Search Results - "Wodak, J"

Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition by Lensink, Marc F., Velankar, Sameer, Wodak, Shoshana J.

“…ABSTRACT We present the sixth report evaluating the performance of methods for predicting the atomic resolution structures of protein complexes offered as…”
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Docking, scoring, and affinity prediction in CAPRI by Lensink, Marc F., Wodak, Shoshana J.

“…ABSTRACT We present the fifth evaluation of docking and related scoring methods used in the community‐wide experiment on the Critical Assessment of Predicted…”
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Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition by Lensink, Marc F., Nadzirin, Nurul, Velankar, Sameer, Wodak, Shoshana J.

“…ABSTRACT We present the seventh report on the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to…”
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Docking and scoring protein interactions: CAPRI 2009 by Lensink, Marc F., Wodak, Shoshana J.

“…Protein docking algorithms are assessed by evaluating blind predictions performed during 2007–2009 in Rounds 13–19 of the community‐wide experiment on critical…”
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Allostery in Its Many Disguises: From Theory to Applications by Wodak, Shoshana J., Paci, Emanuele, Dokholyan, Nikolay V., Berezovsky, Igor N., Horovitz, Amnon, Li, Jing, Hilser, Vincent J., Bahar, Ivet, Karanicolas, John, Stock, Gerhard, Hamm, Peter, Stote, Roland H., Eberhardt, Jerome, Chebaro, Yassmine, Dejaegere, Annick, Cecchini, Marco, Changeux, Jean-Pierre, Bolhuis, Peter G., Vreede, Jocelyne, Faccioli, Pietro, Orioli, Simone, Ravasio, Riccardo, Yan, Le, Brito, Carolina, Wyart, Matthieu, Gkeka, Paraskevi, Rivalta, Ivan, Palermo, Giulia, McCammon, J. Andrew, Panecka-Hofman, Joanna, Wade, Rebecca C., Di Pizio, Antonella, Niv, Masha Y., Nussinov, Ruth, Tsai, Chung-Jung, Jang, Hyunbum, Padhorny, Dzmitry, Kozakov, Dima, McLeish, Tom

“…Allosteric regulation plays an important role in many biological processes, such as signal transduction, transcriptional regulation, and metabolism. Allostery…”
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The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment by Lensink, Marc F., Velankar, Sameer, Baek, Minkyung, Heo, Lim, Seok, Chaok, Wodak, Shoshana J.

“…We present the quality assessment of 5613 models submitted by predictor groups from both CAPRI and CASP for the total of 15 most tractable targets from the…”
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A Census of Human Soluble Protein Complexes by Havugimana, Pierre C., Hart, G. Traver, Nepusz, Tamás, Yang, Haixuan, Turinsky, Andrei L., Li, Zhihua, Wang, Peggy I., Boutz, Daniel R., Fong, Vincent, Phanse, Sadhna, Babu, Mohan, Craig, Stephanie A., Hu, Pingzhao, Wan, Cuihong, Vlasblom, James, Dar, Vaqaar-un-Nisa, Bezginov, Alexandr, Clark, Gregory W., Wu, Gabriel C., Wodak, Shoshana J., Tillier, Elisabeth R.M., Paccanaro, Alberto, Marcotte, Edward M., Emili, Andrew

“…Cellular processes often depend on stable physical associations between proteins. Despite recent progress, knowledge of the composition of human protein…”
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Integration of Data from Liquid-Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers by Farahi, Nazanin, Lazar, Tamas, Wodak, Shoshana J, Tompa, Peter, Pancsa, Rita

“…Liquid-liquid phase separation (LLPS) is a molecular process that leads to the formation of membraneless organelles, representing functionally specialized…”
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The Balancing Act of Intrinsically Disordered Proteins: Enabling Functional Diversity while Minimizing Promiscuity by Macossay-Castillo, Mauricio, Marvelli, Giulio, Guharoy, Mainak, Jain, Aashish, Kihara, Daisuke, Tompa, Peter, Wodak, Shoshana J.

“…Intrinsically disordered proteins (IDPs) or regions (IDRs) perform diverse cellular functions, but are also prone to forming promiscuous and potentially…”
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Docking and scoring protein complexes: CAPRI 3rd Edition by Lensink, Marc F., Méndez, Raúl, Wodak, Shoshana J.

