| Year |
Citation |
Score |
| 2021 |
Orti F, Navarro AM, Rabinovich A, Wodak SJ, Marino-Buslje C. Insight into membraneless organelles and their associated proteins: Drivers, Clients and Regulators. Computational and Structural Biotechnology Journal. 19: 3964-3977. PMID 34377363 DOI: 10.1016/j.csbj.2021.06.042 |
0.311 |
|
| 2021 |
Farahi N, Lazar T, Wodak SJ, Tompa P, Pancsa R. Integration of Data from Liquid-Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers. International Journal of Molecular Sciences. 22. PMID 33809541 DOI: 10.3390/ijms22063017 |
0.75 |
|
| 2021 |
Turinsky AL, Dupont S, Botzki A, Razick S, Turner B, Donaldson IM, Wodak SJ. Navigating the Global Protein-Protein Interaction Landscape Using iRefWeb. Methods in Molecular Biology (Clifton, N.J.). 2199: 191-207. PMID 33125652 DOI: 10.1007/978-1-0716-0892-0_12 |
0.302 |
|
| 2020 |
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, et al. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000research. 9. PMID 32566135 DOI: 10.12688/F1000Research.20559.1 |
0.534 |
|
| 2020 |
Lazar T, Guharoy M, Vranken W, Rauscher S, Wodak SJ, Tompa P. Distance-Based Metrics for Comparing Conformational Ensembles of Intrinsically Disordered Proteins. Biophysical Journal. 118: 2952-2965. PMID 32502383 DOI: 10.1016/J.Bpj.2020.05.015 |
0.764 |
|
| 2020 |
Wodak SJ, Velankar S, Sternberg MJE. Modeling protein interactions and complexes in CAPRI 7 CAPRI evaluation meeting April 3-5 EMBL-EBI, Hinxton UK. Proteins. PMID 32077154 DOI: 10.1002/Prot.25883 |
0.374 |
|
| 2020 |
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AM, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, et al. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) F1000research. 9: 278. DOI: 10.12688/f1000research.20559.1 |
0.478 |
|
| 2019 |
Lensink MF, Nadzirin N, Velankar S, Wodak SJ. Modeling protein-protein, protein-peptide and protein-oligosaccharide complexes: CAPRI 7 edition. Proteins. PMID 31886916 DOI: 10.1002/Prot.25870 |
0.452 |
|
| 2019 |
Lensink MF, Brysbaert G, Nadzirin N, Velankar S, Chaleil RAG, Gerguri T, Bates PA, Laine E, Carbone A, Grudinin S, Kong R, Liu RR, Xu XM, Shi H, Chang S, ... ... Wodak SJ, et al. Blind prediction of homo- and hetero- protein complexes: The CASP13-CAPRI experiment. Proteins. PMID 31612567 DOI: 10.1002/Prot.25838 |
0.367 |
|
| 2019 |
Macossay-Castillo M, Marvelli G, Guharoy M, Jain A, Kihara D, Tompa P, Wodak SJ. The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity. Journal of Molecular Biology. PMID 30878482 DOI: 10.1016/J.Jmb.2019.03.008 |
0.779 |
|
| 2019 |
Wodak SJ, Paci E, Dokholyan NV, Berezovsky IN, Horovitz A, Li J, Hilser VJ, Bahar I, Karanicolas J, Stock G, Hamm P, Stote RH, Eberhardt J, Chebaro Y, Dejaegere A, et al. Allostery in Its Many Disguises: From Theory to Applications. Structure (London, England : 1993). PMID 30744993 DOI: 10.1016/J.Str.2019.01.003 |
0.302 |
|
| 2018 |
Costain G, Callewaert B, Gabriel H, Tan TY, Walker S, Christodoulou J, Lazar T, Menten B, Orkin J, Sadedin S, Snell M, Vanlander A, Vergult S, White SM, Scherer SW, ... ... Wodak SJ, et al. De novo missense variants in RAC3 cause a novel neurodevelopmental syndrome. Genetics in Medicine : Official Journal of the American College of Medical Genetics. PMID 30293988 DOI: 10.1038/S41436-018-0323-Y |
0.656 |
|
| 2018 |
Garton M, MacKinnon SS, Malevanets A, Wodak SJ. Interplay of self-association and conformational flexibility in regulating protein function. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 373. PMID 29735742 DOI: 10.1098/Rstb.2017.0190 |
0.412 |
|
| 2018 |
Schneider B, Orengo C, Schwede T, Sussman JL, Thornton JM, Velankar S, Wodak S. Coordination of structural bioinformatics activities across Europe Acta Crystallographica Section a Foundations and Advances. 74: e231-e231. DOI: 10.7490/F1000Research.1115607.1 |
0.504 |
|
| 2017 |
Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ. The challenge of modeling protein assemblies: The CASP12-CAPRI experiment. Proteins. PMID 29127686 DOI: 10.1002/Prot.25419 |
0.393 |
|
| 2017 |
Malevanets A, Chong PA, Hansen DF, Rizk P, Sun Y, Lin H, Muhandiram R, Chakrabartty A, Kay LE, Forman-Kay JD, Wodak SJ. Interplay of buried histidine protonation and protein stability in prion misfolding. Scientific Reports. 7: 882. PMID 28408762 DOI: 10.1038/S41598-017-00954-7 |
0.309 |
|
| 2016 |
