to integrin I domains Hänel, Karen; Stangler, Thomas; Stoldt, Matthias; Willbold, Dieter 2005 2005-11-23 PMC N PMC7089389 16328780.0 10.1007/s11373-005-9043-9 4dbksw3l 0.532049 Ivarsson_2012, UNKNOWN_1987 Tsai_2010, Voß_D_2009
56 Bartlam_2007 Structural proteomics of the SARS coronavirus: a model response to emerging infectious diseases Bartlam, Mark; Xu, Yuanyuan; Rao, Zihe 2007 2007-08-07 PMC N PMC7088133 17680348.0 10.1007/s10969-007-9024-5 08yraaz7 0.529525
57 Bissaro_2020 Exploring the RNA-Recognition Mechanism Using Supervised Molecular Dynamics (SuMD) Simulations: Toward a Rational Design for Ribonucleic-Targeting Molecules? Bissaro, Maicol; Sturlese, Mattia; Moro, Stefano 2020 2020-02-27 COMM-USE N PMC7057144 32175307.0 10.3389/fchem.2020.00107 i2mac4xm 0.528433 Liu_Z_2008, Ivarsson_2012 Moulaei_2010, Kanitz_2019, Wang_2013
58 Robinson_2013 Max Bergmann lecture Protein epitope mimetics in the age of structural vaccinology‡ Robinson, John A 2013 2013-01-24 COMM-USE N PMC3592999 23349031.0 10.1002/psc.2482 njlqgih3 0.524484 Ivarsson_2012
59 Rossmann_2005 Combining X-Ray Crystallography and Electron Microscopy Rossmann, Michael G.; Morais, Marc C.; Leiman, Petr G.; Zhang, Wei 2005 2005-03-31 PMC N 15766536.0 10.1016/j.str.2005.01.005 qnh6tlnm 0.519563 DiMaio_2016
60 Vajda_2018 Cryptic binding sites on proteins: definition, detection, and druggability Vajda, Sandor; Beglov, Dmitri; Wakefield, Amanda E; Egbert, Megan; Whitty, Adrian 2018 2018-06-30 PMC N PMC6088748 29800865.0 10.1016/j.cbpa.2018.05.003 1csbxa8f 0.518736 Liu_Z_2008, Kirillova_2009
61 Pedro_2019 Smoothing membrane protein structure determination by initial upstream stage improvements Pedro, Augusto Quaresma; Queiroz, João António; Passarinha, Luís António 2019 2019-05-24 PMC N PMC7079970 31127356.0 10.1007/s00253-019-09873-1 3riv0oh3 0.503512 Liu_Z_2008 Pandey_2016, Faaberg_1996, Voß_D_2009
62 Jonić_2016 Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes Jonić, Slavica 2016 2016-10-14 COMM-USE N PMC5072154 27800126.0 10.1016/j.csbj.2016.10.002 toglzyci 0.500286 DiMaio_2016, Subramaniam_2016
63 Kolchanov_1996 Chemical and Computer Probing of RNA Structure 1 Kolchanov, N.A.; Titov, I.I.; Vlassova, I.E.; Vlassov, V.V. 1996 1996-12-31 PMC N 8650302.0 10.1016/s0079-6603(08)60144-0 xuxlw4c0 0.500192 Myllykoski_2017
64 Yamasaki_2019 ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow Yamasaki, Satoshi; Amemiya, Takayuki; Yabuki, Yukimitsu; Horimoto, Katsuhisa; Fukui, Kazuhiko 2019 2019-03-06 PMC N PMC7088279 30840170.0 10.1007/s10822-019-00195-y 7cwp2xbw 0.491186
65 Mascarenhas_2017 Understanding protein domain-swapping using structure-based models of protein folding Mascarenhas, Nahren Manuel; Gosavi, Shachi 2017 2017-09-30 PMC N PMC7127520 27867057.0 10.1016/j.pbiomolbio.2016.09.013 2paaybd0 0.478546 Ivarsson_2012, Kinjo_2012, Liu_Z_2008 Ziółkowska_2006, Hayashi_2016, Tong_2009
