Search Results - "Novotny, Marian"

PrankWeb: a web server for ligand binding site prediction and visualization by Jendele, Lukas, Krivak, Radoslav, Skoda, Petr, Novotny, Marian, Hoksza, David

“…PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free…”
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Secondary Structures of Proteins Follow Menzerath-Altmann Law by Matlach, Vladimír, Dostál, Daniel, Novotný, Marian

“…This article examines the presence of the empirical tendency known as the Menzerath-Altmann Law (MAL) on protein secondary structures. MAL is related to…”
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DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation by Quaglia, Federica, Mészáros, Bálint, Salladini, Edoardo, Hatos, András, Pancsa, Rita, Chemes, Lucía B, Pajkos, Mátyás, Lazar, Tamas, Peña-Díaz, Samuel, Santos, Jaime, Ács, Veronika, Farahi, Nazanin, Fichó, Erzsébet, Aspromonte, Maria Cristina, Bassot, Claudio, Chasapi, Anastasia, Davey, Norman E, Davidović, Radoslav, Dobson, Laszlo, Elofsson, Arne, Erdős, Gábor, Gaudet, Pascale, Giglio, Michelle, Glavina, Juliana, Iserte, Javier, Iglesias, Valentín, Kálmán, Zsófia, Lambrughi, Matteo, Leonardi, Emanuela, Longhi, Sonia, Macedo-Ribeiro, Sandra, Maiani, Emiliano, Marchetti, Julia, Marino-Buslje, Cristina, Mészáros, Attila, Monzon, Alexander Miguel, Minervini, Giovanni, Nadendla, Suvarna, Nilsson, Juliet F, Novotný, Marian, Ouzounis, Christos A, Palopoli, Nicolás, Papaleo, Elena, Pereira, Pedro José Barbosa, Pozzati, Gabriele, Promponas, Vasilis J, Pujols, Jordi, Rocha, Alma Carolina Sanchez, Salas, Martin, Sawicki, Luciana Rodriguez, Schad, Eva, Shenoy, Aditi, Szaniszló, Tamás, Tsirigos, Konstantinos D, Veljkovic, Nevena, Parisi, Gustavo, Ventura, Salvador, Dosztányi, Zsuzsanna, Tompa, Peter, Tosatto, Silvio C E, Piovesan, Damiano

“…Abstract The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of…”
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Positive selection and convergent evolution shape molecular phenotypic traits of innate immunity receptors in tits (Paridae) by Těšický, Martin, Velová, Hana, Novotný, Marian, Kreisinger, Jakub, Beneš, Vladimír, Vinkler, Michal

“…Despite widespread variability and redundancy abounding animal immunity, little is currently known about the rate of evolutionary convergence (functionally…”
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Divergent evolution drives high diversity of toll-like receptors (TLRs) in passerine birds: Buntings and finches by Włodarczyk, Radosław, Těšický, Martin, Vinkler, Michal, Novotný, Marian, Remisiewicz, Magdalena, Janiszewski, Tomasz, Minias, Piotr

“…Toll-like receptors (TLRs) form a key component of animal innate immunity, being responsible for recognition of conserved microbial structures. As such, TLRs…”
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SH3 domain tyrosine phosphorylation--sites, role and evolution by Tatárová, Zuzana, Brábek, Jan, Rösel, Daniel, Novotný, Marian

“…SH3 domains are eukaryotic protein domains that participate in a plethora of cellular processes including signal transduction, proliferation, and cellular…”
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Signatures of diversifying selection and convergence acting on passerine Toll‐like receptor 4 in an evolutionary context by Králová, Tereza, Albrecht, Tomáš, Bryja, Josef, Hořák, David, Johnsen, Arild, Lifjeld, Jan T., Novotný, Marian, Sedláček, Ondřej, Velová, Hana, Vinkler, Michal

“…Positive selection acting on Toll‐like receptors (TLRs) has been recently investigated to reveal evolutionary mechanisms of host–pathogen molecular…”
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The Diversity of Yellow-Related Proteins in Sand Flies (Diptera: Psychodidae) by Sima, Michal, Novotny, Marian, Pravda, Lukas, Sumova, Petra, Rohousova, Iva, Volf, Petr

“…Yellow-related proteins (YRPs) present in sand fly saliva act as affinity binders of bioamines, and help the fly to complete a bloodmeal by scavenging the…”
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Nineteen complex-related factor Prp45 is required for the early stages of cotranscriptional spliceosome assembly by Hálová, Martina, Gahura, Ondřej, Převorovský, Martin, Cit, Zdeněk, Novotný, Marian, Valentová, Anna, Abrhámová, Kateřina, Půta, František, Folk, Petr