Wodak SJ, Janin J. Modeling protein assemblies: CAPRI 15 years hence 6(th) CAPRI evaluation meeting April 17-19 Tel-Aviv Israel. Proteins. PMID 28019680 DOI: 10.1002/Prot.25233 |
0.318 |
|
| 2016 |
Molinski SV, Shahani VM, MacKinnon SS, Morayniss LD, Laforet M, Woollard G, Kurji N, Sanchez CG, Wodak SJ, Windemuth A. Computational proteome-wide screening predicts neurotoxic drug-protein interactome for the investigational analgesic BIA 10-2474. Biochemical and Biophysical Research Communications. PMID 28007597 DOI: 10.1016/J.Bbrc.2016.12.115 |
0.384 |
|
| 2016 |
Shukla AK, Wodak SJ. Editorial overview: Multi-protein assemblies in signaling. Current Opinion in Structural Biology. PMID 27889113 DOI: 10.1016/J.Sbi.2016.11.010 |
0.335 |
|
| 2016 |
Lensink MF, Velankar S, Wodak SJ. Modeling protein-protein and protein-peptide complexes: CAPRI 6(th) edition. Proteins. PMID 27865038 DOI: 10.1002/Prot.25215 |
0.445 |
|
| 2016 |
Schueler-Furman O, Wodak SJ. Computational approaches to investigating allostery. Current Opinion in Structural Biology. 41: 159-171. PMID 27607077 DOI: 10.1016/J.Sbi.2016.06.017 |
0.303 |
|
| 2016 |
Bohnuud T, Luo L, Wodak SJ, Bonvin AM, Weng Z, Vajda S, Schueler-Furman O, Kozakov D. A benchmark testing ground for integrating homology modeling and protein docking. Proteins. PMID 27172383 DOI: 10.1002/Prot.25063 |
0.472 |
|
| 2016 |
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, ... ... Wodak SJ, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007 |
0.422 |
|
| 2015 |
Wodak SJ, Malevanets A, MacKinnon SS. The Landscape of Intertwined Associations in Homooligomeric Proteins. Biophysical Journal. 109: 1087-100. PMID 26340815 DOI: 10.1016/J.Bpj.2015.08.010 |
0.413 |
|
| 2015 |
Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, ... ... Wodak SJ, et al. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nature Methods. PMID 26121405 DOI: 10.1038/Nmeth.3472 |
0.317 |
|
| 2015 |
Pu S, Vlasblom J, Turinsky A, Marcon E, Phanse S, Trimble SS, Olsen J, Greenblatt J, Emili A, Wodak SJ. Extracting high confidence protein interactions from affinity purification data: at the crossroads. Journal of Proteomics. 118: 63-80. PMID 25782749 DOI: 10.1016/J.Jprot.2015.03.009 |
0.351 |
|
| 2015 |
MacKinnon SS, Wodak SJ. Landscape of intertwined associations in multi-domain homo-oligomeric proteins. Journal of Molecular Biology. 427: 350-70. PMID 25451036 DOI: 10.1016/J.Jmb.2014.11.003 |
0.349 |
|
| 2014 |
Lensink MF, Wodak SJ. Score_set: a CAPRI benchmark for scoring protein complexes. Proteins. 82: 3163-9. PMID 25179222 DOI: 10.7490/F1000Research.1096787.1 |
0.346 |
|
| 2014 |
Marcon E, Ni Z, Pu S, Turinsky AL, Trimble SS, Olsen JB, Silverman-Gavrila R, Silverman-Gavrila L, Phanse S, Guo H, Zhong G, Guo X, Young P, Bailey S, Roudeva D, ... ... Wodak SJ, et al. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Cell Reports. 8: 297-310. PMID 24981860 DOI: 10.1016/J.Celrep.2014.05.050 |
0.438 |
|
| 2014 |
Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. Navigating the global protein-protein interaction landscape using iRefWeb. Methods in Molecular Biology (Clifton, N.J.). 1091: 315-31. PMID 24203342 DOI: 10.1007/978-1-62703-691-7_22 |
0.427 |
|
| 2014 |
Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, ... ... Wodak SJ, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/Prot.24439 |
0.367 |
|
| 2013 |
Lensink MF, Wodak SJ. Docking, scoring, and affinity prediction in CAPRI. Proteins. 81: 2082-95. PMID 24115211 DOI: 10.1002/Prot.24428 |
0.373 |
|
| 2013 |
Wodak SJ, Vlasblom J, Turinsky AL, Pu S. Protein-protein interaction networks: the puzzling riches. Current Opinion in Structural Biology. 23: 941-53. PMID 24007795 DOI: 10.1016/J.Sbi.2013.08.002 |
0.378 |
|
| 2013 |
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Wodak SJ, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/Prot.24356 |
0.375 |
|
| 2013 |
Mackinnon SS, Malevanets A, Wodak SJ. Intertwined associations in structures of homooligomeric proteins. Structure (London, England : 1993). 21: 638-49. PMID 23523426 DOI: 10.1016/J.Str.2013.01.019 |
0.458 |
|
| 2013 |
Wodak SJ, Garton M, Malevanets A, McKinnon S. 174 Self-association prompts proteins for new function: The role of altered dynamic properties Journal of Biomolecular Structure and Dynamics. 31: 112-112. DOI: 10.1080/07391102.2013.786416 |
0.394 |
|
| 2012 |