66 Das_J_2016 Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids Das, Jayanta Kumar; Das, Provas; Ray, Korak Kumar; Choudhury, Pabitra Pal; Jana, Siddhartha Sankar 2016 2016-12-08 COMM-USE N PMC5145171 27930687.0 10.1371/journal.pone.0167651 ifebw24e 0.478465 Ivarsson_2012 Das_J_2017
67 Sivanesam_2019 Pre-structured hydrophobic peptide β-strands: A universal amyloid trap? Sivanesam, Kalkena; Andersen, Niels 2019 2019-03-30 PMC N PMC7094768 30707943.0 10.1016/j.abb.2019.01.032 c6hqrnj2 0.477775 Ivarsson_2012, Kirillova_2009 Abad_2009, Robinson_2013, Ghosh_2015
68 Rettinger_2016 Examples of Applications of Electrophysiology Rettinger, Jürgen; Schwarz, Silvia; Schwarz, Wolfgang 2016 2016-06-03 PMC N PMC7123767 10.1007/978-3-319-30012-2_8 subm50ld 0.475583 Ivarsson_2012, Liu_Z_2008
69 Polanco_2018 On the Regularities of the Polar Profiles of Proteins Related to Ebola Virus Infection and their Functional Domains Polanco, Carlos; Samaniego Mendoza, José Lino; Buhse, Thomas; Uversky, Vladimir N.; Bañuelos Chao, Ingrid Paola; Bañuelos Cedano, Marcela Angola; Tavera, Fernando Michel; Tavera, Daniel Michel; Falconi, Manuel; Ponce de León, Abelardo Vela 2018 2018-03-06 PMC N PMC7090660 29511990.0 10.1007/s12013-018-0839-4 6tkrctgc 0.472268 UNKNOWN_1987, Callison_1999 Kumar_2013
70 Milanetti_2020 In-Silico evidence for two receptors based strategy of SARS-CoV-2 Edoardo Milanetti; Mattia Miotto; Lorenzo Di Rienzo; Michele Monti; Giorgio Gosti; Giancarlo Ruocco 2020 2020-03-27 BioRxiv Y 10.1101/2020.03.24.006197 ob37jivi 0.461116 Zhang_2009, Yap_Y_2005
71 Amacher_2020 Specificity in PDZ-peptide interaction networks: Computational analysis and review Amacher, Jeanine F.; Brooks, Lionel; Hampton, Thomas H.; Madden, Dean R. 2020 2020-12-31 None N PMC7138185 10.1016/j.yjsbx.2020.100022 gy8aata6 0.450310 Ivarsson_2012, Choudhury_2017 Liu_X_2019
72 Roy_K_2015 Chapter 10 Other Related Techniques Roy, Kunal; Kar, Supratik; Das, Rudra Narayan 2015 2015-12-31 PMC N PMC7149793 10.1016/b978-0-12-801505-6.00010-7 a9q0tcgz 0.448752 Liu_Z_2008 Zhang_2018
73 Badtke_2006 Combining genetic and biochemical approaches to identify functional molecular contact points Badtke, Matthew P.; Cao, Feng; Tavis, John E. 2006 2006-08-10 PMC N PMC1592461 17033698.0 10.1251/bpo121 yagdt1a2 0.445165
74 Kainosho_2017 Isotope-Aided Methods for Biological NMR Spectroscopy: Past, Present, and Future Kainosho, Masatsune; Miyanoiri, Yohei; Takeda, Mitsuhiro 2017 2017-07-24 PMC N PMC7122432 10.1007/978-981-10-5966-7_2 9hkg34u6 0.444742 Liu_Z_2008, Ivarsson_2012, Kinjo_2012 Miyanoiri_2018
75 Wu_G_2007 Prediction of mutations engineered by randomness in H5N1 hemagglutinins of influenza A virus Wu, G.; Yan, S. 2007 2007-11-02 PMC N PMC7088403 17973072.0 10.1007/s00726-007-0602-4 rx0os4ke 0.434429
