Search Results - "Punta, Marco"

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions by Mistry, Jaina, Finn, Robert D, Eddy, Sean R, Bateman, Alex, Punta, Marco

“…Detection of protein homology via sequence similarity has important applications in biology, from protein structure and function prediction to reconstruction…”
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The InterPro protein families database: the classification resource after 15 years by Mitchell, Alex, Chang, Hsin-Yu, Daugherty, Louise, Fraser, Matthew, Hunter, Sarah, Lopez, Rodrigo, McAnulla, Craig, McMenamin, Conor, Nuka, Gift, Pesseat, Sebastien, Sangrador-Vegas, Amaia, Scheremetjew, Maxim, Rato, Claudia, Yong, Siew-Yit, Bateman, Alex, Punta, Marco, Attwood, Teresa K, Sigrist, Christian J A, Redaschi, Nicole, Rivoire, Catherine, Xenarios, Ioannis, Kahn, Daniel, Guyot, Dominique, Bork, Peer, Letunic, Ivica, Gough, Julian, Oates, Matt, Haft, Daniel, Huang, Hongzhan, Natale, Darren A, Wu, Cathy H, Orengo, Christine, Sillitoe, Ian, Mi, Huaiyu, Thomas, Paul D, Finn, Robert D

“…The InterPro database (http://www.ebi.ac.uk/interpro/) is a freely available resource that can be used to classify sequences into protein families and to…”
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PredictProtein--an open resource for online prediction of protein structural and functional features by Yachdav, Guy, Kloppmann, Edda, Kajan, Laszlo, Hecht, Maximilian, Goldberg, Tatyana, Hamp, Tobias, Hönigschmid, Peter, Schafferhans, Andrea, Roos, Manfred, Bernhofer, Michael, Richter, Lothar, Ashkenazy, Haim, Punta, Marco, Schlessinger, Avner, Bromberg, Yana, Schneider, Reinhard, Vriend, Gerrit, Sander, Chris, Ben-Tal, Nir, Rost, Burkhard

“…PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a…”
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Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer by Woolston, Andrew, Khan, Khurum, Spain, Georgia, Barber, Louise J., Griffiths, Beatrice, Gonzalez-Exposito, Reyes, Hornsteiner, Lisa, Punta, Marco, Patil, Yatish, Newey, Alice, Mansukhani, Sonia, Davies, Matthew N., Furness, Andrew, Sclafani, Francesco, Peckitt, Clare, Jiménez, Mirta, Kouvelakis, Kyriakos, Ranftl, Romana, Begum, Ruwaida, Rana, Isma, Thomas, Janet, Bryant, Annette, Quezada, Sergio, Wotherspoon, Andrew, Khan, Nasir, Fotiadis, Nikolaos, Marafioti, Teresa, Powles, Thomas, Lise, Stefano, Calvo, Fernando, Guettler, Sebastian, von Loga, Katharina, Rao, Sheela, Watkins, David, Starling, Naureen, Chau, Ian, Sadanandam, Anguraj, Cunningham, David, Gerlinger, Marco

“…Despite biomarker stratification, the anti-EGFR antibody cetuximab is only effective against a subgroup of colorectal cancers (CRCs). This genomic and…”
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Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation by Russo, Elena Tea, Laio, Alessandro, Punta, Marco

“…The identification of protein families is of outstanding practical importance for in silico protein annotation and is at the basis of several bioinformatic…”
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Improved disorder prediction by combination of orthogonal approaches by Schlessinger, Avner, Punta, Marco, Yachdav, Guy, Kajan, Laszlo, Rost, Burkhard

“…Disordered proteins are highly abundant in regulatory processes such as transcription and cell-signaling. Different methods have been developed to predict…”
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The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function by Punta, Marco, Ofran, Yanay

“…  [...]although higher sequence similarity increases confidence in function annotation transfer, there is no threshold that can be considered safe. [...]in…”
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Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer by von Loga, Katharina, Woolston, Andrew, Punta, Marco, Barber, Louise J., Griffiths, Beatrice, Semiannikova, Maria, Spain, Georgia, Challoner, Benjamin, Fenwick, Kerry, Simon, Ronald, Marx, Andreas, Sauter, Guido, Lise, Stefano, Matthews, Nik, Gerlinger, Marco

“…Mismatch repair deficient (dMMR) gastro-oesophageal adenocarcinomas (GOAs) show better outcomes than their MMR-proficient counterparts and high immunotherapy…”
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DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets by Russo, Elena Tea, Barone, Federico, Bateman, Alex, Cozzini, Stefano, Punta, Marco, Laio, Alessandro