Babu M, Vlasblom J, Pu S, Guo X, Graham C, Bean BD, Burston HE, Vizeacoumar FJ, Snider J, Phanse S, Fong V, Tam YY, Davey M, Hnatshak O, Bajaj N, ... ... Wodak SJ, et al. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Nature. 489: 585-9. PMID 22940862 DOI: 10.1038/Nature11354 |
0.367 |
|
| 2012 |
Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, ... ... Wodak SJ, et al. A census of human soluble protein complexes. Cell. 150: 1068-81. PMID 22939629 DOI: 10.1016/J.Cell.2012.08.011 |
0.417 |
|
| 2012 |
Wodak SJ. Next-generation protein engineering targets influenza. Nature Biotechnology. 30: 502-4. PMID 22678386 DOI: 10.1038/Nbt.2268 |
0.322 |
|
| 2012 |
Wodak SJ, Vagin AA, Richelle J, Das U, Pontius J, Berman HM. Chapter 21.2 Assessing the quality of macromolecular structures International Tables For Crystallography. DOI: 10.1107/97809553602060000880 |
0.336 |
|
| 2011 |
Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Wodak SJ, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/J.Jmb.2011.09.031 |
0.731 |
|
| 2011 |
Leung E, Datti A, Cossette M, Goodreid J, McCaw SE, Mah M, Nakhamchik A, Ogata K, El Bakkouri M, Cheng YQ, Wodak SJ, Eger BT, Pai EF, Liu J, Gray-Owen S, et al. Activators of cylindrical proteases as antimicrobials: identification and development of small molecule activators of ClpP protease. Chemistry & Biology. 18: 1167-78. PMID 21944755 DOI: 10.1016/J.Chembiol.2011.07.023 |
0.314 |
|
| 2011 |
Wodak SJ, Vlasblom J, Pu S. High-throughput analyses and curation of protein interactions in yeast. Methods in Molecular Biology (Clifton, N.J.). 759: 381-406. PMID 21863499 DOI: 10.1007/978-1-61779-173-4_22 |
0.412 |
|
| 2011 |
Malevanets A, Wodak SJ. Multiple replica repulsion technique for efficient conformational sampling of biological systems. Biophysical Journal. 101: 951-60. PMID 21843487 DOI: 10.1016/J.Bpj.2011.06.043 |
0.38 |
|
| 2011 |
Hao Y, Merkoulovitch A, Vlasblom J, Pu S, Turinsky AL, Roudeva D, Turner B, Greenblatt J, Wodak SJ. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms. Bioinformatics (Oxford, England). 27: 883-4. PMID 21257609 DOI: 10.1093/Bioinformatics/Btr035 |
0.342 |
|
| 2011 |
Turinsky AL, Turner B, Borja RC, Gleeson JA, Heath M, Pu S, Switzer T, Dong D, Gong Y, On T, Xiong X, Emili A, Greenblatt J, Parkinson J, Zhang Z, ... Wodak SJ, et al. DAnCER: disease-annotated chromatin epigenetics resource. Nucleic Acids Research. 39: D889-94. PMID 20876685 DOI: 10.1093/Nar/Gkq857 |
0.375 |
|
| 2010 |
Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ. Literature curation of protein interactions: measuring agreement across major public databases. Database : the Journal of Biological Databases and Curation. 2010: baq026. PMID 21183497 DOI: 10.1093/Database/Baq026 |
0.387 |
|
| 2010 |
Turner B, Razick S, Turinsky AL, Vlasblom J, Crowdy EK, Cho E, Morrison K, Donaldson IM, Wodak SJ. iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence. Database : the Journal of Biological Databases and Curation. 2010: baq023. PMID 20940177 DOI: 10.1093/Database/Baq023 |
0.399 |
|
| 2010 |
Lensink MF, Wodak SJ. Blind predictions of protein interfaces by docking calculations in CAPRI. Proteins. 78: 3085-95. PMID 20839234 DOI: 10.1002/Prot.22850 |
0.409 |
|
| 2010 |
Lensink MF, Wodak SJ. Docking and scoring protein interactions: CAPRI 2009. Proteins. 78: 3073-84. PMID 20806235 DOI: 10.1002/Prot.22818 |
0.439 |
|
| 2010 |
Santos MA, Turinsky AL, Ong S, Tsai J, Berger MF, Badis G, Talukder S, Gehrke AR, Bulyk ML, Hughes TR, Wodak SJ. Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences. Nucleic Acids Research. 38: 7927-42. PMID 20705649 DOI: 10.1093/Nar/Gkq714 |
0.357 |
|
| 2010 |
Ogata K, Isomura T, Kawata S, Yamashita H, Kubodera H, Wodak SJ. Lead generation and optimization based on protein-ligand complementarity. Molecules (Basel, Switzerland). 15: 4382-400. PMID 20657448 DOI: 10.3390/Molecules15064382 |
0.397 |
|
| 2010 |
On T, Xiong X, Pu S, Turinsky A, Gong Y, Emili A, Zhang Z, Greenblatt J, Wodak SJ, Parkinson J. The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins. 78: 2075-89. PMID 20455264 DOI: 10.1002/Prot.22723 |
0.352 |
|
| 2010 |
Wodak SJ, Janin J. Analytical approximation to the accessible surface area of proteins. Proceedings of the National Academy of Sciences of the United States of America. 77: 1736-40. PMID 16592793 DOI: 10.1073/Pnas.77.4.1736 |
0.38 |
|
| 2009 |
Vlasblom J, Wodak SJ. Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. Bmc Bioinformatics. 10: 99. PMID 19331680 DOI: 10.1186/1471-2105-10-99 |
0.341 |
|
| 2009 |