76 Bahramali_2016 Chameleon sequences in neurodegenerative diseases Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali 2016 2016-03-25 None N PMC7124260 26920059.0 10.1016/j.bbrc.2016.01.187 yjn0egy6 0.432017 Callison_1999, UNKNOWN_1987 Wang_2013, Kumar_2013
77 Liu_Z_2013 Evidences for the unfolding mechanism of three-dimensional domain swapping Liu, Zhirong; Huang, Yongqi 2013 2013-01-17 PMC N PMC3595458 23238853.0 10.1002/pro.2209 ehd837s5 0.429387 Ivarsson_2012, Smith_2003, UNKNOWN_1987, Chang_2000 Hayashi_2016
78 Miyanoiri_2018 Stable-Isotope-Aided NMR Spectroscopy Miyanoiri, Yohei; Takeda, Mitsuhiro; Kainosho, Masatsune 2018 2018-02-09 PMC N PMC7123952 10.1007/978-3-319-28388-3_48 8sv9256h 0.427912 Takeda_2012, Liu_Z_2008 Kainosho_2017
79 Christensen_2019 PDZ Domains as Drug Targets Christensen, Nikolaj R.; Čalyševa, Jelena; Fernandes, Eduardo F. A.; Lüchow, Susanne; Clemmensen, Louise S.; Haugaard‐Kedström, Linda M.; Strømgaard, Kristian 2019 2019-04-24 PMC N PMC7161847 10.1002/adtp.201800143 0ac6rq14 0.426412 Ivarsson_2012, Choudhury_2017, Liu_X_2019
80 Ghosh_2015 Self-Assembly of a 9-Residue Amyloid-Forming Peptide Fragment of SARS Corona Virus E-protein: Mechanism of Self Aggregation and Amyloid-Inhibition of hIAPP Ghosh, Anirban; Pithadia, Amit S.; Bhat, Jyotsna; Bera, Supriyo; Midya, Anupam; Fierke, Carol A.; Ramamoorthy, Ayyalusamy; Bhunia, Anirban 2015 2015-03-24 PMC N PMC4903029 25785896.0 10.1021/acs.biochem.5b00061 b0v178qy 0.419095 Ivarsson_2012, Sivanesam_2019 Voß_D_2009, Guillén_2009, Abad_2009
81 Wang_2018 A Comprehensive In Silico Method to Study the QSTR of the Aconitine Alkaloids for Designing Novel Drugs Wang, Ming-Yang; Liang, Jing-Wei; Mohamed Olounfeh, Kamara; Sun, Qi; Zhao, Nan; Meng, Fan-Hao 2018 2018-09-18 COMM-USE N PMC6225272 30231506.0 10.3390/molecules23092385 fewy8y4a 0.415733 Liu_Z_2008
82 Pina_2014 Challenges and opportunities in the purification of recombinant tagged proteins Pina, Ana Sofia; Lowe, Christopher R.; Roque, Ana Cecília A. 2014 2014-04-30 PMC N PMC7125906 24334194.0 10.1016/j.biotechadv.2013.12.001 vlvu75mf 0.411756 Ivarsson_2012 Sadilkova_2008
83 Apgar_2008 Predicting helix orientation for coiled-coil dimers Apgar, James R.; Gutwin, Karl N.; Keating, Amy E. 2008 2008-05-27 PMC N PMC2562949 18506779.0 10.1002/prot.22118 l7p84aur 0.407117 Ivarsson_2012, Kinjo_2012 Lupas_2017, Deng_2006, McFarlane_2009
84 Singh_1999 LearnCoil-VMF: computational evidence for coiled-coil-like motifs in many viral membrane-fusion proteins 1 1 Edited by F. E. Cohen Singh, Mona; Berger, Bonnie; Kim, Peter S 1999 1999-07-30 PMC N PMC7125536 10438601.0 10.1006/jmbi.1999.2796 bdjiqym8 0.406874 Ivarsson_2012 Peisajovich_2000
85 Lupas_2017 The Structure and Topology of α-Helical Coiled Coils Lupas, Andrei N.; Bassler, Jens; Dunin-Horkawicz, Stanislaw 2017 2017-01-19 PMC N PMC7122542 28101860.0 10.1007/978-3-319-49674-0_4 g4mwhg7l 0.402841 Apgar_2008, Ivarsson_2012, Deng_2008 Apgar_2008, McFarlane_2009