“…The performance of methods for predicting protein–protein interactions at the atomic scale is assessed by evaluating blind predictions performed during…”
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The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies by Waman, Vaishali P, Sen, Neeladri, Varadi, Mihaly, Daina, Antoine, Wodak, Shoshana J, Zoete, Vincent, Velankar, Sameer, Orengo, Christine

“…Abstract SARS-CoV-2 is the causative agent of COVID-19, the ongoing global pandemic. It has posed a worldwide challenge to human health as no effective…”
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Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae by Babu, Mohan, Vlasblom, James, Pu, Shuye, Guo, Xinghua, Graham, Chris, Bean, Björn D. M., Burston, Helen E., Vizeacoumar, Franco J., Snider, Jamie, Phanse, Sadhna, Fong, Vincent, Tam, Yuen Yi C., Davey, Michael, Hnatshak, Olha, Bajaj, Navgeet, Chandran, Shamanta, Punna, Thanuja, Christopolous, Constantine, Wong, Victoria, Yu, Analyn, Zhong, Gouqing, Li, Joyce, Stagljar, Igor, Conibear, Elizabeth, Wodak, Shoshana J., Emili, Andrew, Greenblatt, Jack F.

“…A survey of 1,590 putative integral, peripheral and lipid-anchored membrane proteins from Saccharomyces cerevisiae reveals unexpected physical associations…”
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Blind predictions of protein interfaces by docking calculations in CAPRI by Lensink, Marc F., Wodak, Shoshana J.

“…Reliable prediction of the amino acid residues involved in protein–protein interfaces can provide valuable insight into protein function, and inform…”
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Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures by Méndez, Raúl, Leplae, Raphaël, Lensink, Marc F., Wodak, Shoshana J.

“…The current status of docking procedures for predicting protein–protein interactions starting from their three‐dimensional (3D) structure is reassessed by…”
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Assessment of blind predictions of protein-protein interactions: Current status of docking methods by Méndez, Raúl, Leplae, Raphaël, De Maria, Leonardo, Wodak, Shoshana J.

“…The current status of docking procedures for predicting protein–protein interactions starting from their three‐dimensional structure is assessed from a first…”
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Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways by Babu, Mohan, Díaz-Mejía, J Javier, Vlasblom, James, Gagarinova, Alla, Phanse, Sadhna, Graham, Chris, Yousif, Fouad, Ding, Huiming, Xiong, Xuejian, Nazarians-Armavil, Anaies, Alamgir, Md, Ali, Mehrab, Pogoutse, Oxana, Pe'er, Asaf, Arnold, Roland, Michaut, Magali, Parkinson, John, Golshani, Ashkan, Whitfield, Chris, Wodak, Shoshana J, Moreno-Hagelsieb, Gabriel, Greenblatt, Jack F, Emili, Andrew

“…As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis…”
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The Landscape of Intertwined Associations in Homooligomeric Proteins by Wodak, Shoshana J., Malevanets, Anatoly, MacKinnon, Stephen S.

“…We present an overview of the full repertoire of intertwined associations in homooligomeric proteins. This overview summarizes recent findings on the different…”
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CAPRI: A Critical Assessment of PRedicted Interactions by Janin, Joël, Henrick, Kim, Moult, John, Eyck, Lynn Ten, Sternberg, Michael J. E., Vajda, Sandor, Vakser, Ilya, Wodak, Shoshana J.

“…CAPRI is a communitywide experiment to assess the capacity of protein‐docking methods to predict protein–protein interactions. Nineteen groups participated in…”
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Insight into membraneless organelles and their associated proteins: Drivers, Clients and Regulators by Orti, Fernando, Navarro, Alvaro M., Rabinovich, Andres, Wodak, Shoshana J., Marino-Buslje, Cristina

“…[Display omitted] •Membraneless organelles (MLO) carry out a large number of functions within the cell.•LLPS databases focus on different aspects, representing…”
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Human-Chromatin-Related Protein Interactions Identify a Demethylase Complex Required for Chromosome Segregation by Marcon, Edyta, Ni, Zuyao, Pu, Shuye, Turinsky, Andrei L., Trimble, Sandra Smiley, Olsen, Jonathan B., Silverman-Gavrila, Rosalind, Silverman-Gavrila, Lorelei, Phanse, Sadhna, Guo, Hongbo, Zhong, Guoqing, Guo, Xinghua, Young, Peter, Bailey, Swneke, Roudeva, Denitza, Zhao, Dorothy, Hewel, Johannes, Li, Joyce, Gräslund, Susanne, Paduch, Marcin, Kossiakoff, Anthony A., Lupien, Mathieu, Emili, Andrew, Wodak, Shoshana J., Greenblatt, Jack

“…Chromatin regulation is driven by multicomponent protein complexes, which form functional modules. Deciphering the components of these modules and their…”
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