Pu S, Wong J, Turner B, Cho E, Wodak SJ. Up-to-date catalogues of yeast protein complexes. Nucleic Acids Research. 37: 825-31. PMID 19095691 DOI: 10.1093/Nar/Gkn1005 |
0.379 |
|
| 2009 |
Wodak SJ, Pu S, Vlasblom J, Séraphin B. Challenges and rewards of interaction proteomics. Molecular & Cellular Proteomics : McP. 8: 3-18. PMID 18799807 DOI: 10.1074/Mcp.R800014-Mcp200 |
0.402 |
|
| 2008 |
Malevanets A, Sirota FL, Wodak SJ. Mechanism and energy landscape of domain swapping in the B1 domain of protein G. Journal of Molecular Biology. 382: 223-35. PMID 18588900 DOI: 10.1016/J.Jmb.2008.06.025 |
0.387 |
|
| 2008 |
Sirota FL, Héry-Huynh S, Maurer-Stroh S, Wodak SJ. Role of the amino acid sequence in domain swapping of the B1 domain of protein G. Proteins. 72: 88-104. PMID 18186476 DOI: 10.1002/Prot.21901 |
0.402 |
|
| 2008 |
Dessailly BH, Lensink MF, Orengo CA, Wodak SJ. LigASite--a database of biologically relevant binding sites in proteins with known apo-structures. Nucleic Acids Research. 36: D667-73. PMID 17933762 DOI: 10.1093/Nar/Gkm839 |
0.415 |
|
| 2007 |
Lensink MF, Méndez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins. 69: 704-18. PMID 17918726 DOI: 10.1002/Prot.21804 |
0.426 |
|
| 2007 |
Launay G, Mendez R, Wodak S, Simonson T. Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets. Bmc Bioinformatics. 8: 270. PMID 17662112 DOI: 10.1186/1471-2105-8-270 |
0.422 |
|
| 2007 |
Janin J, Wodak S. The third CAPRI assessment meeting Toronto, Canada, April 20-21, 2007. Structure (London, England : 1993). 15: 755-9. PMID 17637336 DOI: 10.1016/J.Str.2007.06.007 |
0.422 |
|
| 2007 |
Dessailly BH, Lensink MF, Wodak SJ. Relating destabilizing regions to known functional sites in proteins. Bmc Bioinformatics. 8: 141. PMID 17470296 DOI: 10.1186/1471-2105-8-141 |
0.413 |
|
| 2007 |
Pu S, Vlasblom J, Emili A, Greenblatt J, Wodak SJ. Identifying functional modules in the physical interactome of Saccharomyces cerevisiae. Proteomics. 7: 944-60. PMID 17370254 DOI: 10.1002/Pmic.200600636 |
0.392 |
|
| 2006 |
Simonis N, Gonze D, Orsi C, van Helden J, Wodak SJ. Modularity of the transcriptional response of protein complexes in yeast. Journal of Molecular Biology. 363: 589-610. PMID 16973176 DOI: 10.1016/J.Jmb.2006.06.024 |
0.309 |
|
| 2006 |
Billingsley G, Santhiya ST, Paterson AD, Ogata K, Wodak S, Hosseini SM, Manisastry SM, Vijayalakshmi P, Gopinath PM, Graw J, Héon E. CRYBA4, a novel human cataract gene, is also involved in microphthalmia. American Journal of Human Genetics. 79: 702-9. PMID 16960806 DOI: 10.1086/507712 |
0.341 |
|
| 2006 |
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, PeregrÃn-Alvarez JM, Shales M, Zhang X, Davey M, ... ... Wodak SJ, et al. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 440: 637-43. PMID 16554755 DOI: 10.1038/Nature04670 |
0.435 |
|
| 2006 |
Wodak SJ, Vagin AA, Richelle J, Das U, Pontius J, Berman HM. Assessing the quality of macromolecular structures International Tables For Crystallography. DOI: 10.1107/97809553602060000708 |
0.338 |
|
| 2005 |
Méndez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins. 60: 150-69. PMID 15981261 DOI: 10.1002/Prot.20551 |
0.428 |
|
| 2005 |
Güldener U, Münsterkötter M, Kastenmüller G, Strack N, van Helden J, Lemer C, Richelles J, Wodak SJ, García-Martínez J, Pérez-Ortín JE, Michael H, Kaps A, Talla E, Dujon B, André B, et al. CYGD: The Comprehensive Yeast Genome Database Nucleic Acids Research. 33. PMID 15608217 DOI: 10.1093/Nar/Gki053 |
0.334 |
|
| 2005 |
Jaramillo A, Wodak SJ. Computational protein design is a challenge for implicit solvation models. Biophysical Journal. 88: 156-71. PMID 15377512 DOI: 10.1529/Biophysj.104.042044 |
0.689 |
|
| 2004 |
Wodak SJ, Castura J, Orsi C. Integrative bioinformatics: making sense of the networks. Drug Discovery Today. Technologies. 1: 179-87. PMID 24981389 DOI: 10.1016/J.Ddtec.2004.10.001 |
0.318 |
|
| 2004 |
Giraldo J, De Maria L, Wodak SJ. Shift in nucleotide conformational equilibrium contributes to increased rate of catalysis of GpAp versus GpA in barnase. Proteins. 56: 261-76. PMID 15211510 DOI: 10.1002/Prot.20137 |
0.337 |
|
| 2004 |
Simonis N, van Helden J, Cohen GN, Wodak SJ. Transcriptional regulation of protein complexes in yeast. Genome Biology. 5: R33. PMID 15128447 DOI: 10.1186/Gb-2004-5-5-R33 |
0.306 |
|
| 2004 |
Wodak SJ, Méndez R. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Current Opinion in Structural Biology. 14: 242-9. PMID 15093840 DOI: 10.1016/J.Sbi.2004.02.003 |