86 Takeda_2012 1.12 Labeling Techniques Takeda, M.; Kainosho, M. 2012 2012-12-31 PMC N PMC7151895 10.1016/b978-0-12-374920-8.00116-8 cvib20ca 0.401240 DiMaio_2016 Miyanoiri_2018, Kainosho_2017
87 Bassetto_2016 Structural biology in antiviral drug discovery Bassetto, Marcella; Massarotti, Alberto; Coluccia, Antonio; Brancale, Andrea 2016 2016-10-31 PMC N 27611878.0 10.1016/j.coph.2016.08.014 3eoio8uk 0.398245 Ivarsson_2012, Liu_Z_2008 Robinson_2013
88 Fan_S_2009 Conformational changes in redox pairs of protein structures Fan, Samuel W; George, Richard A; Haworth, Naomi L; Feng, Lina L; Liu, Jason Y; Wouters, Merridee A 2009 2009-08-01 PMC N PMC2776962 19598234.0 10.1002/pro.175 d3gcfepx 0.396969 Ivarsson_2012, Langosch_2011, Smith_2003 Myllykoski_2017
89 Zaucha_2020 Deep learning model can predict water binding sites on the surface of proteins using limited-resolution data Jan Zaucha; Charlotte A. Softley; Michael Sattler; Grzegorz M. Popowicz 2020 2020-04-21 BioRxiv Y 10.1101/2020.04.20.050393 sy3n8v7f 0.386237 Kirillova_2009
90 Liu_L_2012 3.8 Protein and Nucleic Acid Folding: Domain Swapping in Proteins Liu, L.; Gronenborn, A.M. 2012 2012-12-31 PMC N PMC7152442 10.1016/b978-0-12-374920-8.00309-x n4nzocp5 0.384472 Ivarsson_2012, UNKNOWN_1987 Mascarenhas_2017, Tong_2009, Myllykoski_2017
91 Spiga_2003 Molecular modelling of S1 and S2 subunits of SARS coronavirus spike glycoprotein Spiga, Ottavia; Bernini, Andrea; Ciutti, Arianna; Chiellini, Stefano; Menciassi, Nicola; Finetti, Francesca; Causarono, Vincenza; Anselmi, Francesca; Prischi, Filippo; Niccolai, Neri 2003 2003-10-10 PMC N PMC7110993 14511651.0 10.1016/j.bbrc.2003.08.122 imyfo83x 0.375894 Callison_1999 Guillén_2009, Voß_D_2009, Shajahan_2020
92 Stehle_2003 Structural evidence for common functions and ancestry of the reovirus and adenovirus attachment proteins Stehle, Thilo; Dermody, Terence S. 2003 2003-02-28 PMC N PMC7169122 12627395.0 10.1002/rmv.379 zgoi2lkv 0.374363 Ivarsson_2012
93 Popot_1993 Integral membrane protein structure: transmembrane α-helices as autonomous folding domains Current opinion in structural biology 1993, 3: 532–540 Popot, Jean-Luc 1993 1993-08-31 PMC N PMC7126879 10.1016/0959-440x(93)90079-z cx0m54dd 0.364498 Ivarsson_2012, UNKNOWN_1987, UNKNOWN_1993, Modis_2013 Faaberg_1996, UNKNOWN_1995
94 Jin_F_2013 Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins Jin, Fan; Yu, Chen; Lai, Luhua; Liu, Zhirong 2013 2013-10-03 COMM-USE N PMC3789766 24098099.0 10.1371/journal.pcbi.1003249 5l0fthw3 0.362807 Ivarsson_2012, Smith_2003, Chan_2016, Kirillova_2009 Wang_2013, RAMAKRISHNA_2015, Liou_2014
95 Guo_H_2007 Computational studies for the structure and function of mRPE65 Guo, Hao; Zheng, Chong; Gaillard, Elizabeth R. 2007 2007-03-21 PMC N PMC7094118 17123547.0 10.1016/j.jtbi.2006.10.002 mfm96d2q 0.359370 Ivarsson_2012, Kirillova_2009, Liu_Z_2008 Myllykoski_2017, RAMAKRISHNA_2015