“…Proteins that are known only at a sequence level outnumber those with an experimental characterization by orders of magnitude. Classifying protein regions…”
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Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity by Heindl, Andreas, Khan, Adnan Mujahid, Rodrigues, Daniel Nava, Eason, Katherine, Sadanandam, Anguraj, Orbegoso, Cecilia, Punta, Marco, Sottoriva, Andrea, Lise, Stefano, Banerjee, Susana, Yuan, Yinyin

“…How tumor microenvironmental forces shape plasticity of cancer cell morphology is poorly understood. Here, we conduct automated histology image and spatial…”
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Natively unstructured regions in proteins identified from contact predictions by Schlessinger, Avner, Punta, Marco, Rost, Burkhard

“…Motivation: Natively unstructured (also dubbed intrinsically disordered) regions in proteins lack a defined 3D structure under physiological conditions and…”
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The Immunogenic Potential of Recurrent Cancer Drug Resistance Mutations: An In Silico Study by Punta, Marco, Jennings, Victoria A, Melcher, Alan A, Lise, Stefano

“…Cancer somatic mutations have been identified as a source of antigens that can be targeted by cancer immunotherapy. In this work, expanding on previous…”
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Homologue structure of the SLAC1 anion channel for closing stomata in leaves by Hendrickson, Wayne A, Chen, Yu-hang, Hu, Lei, Punta, Marco, Bruni, Renato, Hillerich, Brandan, Kloss, Brian, Rost, Burkhard, Love, James, Siegelbaum, Steven A

“…The plant SLAC1 anion channel controls turgor pressure in the aperture-defining guard cells of plant stomata, thereby regulating the exchange of water vapour…”
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Protein family annotation for the Unified Human Gastrointestinal Proteome by DPCfam clustering by Barone, Federico, Russo, Elena Tea, Villegas Garcia, Edith Natalia, Punta, Marco, Cozzini, Stefano, Ansuini, Alessio, Cazzaniga, Alberto

“…Technological advances in massively parallel sequencing have led to an exponential growth in the number of known protein sequences. Much of this growth…”
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T-cell receptor determinants of response to chemoradiation in locally-advanced HPV16-driven malignancies by Nenclares, Pablo, Larkeryd, Adrian, Manodoro, Floriana, Lee, Jen Y, Lalondrelle, Susan, Gilbert, Duncan C, Punta, Marco, O'Leary, Ben, Rullan, Antonio, Sadanandam, Anguraj, Chain, Benny, Melcher, Alan, Harrington, Kevin J, Bhide, Shreerang A

“…The effect of chemoradiation on the anti-cancer immune response is being increasingly acknowledged; however, its clinical implications in treatment responses…”
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Crystal structure of a potassium ion transporter, TrkH by Cao, Yu, Jin, Xiangshu, Huang, Hua, Derebe, Mehabaw Getahun, Levin, Elena J., Kabaleeswaran, Venkataraman, Pan, Yaping, Punta, Marco, Love, James, Weng, Jun, Quick, Matthias, Ye, Sheng, Kloss, Brian, Bruni, Renato, Martinez-Hackert, Erik, Hendrickson, Wayne A., Rost, Burkhard, Javitch, Jonathan A., Rajashankar, Kanagalaghatta R., Jiang, Youxing, Zhou, Ming

“…The TrkH/TrkG/KtrB proteins mediate K + uptake in bacteria and probably evolved from simple K + channels by multiple gene duplications or fusions. Here we…”
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Driver mutations in GNAQ and GNA11 genes as potential targets for precision immunotherapy in uveal melanoma patients by García-Mulero, Sandra, Fornelino, Roberto, Punta, Marco, Lise, Stefano, Varela, Mar, del Carpio, Luis P., Moreno, Rafael, Costa-García, Marcel, Rieder, Dietmar, Trajanoski, Zlatko, Gros, Alena, Alemany, Ramón, Piulats, Josep María, Sanz-Pamplona, Rebeca

“…Uveal melanoma (UM) is the most common ocular malignancy in adults. Nearly 95% of UM patients carry the mutually exclusive mutations in the homologous genes…”
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Protein Folding Rates Estimated from Contact Predictions by Punta, Marco, Rost, Burkhard

“…Folding rates of small single-domain proteins that fold through simple two-state kinetics can be estimated from details of the three-dimensional protein…”
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MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence by Lippi, Marco, Passerini, Andrea, Punta, Marco, Rost, Burkhard, Frasconi, Paolo

“…The web server MetalDetector classifies histidine residues in proteins into one of two states (free or metal bound) and cysteines into one of three states…”
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Author Correction: Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer by von Loga, Katharina, Woolston, Andrew, Punta, Marco, Barber, Louise J., Griffiths, Beatrice, Semiannikova, Maria, Spain, Georgia, Challoner, Benjamin, Fenwick, Kerry, Simon, Ronald, Marx, Andreas, Sauter, Guido, Lise, Stefano, Matthews, Nik, Gerlinger, Marco

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
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