0.468 |
|
| 2004 |
Ochagavía ME, Wodak S. Progressive combinatorial algorithm for multiple structural alignments: application to distantly related proteins. Proteins. 55: 436-54. PMID 15048834 DOI: 10.1002/Prot.10587 |
0.483 |
|
| 2004 |
Lemer C, Antezana E, Couche F, Fays F, Santolaria X, Janky R, Deville Y, Richelle J, Wodak SJ. The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Research. 32: D443-8. PMID 14681453 DOI: 10.1093/Nar/Gkh139 |
0.315 |
|
| 2004 |
Leplae R, Hebrant A, Wodak SJ, Toussaint A. ACLAME: a CLAssification of Mobile genetic Elements. Nucleic Acids Research. 32: D45-9. PMID 14681355 DOI: 10.1093/Nar/Gkh084 |
0.326 |
|
| 2003 |
Méndez R, Leplae R, De Maria L, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins. 52: 51-67. PMID 12784368 DOI: 10.1002/Prot.10393 |
0.447 |
|
| 2003 |
Janin J, Henrick K, Moult J, Eyck LT, Sternberg MJ, Vajda S, Vakser I, Wodak SJ. CAPRI: a Critical Assessment of PRedicted Interactions. Proteins. 52: 2-9. PMID 12784359 DOI: 10.1002/Prot.10381 |
0.467 |
|
| 2003 |
Wernisch L, Wodak SJ. Identifying structural domains in proteins. Methods of Biochemical Analysis. 44: 365-85. PMID 12647395 DOI: 10.1002/0471721204.Ch18 |
0.355 |
|
| 2003 |
Govaerts C, Bondue A, Springael JY, Olivella M, Deupi X, Le Poul E, Wodak SJ, Parmentier M, Pardo L, Blanpain C. Activation of CCR5 by chemokines involves an aromatic cluster between transmembrane helices 2 and 3. The Journal of Biological Chemistry. 278: 1892-903. PMID 12411445 DOI: 10.1074/Jbc.M205685200 |
0.357 |
|
| 2003 |
Ogata K, Jaramillo A, Cohen W, Briand JP, Connan F, Choppin J, Muller S, Wodak SJ. Automatic sequence design of major histocompatibility complex class I binding peptides impairing CD8+ T cell recognition. The Journal of Biological Chemistry. 278: 1281-90. PMID 12411444 DOI: 10.1074/Jbc.M206853200 |
0.62 |
|
| 2002 |
Wodak SJ, Janin J. Structural basis of macromolecular recognition. Advances in Protein Chemistry. 61: 9-73. PMID 12461820 DOI: 10.1016/S0065-3233(02)61001-0 |
0.317 |
|
| 2002 |
Janin J, Wodak SJ. Protein modules and protein-protein interaction. Introduction. Advances in Protein Chemistry. 61: 1-8. PMID 12461819 DOI: 10.1016/S0065-3233(02)61000-9 |
0.418 |
|
| 2002 |
Radresa O, Ogata K, Wodak S, Ruysschaert JM, Goormaghtigh E. Modeling the three-dimensional structure of H+-ATPase of Neurospora crassa. European Journal of Biochemistry / Febs. 269: 5246-58. PMID 12392557 DOI: 10.1046/J.1432-1033.2002.03236.X |
0.319 |
|
| 2002 |
Jaramillo A, Wernisch L, Héry S, Wodak SJ. Folding free energy function selects native-like protein sequences in the core but not on the surface. Proceedings of the National Academy of Sciences of the United States of America. 99: 13554-9. PMID 12368470 DOI: 10.1073/Pnas.212068599 |
0.688 |
|
| 2002 |
Ogata K, Wodak SJ. Conserved water molecules in MHC class-I molecules and their putative structural and functional roles. Protein Engineering. 15: 697-705. PMID 12364585 DOI: 10.1093/Protein/15.8.697 |
0.354 |
|
| 2002 |
Ochagavia ME, Richelle J, Wodak SJ. Advanced pairwise structure alignments of proteins and analysis of conformational changes. Bioinformatics (Oxford, England). 18: 637-40. PMID 12016063 DOI: 10.1093/Bioinformatics/18.4.637 |
0.438 |
|
| 2001 |
Jaramillo A, Wernisch L, Hery S, Wodak SJ. Automatic procedures for protein design. Combinatorial Chemistry & High Throughput Screening. 4: 643-59. PMID 11812260 DOI: 10.2174/1386207013330724 |
0.657 |
|
| 2001 |
Nadassy K, Tomás-Oliveira I, Alberts I, Janin J, Wodak SJ. Standard atomic volumes in double-stranded DNA and packing in protein--DNA interfaces. Nucleic Acids Research. 29: 3362-76. PMID 11504874 DOI: 10.1093/Nar/29.16.3362 |
0.346 |
|
| 2001 |
van Helden J, Naim A, Lemer C, Mancuso R, Eldridge M, Wodak SJ. From molecular activities and processes to biological function. Briefings in Bioinformatics. 2: 81-93. PMID 11465065 DOI: 10.1093/Bib/2.1.81 |
0.308 |
|
| 2001 |
Das U, Chen S, Fuxreiter M, Vaguine AA, Richelle J, Berman HM, Wodak SJ. Checking nucleic acid crystal structures. Acta Crystallographica. Section D, Biological Crystallography. 57: 813-28. PMID 11375501 DOI: 10.1107/S0907444901003936 |
0.322 |
|
| 2001 |
Govaerts C, Lefort A, Costagliola S, Wodak SJ, Ballesteros JA, Van Sande J, Pardo L, Vassart G. A conserved Asn in transmembrane helix 7 is an on/off switch in the activation of the thyrotropin receptor. The Journal of Biological Chemistry. 276: 22991-9. PMID 11312274 DOI: 10.1074/Jbc.M102244200 |