96 Doll_2015 Optimizing the design of protein nanoparticles as carriers for vaccine applications Doll, Tais A.P.F.; Neef, Tobias; Duong, Nha; Lanar, David E.; Ringler, Philippe; Müller, Shirley A.; Burkhard, Peter 2015 2015-10-31 None N PMC4587294 26051652.0 10.1016/j.nano.2015.05.003 mgi6aelt 0.356025
97 Punjani_2020 3D Variability Analysis: Directly resolving continuous flexibility and discrete heterogeneity from single particle cryo-EM images Ali Punjani; David J. Fleet 2020 2020-04-09 BioRxiv N 10.1101/2020.04.08.032466 yxo8oanc 0.355646 Liu_Z_2008 Zhong_2020, Jonić_2016, Punjani_2019, Effantin_2016
98 Kuzmanovic_2008 A novel application of small-angle scattering techniques: Quality assurance testing of virus quantification technology Kuzmanovic, Deborah A.; Elashvili, Ilya; O’Connell, Catherine; Krueger, Susan 2008 2008-03-31 PMC N PMC7127611 10.1016/j.radphyschem.2007.10.004 cz3ce29n 0.355275 Takeda_2012, DiMaio_2016, Molodenskiy_2019
99 Jankauskaitė_2019 SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation Jankauskaitė, Justina; Jiménez-García, Brian; Dapkūnas, Justas; Fernández-Recio, Juan; Moal, Iain H 2019 2019-02-01 COMM-USE N PMC6361233 30020414.0 10.1093/bioinformatics/bty635 vqiipbo8 0.353881 Ivarsson_2012, Callison_1999 Jankauskaitė_2018, Myllykoski_2017
100 Wu_G_2004 Reasoning of spike glycoproteins being more vulnerable to mutations among 158 coronavirus proteins from different species Wu, Guang; Yan, Shaomin 2004 2004-12-09 PMC N PMC7088192 15592899.0 10.1007/s00894-004-0210-0 1gsy43a0 0.350579 Callison_1999, UNKNOWN_1987, Chang_2000 Shajahan_2020
101 Sun_Z_2019 Developing Novel G-Quadruplex Ligands: From Interaction with Nucleic Acids to Interfering with Nucleic Acid–Protein Interaction Sun, Zhi-Yin; Wang, Xiao-Na; Cheng, Sui-Qi; Su, Xiao-Xuan; Ou, Tian-Miao 2019 2019-01-22 COMM-USE N PMC6384609 30678288.0 10.3390/molecules24030396 isvn3wji 0.350376 Ivarsson_2012 Scalabrin_2017
102 Chen_2009 Random dissection to select for protein split sites and its application in protein fragment complementation Chen, Yong; Li, Shuang; Chen, Tingjian; Hua, Hui; Lin, Zhanglin 2009 2009-02-01 PMC N PMC2708047 19165722.0 10.1002/pro.42 a6amhlzy 0.343456
103 Das_J_2017 Chemical property based sequence characterization of PpcA and its homolog proteins PpcB-E: A mathematical approach Das, Jayanta Kumar; Pal Choudhury, Pabitra 2017 2017-03-31 COMM-USE N PMC5376323 28362850.0 10.1371/journal.pone.0175031 2kpxhzbe 0.341367 Callison_1999
104 Woldring_2015 High-Throughput Ligand Discovery Reveals a Sitewise Gradient of Diversity in Broadly Evolved Hydrophilic Fibronectin Domains Woldring, Daniel R.; Holec, Patrick V.; Zhou, Hong; Hackel, Benjamin J. 2015 2015-09-18 None N PMC4575168 26383268.0 10.1371/journal.pone.0138956 6rt3ty64 0.338037 Ivarsson_2012, Kinjo_2012 Moulaei_2010