“…Splicing in has been shown to proceed cotranscriptionally, but the nature of the coupling remains a subject of debate. Here, we examine the effect of nineteen…”
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A Novel Protein Acts as a Negative Regulator of Prophenoloxidase Activation and Melanization in the Freshwater Crayfish Pacifastacus leniusculus by Söderhäll, Irene, Wu, Chenglin, Novotny, Marian, Lee, Bok Luel, Söderhäll, Kenneth

“…Melanization is an important immune component of the innate immune system of invertebrates and is vital for defense as well as for wound healing. In most…”
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Reductive evolution of the mitochondrial processing peptidases of the unicellular parasites trichomonas vaginalis and giardia intestinalis by Smíd, Ondrej, Matusková, Anna, Harris, Simon R, Kucera, Tomás, Novotný, Marián, Horváthová, Lenka, Hrdý, Ivan, Kutejová, Eva, Hirt, Robert P, Embley, T Martin, Janata, Jirí, Tachezy, Jan

“…Mitochondrial processing peptidases are heterodimeric enzymes (alpha/betaMPP) that play an essential role in mitochondrial biogenesis by recognizing and…”
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Evaluation of protein fold comparison servers by Novotny, Marian, Madsen, Dennis, Kleywegt, Gerard J.

“…When a new protein structure has been determined, comparison with the database of known structures enables classification of its fold as new or belonging to a…”
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On the precision of calculated solvent-accessible surface areas by Novotny, Marian, Seibert, Marvin, Kleywegt, Gerard J.

“…The fact that protein structures are dynamic by nature and that structure models determined by X‐ray crystallography, electron microscopy (EM) and nuclear…”
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cpRAS: a novel circularly permuted RAS-like GTPase domain with a highly scattered phylogenetic distribution by Elias, Marek, Novotny, Marian

“…A recent systematic survey suggested that the YRG (or YawG/YlqF) family with the G4-G5-G1-G2-G3 order of the conserved GTPase motifs represents the only…”
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PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures by Jakubec, David, Skoda, Petr, Krivak, Radoslav, Novotny, Marian, Hoksza, David

“…Abstract Knowledge of protein–ligand binding sites (LBSs) enables research ranging from protein function annotation to structure-based drug design. To this…”
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Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis by Makki, Abhijith, Rada, Petr, Žárský, Vojtěch, Kereïche, Sami, Kováčik, Lubomír, Novotný, Marian, Jores, Tobias, Rapaport, Doron, Tachezy, Jan

“…Mitochondria originated from proteobacterial endosymbionts, and their transition to organelles was tightly linked to establishment of the protein import…”
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Cryptic binding site prediction with protein language models by Skrhak, Vit, Novotny, Marian, Riedlova, Kamila, Hoksza, David

“…Structure-based identification of protein-ligand binding sites plays a crucial role in the initial stages of rational drug discovery pipelines. As machine…”
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Tyrosine phosphorylation within the SH3 domain regulates CAS subcellular localization, cell migration, and invasiveness by Janoštiak, Radoslav, Tolde, Ondřej, Brůhová, Zuzana, Novotný, Marian, Hanks, Steven K, Rösel, Daniel, Brábek, Jan

“…Crk-associated substrate (CAS) is a major tyrosine-phosphorylated protein in cells transformed by v-crk and v-src oncogenes and plays an important role in…”
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Cathepsins B1 and B2 of Trichobilharzia SPP., bird schistosomes causing cercarial dermatitis by Kašný, Martin, Mikeš, Libor, Dolečková, Kateřina, Hampl, Vladimír, Dvořák, Jan, Novotný, Marian, Horák, Petr

“…Trichobilharzia regenti and T. szidati are schistosomes that infect birds. although T. regenti/T. szidati can only complete their life cycle in specific bird…”
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Structural characterization of CAS SH3 domain selectivity and regulation reveals new CAS interaction partners by Gemperle, Jakub, Hexnerová, Rozálie, Lepšík, Martin, Tesina, Petr, Dibus, Michal, Novotný, Marian, Brábek, Jan, Veverka, Václav, Rosel, Daniel

“…CAS is a docking protein downstream of the proto-oncogene Src with a role in invasion and metastasis of cancer cells. The CAS SH3 domain is indispensable for…”
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