0.325 |
|
| 2001 |
Martins JC, Enassar M, Willem R, Wieruzeski JM, Lippens G, Wodak SJ. Solution structure of the main alpha-amylase inhibitor from amaranth seeds. European Journal of Biochemistry. 268: 2379-89. PMID 11298757 DOI: 10.1046/J.1432-1327.2001.02118.X |
0.368 |
|
| 2001 |
Govaerts C, Blanpain C, Deupi X, Ballet S, Ballesteros JA, Wodak SJ, Vassart G, Pardo L, Parmentier M. The TXP motif in the second transmembrane helix of CCR5. A structural determinant of chemokine-induced activation. The Journal of Biological Chemistry. 276: 13217-25. PMID 11278962 DOI: 10.1074/Jbc.M011670200 |
0.357 |
|
| 2001 |
van Helden J, Naim A, Mancuso R, Eldridge M, Wernisch L, Gilbert D, Wodak SJ. Representing and analysing molecular and cellular function using the computer. Biological Chemistry. 381: 921-35. PMID 11076023 DOI: 10.1515/Bc.2000.113 |
0.345 |
|
| 2001 |
Boutonnet N, Van Belle D, Wodak SJ. Influence of ligand binding on the conformation of Torpedo californica acetylcholinesterase Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 106: 10-21. DOI: 10.1007/S002140000226 |
0.33 |
|
| 2000 |
Wernisch L, Hery S, Wodak SJ. Automatic protein design with all atom force-fields by exact and heuristic optimization. Journal of Molecular Biology. 301: 713-36. PMID 10966779 DOI: 10.1006/Jmbi.2000.3984 |
0.4 |
|
| 2000 |
Van Belle D, De Maria L, Iurcu G, Wodak SJ. Pathways of ligand clearance in acetylcholinesterase by multiple copy sampling. Journal of Molecular Biology. 298: 705-26. PMID 10788331 DOI: 10.1006/Jmbi.2000.3698 |
0.331 |
|
| 1999 |
Morel N, Bon S, Greenblatt HM, Van Belle D, Wodak SJ, Sussman JL, Massoulié J, Silman I. Effect of mutations within the peripheral anionic site on the stability of acetylcholinesterase. Molecular Pharmacology. 55: 982-92. PMID 10347238 DOI: 10.1124/mol.55.6.982 |
0.444 |
|
| 1999 |
Wernisch L, Hunting M, Wodak SJ. Identification of structural domains in proteins by a graph heuristic. Proteins. 35: 338-52. PMID 10328269 DOI: 10.1002/(Sici)1097-0134(19990515)35:3<338::Aid-Prot8>3.0.Co;2-I |
0.416 |
|
| 1999 |
Vaguine AA, Richelle J, Wodak SJ. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallographica. Section D, Biological Crystallography. 55: 191-205. PMID 10089410 DOI: 10.1107/S0907444998006684 |
0.311 |
|
| 1999 |
Alberts IL, Nadassy K, Wodak SJ. Analysis of zinc binding sites in protein crystal structures. Protein Science : a Publication of the Protein Society. 7: 1700-16. PMID 10082367 DOI: 10.1002/Pro.5560070805 |
0.387 |
|
| 1999 |
Nadassy K, Wodak SJ, Janin J. Structural features of protein-nucleic acid recognition sites Biochemistry. 38: 1999-2017. PMID 10026283 DOI: 10.1021/Bi982362D |
0.422 |
|
| 1998 |
Giraldo J, Wodak SJ, van Belle D. Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods. Journal of Molecular Biology. 283: 863-82. PMID 9790845 DOI: 10.1006/Jmbi.1998.2139 |
0.319 |
|
| 1998 |
Wintjens R, Wodak SJ, Rooman M. Typical interaction patterns in alphabeta and betaalpha turn motifs. Protein Engineering. 11: 505-22. PMID 9740369 DOI: 10.1093/Protein/11.7.505 |
0.365 |
|
| 1996 |
Kocher JP, Prévost M, Wodak SJ, Lee B. Properties of the protein matrix revealed by the free energy of cavity formation. Structure (London, England : 1993). 4: 1517-29. PMID 8994976 DOI: 10.1016/S0969-2126(96)00157-8 |
0.421 |
|
| 1996 |
Pontius J, Richelle J, Wodak SJ. Deviations from standard atomic volumes as a quality measure for protein crystal structures. Journal of Molecular Biology. 264: 121-36. PMID 8950272 DOI: 10.1006/Jmbi.1996.0628 |
0.366 |
|
| 1996 |
Gray PM, Kemp GJ, Rawlings CJ, Brown NP, Sander C, Thornton JM, Orengo CM, Wodak SJ, Richelle J. Macromolecular structure information and databases. The EU BRIDGE Database Project Consortium. Trends in Biochemical Sciences. 21: 251-6. PMID 8755246 DOI: 10.1016/0968-0004(96)10037-2 |
0.304 |
|
| 1996 |
Rooman MJ, Wodak SJ. Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Engineering. 8: 849-58. PMID 8746722 DOI: 10.1093/Protein/8.9.849 |
0.412 |
|
| 1996 |
Lemer CM, Rooman MJ, Wodak SJ. Protein structure prediction by threading methods: evaluation of current techniques. Proteins. 23: 337-55. PMID 8710827 DOI: 10.1002/Prot.340230308 |
0.449 |
|
| 1996 |
Wodak SJ. Extending molecular systematics to the third dimension. Nature Structural Biology. 3: 575-8. PMID 8673597 DOI: 10.1038/Nsb0796-575 |