105 Lo_M_2014 Evolution and Structural Organization of the C Proteins of Paramyxovirinae Lo, Michael K.; Søgaard, Teit Max; Karlin, David G. 2014 2014-02-25 COMM-USE N PMC3934983 24587180.0 10.1371/journal.pone.0090003 vnafx1ng 0.337867 UNKNOWN_1987, Callison_1999
106 Gulzar_2020 Bioinformatics Study on Structural Protein of Severe Acute Respiratory Syndrome Coronavirus 2 (Sars-Cov-2) For Better Understanding the Vaccine Development Sumaira Gulzar; Saqib Hussain 2020 2020-04-21 BioRxiv Y 10.1101/2020.04.21.053199 ien7z5gd 0.336398 UNKNOWN_1987, Chang_2000
107 Wu_J_2012 Identification, Characterization and Application of a G-Quadruplex Structured DNA Aptamer against Cancer Biomarker Protein Anterior Gradient Homolog 2 Wu, Jie; Wang, Chi; Li, Xilan; Song, Yanling; Wang, Wei; Li, Cong; Hu, Jia; Zhu, Zhi; Li, Jiuxing; Zhang, Weiyun; Lu, Zhongxian; Yang, Chaoyong James 2012 2012-09-28 COMM-USE N PMC3460915 23029506.0 10.1371/journal.pone.0046393 rhsgqprf 0.333733 Ivarsson_2012, Tosoni_2015, Choudhury_2017
108 Liu_X_2019 Chapter Five Emerging Themes in PDZ Domain Signaling Structure, Function, and Inhibition Liu, Xu; Fuentes, Ernesto J. 2019 2019-12-31 PMC N 30712672.0 10.1016/bs.ircmb.2018.05.013 nfcolowc 0.331710 Ivarsson_2012, Smith_2003, Choudhury_2017
109 Vani_2009 Structural basis for the function of anti-idiotypic antibody in immune memory Vani, J.; Chatterjee, Jhinuk; Shaila, M.S.; Nayak, R.; Chandra, Nagasuma R. 2009 2009-03-31 PMC N PMC7126318 19157554.0 10.1016/j.molimm.2008.11.019 creoyran 0.331358 Ivarsson_2012
110 Rao_Z_2007 History of protein crystallography in China Rao, Zihe 2007 2007-02-27 PMC N PMC2435569 17327211.0 10.1098/rstb.2007.2032 k46ukxcr 0.329985
111 McFarlane_2009 The use of coiled-coil proteins in drug delivery systems McFarlane, Ainsley A.; Orriss, George L.; Stetefeld, Jörg 2009 2009-12-25 PMC N PMC7094320 19835864.0 10.1016/j.ejphar.2009.05.034 vvs512q6 0.329533 Ivarsson_2012, UNKNOWN_1987, Smith_2003, Chang_2000 Doll_2015
112 Thangapandian_2012 Structural Origins for the Loss of Catalytic Activities of Bifunctional Human LTA4H Revealed through Molecular Dynamics Simulations Thangapandian, Sundarapandian; John, Shalini; Lazar, Prettina; Choi, Sun; Lee, Keun Woo 2012 2012-07-25 COMM-USE N PMC3405069 22848428.0 10.1371/journal.pone.0041063 w9iwmqgq 0.323994 Ivarsson_2012, Smith_2003, Chan_2016, Choudhury_2017, UNKNOWN_1987 Kanitz_2019
113 Apellániz_2014 The three lives of viral fusion peptides Apellániz, Beatriz; Huarte, Nerea; Largo, Eneko; Nieva, José L. 2014 2014-07-31 None N PMC4061400 24704587.0 10.1016/j.chemphyslip.2014.03.003 08d6ed68 0.323070 Ivarsson_2012, UNKNOWN_1987, Modis_2013 Voß_D_2009, Guillén_2008, Peisajovich_2000
114 Uslupehlivan_2020 Glycoinformatics approach for identifying target positions to inhibit initial binding of SARS-CoV-2 S1 protein to the host cell Muhammet Uslupehlivan; Ecem Sener 2020 2020-03-25 BioRxiv Y 10.1101/2020.03.25.007898 x8jgcqts 0.313350 Ivarsson_2012, Callison_1999 Zhang_2009, Guillén_2009, Voß_D_2009
