Search Results - "Serra, Victoria Ruiz"

The structural coverage of the human proteome before and after AlphaFold by Porta-Pardo, Eduard, Ruiz-Serra, Victoria, Valentini, Samuel, Valencia, Alfonso

“…The protein structure field is experiencing a revolution. From the increased throughput of techniques to determine experimental structures, to developments…”
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Assessing the accuracy of contact and distance predictions in CASP14 by Ruiz‐Serra, Victoria, Pontes, Camila, Milanetti, Edoardo, Kryshtafovych, Andriy, Lepore, Rosalba, Valencia, Alfonso

“…We present the results of the assessment of the intramolecular residue–residue contact and distance predictions from groups participating in the 14th round of…”
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A structural biology community assessment of AlphaFold2 applications by Akdel, Mehmet, Pires, Douglas E. V., Pardo, Eduard Porta, Jänes, Jürgen, Zalevsky, Arthur O., Mészáros, Bálint, Bryant, Patrick, Good, Lydia L., Laskowski, Roman A., Pozzati, Gabriele, Shenoy, Aditi, Zhu, Wensi, Kundrotas, Petras, Serra, Victoria Ruiz, Rodrigues, Carlos H. M., Dunham, Alistair S., Burke, David, Borkakoti, Neera, Velankar, Sameer, Frost, Adam, Basquin, Jérôme, Lindorff-Larsen, Kresten, Bateman, Alex, Kajava, Andrey V., Valencia, Alfonso, Ovchinnikov, Sergey, Durairaj, Janani, Ascher, David B., Thornton, Janet M., Davey, Norman E., Stein, Amelie, Elofsson, Arne, Croll, Tristan I., Beltrao, Pedro

“…Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in…”
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Local energetic frustration conservation in protein families and superfamilies by Freiberger, Maria I., Ruiz-Serra, Victoria, Pontes, Camila, Romero-Durana, Miguel, Galaz-Davison, Pablo, Ramírez-Sarmiento, Cesar A., Schuster, Claudio D., Marti, Marcelo A., Wolynes, Peter G., Ferreiro, Diego U., Parra, R. Gonzalo, Valencia, Alfonso

“…Energetic local frustration offers a biophysical perspective to interpret the effects of sequence variability on protein families. Here we present a…”
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Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs by Pontes, Camila, Ruiz-Serra, Victoria, Lepore, Rosalba, Valencia, Alfonso

“…[Display omitted] •Specificity determining positions (SDPs) encode host-cell receptor usage in β-CoVs.•Mutations at SDPs show significantly larger impact on…”
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3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures by Ruiz-Serra, Victoria, Valentini, Samuel, Madroñero, Sergi, Valencia, Alfonso, Porta-Pardo, Eduard

“…Abstract Motivation The interpretation of genomic data is crucial to understand the molecular mechanisms of biological processes. Protein structures play a…”
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Pan-cancer proteogenomics connects oncogenic drivers to functional states by Porta-Pardo, Eduard, Bailey, Matthew H., Yaron, Tomer M., Stathias, Vasileios, Geffen, Yifat, Imbach, Kathleen J., Cao, Song, Anand, Shankara, Akiyama, Yo, Liu, Wenke, Wyczalkowski, Matthew A., Song, Yizhe, Storrs, Erik P., Wendl, Michael C., Zhang, Wubing, Sibai, Mustafa, Ruiz-Serra, Victoria, Terekhanova, Nadezhda V., Rodrigues, Fernanda Martins, Clauser, Karl R., Heiman, David I., Zhang, Qing, Aguet, Francois, Calinawan, Anna P., Birger, Chet, Satpathy, Shankha, Zhou, Daniel Cui, Wang, Liang-Bo, Baral, Jessika, Johnson, Jared L., Huntsman, Emily M., Pugliese, Pietro, Colaprico, Antonio, Iavarone, Antonio, Ricketts, Christopher J., Fenyö, David, Payne, Samuel H., Kumar-Sinha, Chandan, Lazar, Alexander J., Getz, Gad, An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Calinawan, Anna, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Selvan, Myvizhi Esai, Foltz, Steven M., Gonzalez Robles, Tania J., Gümüş, Zeynep H., Hiltke, Tara, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Lei, Jonathan T., Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Ma, Weiping, McKerrow, Wilson, Nesvizhskii, Alexey I., Oldroyd, Robert, Omenn, Gilbert S., Petralia, Francesca, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schadt, Eric E., Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Tan, Jimin, Wang, Joshua M., Wang, Pei, Wen, Bo, Wiznerowicz, Maciej, Yi, Xinpei, Zhang, Bing, Zhang, Xu, Zhang, Zhen

“…Cancer driver events refer to key genetic aberrations that drive oncogenesis; however, their exact molecular mechanisms remain insufficiently understood. Here,…”
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Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families by Parra, R Gonzalo, Freiberger, Maria I, Poley-Gil, Miriam, Fernandez-Martin, Miguel, Radusky, Leandro G, Ruiz-Serra, Victoria, Wolynes, Peter G, Ferreiro, Diego U, Valencia, Alfonso

“…According to the Principle of Minimal Frustration, folded proteins can only have a minimal number of strong energetic conflicts in their native states…”
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Analyzing sex imbalance in EGA and dbGaP biological databases: Recommendations for better practices by Ruiz-Serra, Victoria, Buslón, Nataly, Philippe, Olivier R., Saby, Diego, Morales, María, Pontes, Camila, Andirkó, Alejandro Muñoz, Holliday, Gemma L., Jené, Aina, Moldes, Mauricio, Rambla, Jordi, Valencia, Alfonso, Rementeria, María José, Cortés, Atia, Cirillo, Davide

“…Precision medicine aims at tailoring treatments to individual patient’s characteristics. In this regard, recognizing the significance of sex and gender becomes…”
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