0.367 |
|
| 1996 |
Boutonnet NS, Rooman MJ, Ochagavia ME, Richelle J, Wodak SJ. Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins. Protein Engineering. 8: 647-62. PMID 8577694 DOI: 10.1093/Protein/8.7.647 |
0.43 |
|
| 1996 |
Wintjens RT, Rooman MJ, Wodak SJ. Automatic classification and analysis of alpha alpha-turn motifs in proteins. Journal of Molecular Biology. 255: 235-53. PMID 8568871 DOI: 10.1006/Jmbi.1996.0020 |
0.363 |
|
| 1996 |
Kajava AV, Vassart G, Wodak SJ. Modeling of the three-dimensional structure of proteins with the typical leucine-rich repeats. Structure (London, England : 1993). 3: 867-77. PMID 8535781 DOI: 10.1016/S0969-2126(01)00222-2 |
0.427 |
|
| 1995 |
Lippens G, Najib J, Wodak SJ, Tartar A. NMR sequential assignments and solution structure of chlorotoxin, a small scorpion toxin that blocks chloride channels. Biochemistry. 34: 13-21. PMID 7819188 DOI: 10.1021/Bi00001A003 |
0.32 |
|
| 1995 |
Pugliese L, Prevost M, Wodak SJ. Unfolding simulations of the 85-102 β-hairpin of barnase Journal of Molecular Biology. 251: 432-447. PMID 7650741 DOI: 10.1006/Jmbi.1995.0446 |
0.323 |
|
| 1995 |
Boutonnet NS, Rooman MJ, Wodak SJ. Automatic analysis of protein conformational changes by multiple linkage clustering. Journal of Molecular Biology. 253: 633-47. PMID 7473739 DOI: 10.1006/Jmbi.1995.0578 |
0.405 |
|
| 1994 |
Kocher JP, Rooman MJ, Wodak SJ. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. Journal of Molecular Biology. 235: 1598-613. PMID 8107094 DOI: 10.1006/Jmbi.1994.1109 |
0.443 |
|
| 1994 |
Pintar A, Chollet A, Bradshaw C, Chaffotte A, Cadieux C, Rooman MJ, Hallenga K, Knowles J, Goldberg M, Wodak SJ. Conformational properties of four peptides corresponding to alpha-helical regions of Rhodospirillum cytochrome c2 and bovine calcium binding protein. Biochemistry. 33: 11158-73. PMID 7727367 DOI: 10.1021/Bi00203A012 |
0.301 |
|
| 1994 |
Wintjens RT, Rooman MJ, Wodak SJ. Identification of Short Turn Motifs in Proteins Using Sequence and Structure Fingerprints Israel Journal of Chemistry. 34: 257-269. DOI: 10.1002/Ijch.199400030 |
0.447 |
|
| 1993 |
Janin J, Wodak SJ. The quaternary structure of carbonmonoxy hemoglobin Ypsilanti Proteins: Structure, Function and Genetics. 15: 1-4. PMID 8451234 DOI: 10.1002/Prot.340150102 |
0.303 |
|
| 1993 |
Lippens G, Hallenga K, Van Belle D, Wodak SJ, Nirmala NR, Hill P, Russell KC, Smith DD, Hruby VJ. Transfer nuclear Overhauser effect study of the conformation of oxytocin bound to bovine neurophysin I. Biochemistry. 32: 9423-34. PMID 8369312 DOI: 10.1021/Bi00087A022 |
0.402 |
|
| 1993 |
Wodak SJ, Rooman MJ. Generating and testing protein folds Current Opinion in Structural Biology. 3: 247-259. DOI: 10.1016/S0959-440X(05)80160-5 |
0.455 |
|
| 1992 |
Huysmans M, Richelle J, Wodak SJ. SESAM: a relational database for structure and sequence of macromolecules. Proteins. 11: 59-76. PMID 1961702 DOI: 10.1002/Prot.340110108 |
0.464 |
|
| 1992 |
Rooman MJ, Kocher JP, Wodak SJ. Extracting information on folding from the amino acid sequence: accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions. Biochemistry. 31: 10226-38. PMID 1420144 DOI: 10.1021/Bi00157A009 |
0.454 |
|
| 1992 |
Scheerlinck JPY, Lasters I, Claessens M, Maeyer MD, Pio F, Delhaise P, Wodak S. Recurrent αβ loop structures in TIM barrel motifs show a distinct pattern of conserved structural features Proteins. 12: 299-313. PMID 1374562 DOI: 10.1002/Prot.340120402 |
0.309 |
|
| 1992 |
Rooman MJ, Wodak SJ. Extracting information on folding from the amino acid sequence: consensus regions with preferred conformation in homologous proteins. Biochemistry. 31: 10239-49. PMID 1329944 DOI: 10.1021/Bi00157A010 |
0.47 |
|
| 1991 |
Rooman MJ, Wodak SJ. Weak correlation between predictive power of individual sequence patterns and overall prediction accuracy in proteins. Proteins. 9: 69-78. PMID 2017437 DOI: 10.1002/Prot.340090108 |
0.379 |
|
| 1991 |
Prevost M, Wodak SJ, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase. Proceedings of the National Academy of Sciences of the United States of America. 88: 10880-4. PMID 1961758 DOI: 10.1073/Pnas.88.23.10880 |
0.487 |
|
| 1991 |
Rooman MJ, Kocher JP, Wodak SJ. Prediction of protein backbone conformation based on seven structure assignments. Influence of local interactions. Journal of Molecular Biology. 221: 961-79. PMID 1942039 DOI: 10.1016/0022-2836(91)80186-X |
0.439 |
|