115 Zhang_2007 Computational characterization and design of SARS coronavirus receptor recognition and antibody neutralization Zhang, Yuan; Zheng, Nan; Zhong, Yang 2007 2007-04-30 PMC N PMC7106420 17374510.0 10.1016/j.compbiolchem.2007.02.005 maa8c4a4 0.311211 Ivarsson_2012, Liu_Z_2008
116 Huber_2018 New Antimicrobial Potential and Structural Properties of PAFB: A Cationic, Cysteine-Rich Protein from Penicillium chrysogenum Q176 Huber, Anna; Hajdu, Dorottya; Bratschun-Khan, Doris; Gáspári, Zoltán; Varbanov, Mihayl; Philippot, Stéphanie; Fizil, Ádám; Czajlik, András; Kele, Zoltán; Sonderegger, Christoph; Galgóczy, László; Bodor, Andrea; Marx, Florentine; Batta, Gyula 2018 2018-01-29 None N PMC5788923 29379111.0 10.1038/s41598-018-20002-2 gr8jj6b5 0.310823
117 Zhang_2018 Exploring the Binding Mechanism between Human Profilin (PFN1) and Polyproline-10 through Binding Mode Screening Leili Zhang; David R. Bell; Binquan Luan; Ruhong Zhou 2018 2018-09-16 BioRxiv N 10.1101/418830 40pe21lm 0.308786 Wang_2013, Yap_Y_2005
118 Abad_2009 Membrane topology of gp41 and amyloid precursor protein: Interfering transmembrane interactions as potential targets for HIV and Alzheimer treatment Abad, Concepción; Martínez-Gil, Luis; Tamborero, Silvia; Mingarro, Ismael 2009 2009-10-31 PMC N PMC7094694 19619504.0 10.1016/j.bbamem.2009.07.008 z4zt5873 0.307871 Ivarsson_2012, UNKNOWN_1987, Chang_2000, UNKNOWN_1993 Voß_D_2009, Chen_2009, Guillén_2009
119 Mebs_2010 A simple procedure for the derivation of electron density based surfaces of drug-receptor complexes from a combination of X-ray data and theoretical calculations Mebs, Stefan; Lüth, Anja; Luger, Peter 2010 2010-08-15 PMC N PMC7125671 20634077.0 10.1016/j.bmc.2010.06.080 t6rnpnfc 0.305660 Ivarsson_2012, Kinjo_2012, Liu_Z_2008 Li_G_2009
120 D’Annessa_2020 Differential Antibody Recognition by Novel SARS-CoV-2 and SARS-CoV Spike Protein Receptor Binding Domains: Mechanistic Insights and Implications for the Design of Diagnostics and Therapeutics Ilda D’Annessa; Filippo Marchetti; Giorgio Colombo 2020 2020-03-14 BioRxiv Y 10.1101/2020.03.13.990267 c08ptb1o 0.305060 Ivarsson_2012, Liu_Z_2008 Giron_2020
121 Rossmann_2011 Chapter 5 Future prospects Rossmann, Michael G.; Battisti, Anthony J.; Plevka, Pavel 2011 2011-12-31 PMC N 21501821.0 10.1016/b978-0-12-386507-6.00005-1 u0ycqelc 0.303115 DiMaio_2016, Subramaniam_2016
122 Azoitei_2014 Computational design of protein antigens that interact with the CDR H3 loop of HIV broadly neutralizing antibody 2F5 Azoitei, M.L.; Ban, Y.A.; Kalyuzhny, O.; Guenaga, J.; Schroeter, A.; Porter, J.; Wyatt, R.; Schief, W.R. 2014 2014-07-31 PMC N PMC4437801 25043744.0 10.1002/prot.24641 zgsqriz6 0.302051 Ivarsson_2012, Irving_2010, Zhou_2007, Dey_A_2009