| 1991 |
Karplus M, Prévost M, Tidor B, Wodak S. Simulation analysis of the stability mutants R96H of bacteriophage T4 lysozyme and I96A of barnase. Ciba Foundation Symposium. 161: 63-74. PMID 1814697 DOI: 10.1002/9780470514146.ch5 |
0.398 |
|
| 1991 |
Prévost M, Wodak S, Tidor B, Karplus M. Contribution of the hydrophobic effect to protein stability : molecular dynamics simulations of the lie → Ala mutation in Barnase Journal De Chimie Physique. 88: 2727-2728. DOI: 10.1051/Jcp/1991882727 |
0.566 |
|
| 1990 |
Lasters I, Wodak SJ, Pio F. The design of idealized alpha/beta-barrels: analysis of beta-sheet closure requirements. Proteins. 7: 249-56. PMID 2362946 DOI: 10.1002/Prot.340070306 |
0.3 |
|
| 1990 |
Rooman MJ, Rodriguez J, Wodak SJ. Relations between protein sequence and structure and their significance. Journal of Molecular Biology. 213: 337-50. PMID 2342111 DOI: 10.1016/S0022-2836(05)80195-0 |
0.385 |
|
| 1990 |
Rooman MJ, Rodriguez J, Wodak SJ. Automatic definition of recurrent local structure motifs in proteins. Journal of Molecular Biology. 213: 327-36. PMID 2342110 DOI: 10.1016/S0022-2836(05)80194-9 |
0.356 |
|
| 1989 |
Claessens M, Van Cutsem E, Lasters I, Wodak S. Modelling the polypeptide backbone with 'spare parts' from known protein structures. Protein Engineering. 2: 335-45. PMID 2928296 DOI: 10.1093/Protein/2.5.335 |
0.412 |
|
| 1989 |
Rooman MJ, Wodak SJ, Thornton JM. Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power. Protein Engineering. 3: 23-7. PMID 2813339 DOI: 10.1093/Protein/3.1.23 |
0.398 |
|
| 1988 |
Rooman MJ, Wodak SJ. Identification of predictive sequence motifs limited by protein structure data base size. Nature. 335: 45-9. PMID 3412459 DOI: 10.1038/335045A0 |
0.442 |
|
| 1988 |
Lasters I, Wodak SJ, Alard P, van Cutsem E. Structural principles of parallel beta-barrels in proteins. Proceedings of the National Academy of Sciences of the United States of America. 85: 3338-42. PMID 3368445 DOI: 10.1073/Pnas.85.10.3338 |
0.341 |
|
| 1988 |
Rey F, Jenkins J, Janin J, Lasters I, Alard P, Claessens M, Matthyssens G, Wodak S. Structural analysis of the 2.8 A model of Xylose isomerase from Actinoplanes missouriensis Proteins. 4: 165-172. PMID 3237716 DOI: 10.1002/Prot.340040303 |
0.305 |
|
| 1988 |
Delhaise P, Bardiaux M, De Maeyer M, Prevost M, Van Belle D, Donneux J, Lasters I, Van Custem E, Alard P, Wodak S. The BRUGEL package: toward computer-aided design of macromolecules Journal of Molecular Graphics. 6: 219. DOI: 10.1016/S0263-7855(98)80028-3 |
0.385 |
|
| 1987 |
Wodak SJ. Computer-aided design in protein engineering. Annals of the New York Academy of Sciences. 501: 1-13. PMID 3475005 DOI: 10.1111/J.1749-6632.1987.Tb45678.X |
0.314 |
|
| 1987 |
Van Belle D, Couplet I, Prevost M, Wodak SJ. Calculations of electrostatic properties in proteins. Analysis of contributions from induced protein dipoles. Journal of Molecular Biology. 198: 721-35. PMID 3430627 DOI: 10.1016/0022-2836(87)90213-0 |
0.422 |
|
| 1985 |
Janin J, Wodak SJ. Reaction pathway for the quaternary structure change in hemoglobin. Biopolymers. 24: 509-26. PMID 3986294 DOI: 10.1002/Bip.360240307 |
0.362 |
|
| 1984 |
Delhaise P, Bardiaux M, Wodak S. Interactive computer animation of macromolecules Journal of Molecular Graphics. 2: 103-106. DOI: 10.1016/0263-7855(84)80002-8 |
0.313 |
|
| 1983 |
Janin J, Wodak SJ. Structural domains in proteins and their role in the dynamics of protein function. Progress in Biophysics and Molecular Biology. 42: 21-78. PMID 6353481 DOI: 10.1016/0079-6107(83)90003-2 |
0.314 |
|
| 1982 |
Wodak SJ, Janin J. Location of structural domains in protein. Biochemistry. 20: 6544-52. PMID 7306523 DOI: 10.1021/Bi00526A005 |
0.387 |
|
| 1979 |
Wodak SJ, Janin J. Computer analysis of protein-protein interaction. Journal of Molecular Biology. 124: 323-42. PMID 712840 DOI: 10.1016/0022-2836(78)90302-9 |
0.413 |
|
| 1975 |
Levinthal C, Wodak SJ, Kahn P, Dadivanian AK. Hemoglobin interaction in sickle cell fibers. I: Theoretical approaches to the molecular contacts. Proceedings of the National Academy of Sciences of the United States of America. 72: 1330-4. PMID 1055409 DOI: 10.1073/Pnas.72.4.1330 |
0.585 |
|
| 1973 |
Sussman JL, Wodak SJ. The crystal structure of fulvine: a pyrrolizidine alkaloid Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry. 29: 2918-2926. DOI: 10.1107/S0567740873007740 |
0.476 |
|
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