LIVIVO - The Search Portal for Life Sciences

zur deutschen Oberfläche wechseln
Advanced search

Search results

Result 1 - 10 of total 24

Search options

  1. Article ; Online: The ACPYPE web server for small-molecule MD topology generation.

    Kagami, Luciano / Wilter, Alan / Diaz, Adrian / Vranken, Wim

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 6

    Abstract: Motivation: The generation of parameter files for molecular dynamics (MD) simulations of small molecules that are suitable for force fields commonly applied to proteins and nucleic acids is often challenging. The ACPYPE software and website aid the ... ...

    Abstract Motivation: The generation of parameter files for molecular dynamics (MD) simulations of small molecules that are suitable for force fields commonly applied to proteins and nucleic acids is often challenging. The ACPYPE software and website aid the generation of such parameter files.
    Results: ACPYPE uses OpenBabel and ANTECHAMBER to generate MD input files in Gromacs, AMBER, CHARMM, and CNS formats. It can now take a SMILES string as input, in addition to the original PDB or mol2 coordinate files, with GAFF2 support and GLYCAM force field conversion added. It can be installed locally via Anaconda, PyPI, and Docker distributions, while the web server at https://bio2byte.be/acpype/ was updated with an API, and provides visualization of results for uploaded molecules as well as a pre-generated set of 3738 drug molecules.
    Availability and implementation: The web application is freely available at https://www.bio2byte.be/acpype/ and the open-source code can be found at https://github.com/alanwilter/acpype.
    MeSH term(s) Software ; Computers ; Proteins/metabolism ; Nucleic Acids ; Molecular Dynamics Simulation
    Chemical Substances Proteins ; Nucleic Acids
    Language English
    Publishing date 2023-05-30
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad350
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  2. Article ; Online: ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values.

    Orlando, Gabriele / Raimondi, Daniele / Kagami, Luciano Porto / Vranken, Wim F

    Nucleic acids research

    2020  Volume 48, Issue W1, Page(s) W36–W40

    Abstract: Nuclear magnetic resonance (NMR) spectroscopy data provides valuable information on the behaviour of proteins in solution. The primary data to determine when studying proteins are the per-atom NMR chemical shifts, which reflect the local environment of ... ...

    Abstract Nuclear magnetic resonance (NMR) spectroscopy data provides valuable information on the behaviour of proteins in solution. The primary data to determine when studying proteins are the per-atom NMR chemical shifts, which reflect the local environment of atoms and provide insights into amino acid residue dynamics and conformation. Within an amino acid residue, chemical shifts present multi-dimensional and complexly cross-correlated information, making them difficult to analyse. The ShiftCrypt method, based on neural network auto-encoder architecture, compresses the per-amino acid chemical shift information in a single, interpretable, amino acid-type independent value that reflects the biophysical state of a residue. We here present the ShiftCrypt web server, which makes the method readily available. The server accepts chemical shifts input files in the NMR Exchange Format (NEF) or NMR-STAR format, executes ShiftCrypt and visualises the results, which are also accessible via an API. It also enables the "biophysically-based" pairwise alignment of two proteins based on their ShiftCrypt values. This approach uses Dynamic Time Warping and can optionally include their amino acid code information, and has applications in, for example, the alignment of disordered regions. The server uses a token-based system to ensure the anonymity of the users and results. The web server is available at www.bio2byte.be/shiftcrypt.
    MeSH term(s) Amino Acids/chemistry ; Neural Networks, Computer ; Nuclear Magnetic Resonance, Biomolecular/methods ; Protein Denaturation ; Protein Folding ; Protein Unfolding ; Proteins/chemistry ; Software
    Chemical Substances Amino Acids ; Proteins
    Language English
    Publishing date 2020-05-27
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkaa391
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  3. Article ; Online: Exploring the N1 Position of Biginelli Compounds: New Insights and Trends for Chemical Diversity Generation of Bioactive Derivatives.

    Gonçalves, Itamar Luís / das Neves, Gustavo Machado / Kagami, Luciano Porto / Gonçalves, Guilherme Arraché / Davi, Leonardo / Eifler-Lima, Vera Lucia

    Mini reviews in medicinal chemistry

    2021  Volume 22, Issue 11, Page(s) 1545–1558

    Abstract: Dihydropyrimidinones (DHPMs) are heterocycles obtained by the multicomponent Biginelli reaction. Recently, new synthetic protocols have allowed us to explore functionalisation at less explored positions of DHPMs, such as the N1 position. In this context, ...

    Abstract Dihydropyrimidinones (DHPMs) are heterocycles obtained by the multicomponent Biginelli reaction. Recently, new synthetic protocols have allowed us to explore functionalisation at less explored positions of DHPMs, such as the N1 position. In this context, a full literature survey of N1- substituted DHPMs was performed. We analysed 27 papers and identified 379 compounds with substituents at the N1 position, most of them with alkyl groups, and a total of 28% compounds with aromatic substituents attached at the N1 position. N1-substituted DHPMs were explored mainly due to their effects on cancer cell proliferation via numerous targets, such as kinesin Eg5, heat shock protein 70, heat shock protein 90, and the epidermal growth factor receptor. Similarity analyses were performed using the data of 379 DHPMs from different cheminformatic approaches, i.e., chemical property correlations, principal component analysis, similarity networks, and compound clustering.
    MeSH term(s) Cell Proliferation ; Pyrimidinones/chemistry
    Chemical Substances Pyrimidinones
    Language English
    Publishing date 2021-10-26
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2104081-3
    ISSN 1875-5607 ; 1389-5575
    ISSN (online) 1875-5607
    ISSN 1389-5575
    DOI 10.2174/1389557521666211027105534
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 5891: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  4. Article ; Online: Online biophysical predictions for SARS-CoV-2 proteins.

    Kagami, Luciano / Roca-Martínez, Joel / Gavaldá-García, Jose / Ramasamy, Pathmanaban / Feenstra, K Anton / Vranken, Wim F

    BMC molecular and cell biology

    2021  Volume 22, Issue 1, Page(s) 23

    Abstract: Background: The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins ... ...

    Abstract Background: The SARS-CoV-2 virus, the causative agent of COVID-19, consists of an assembly of proteins that determine its infectious and immunological behavior, as well as its response to therapeutics. Major structural biology efforts on these proteins have already provided essential insights into the mode of action of the virus, as well as avenues for structure-based drug design. However, not all of the SARS-CoV-2 proteins, or regions thereof, have a well-defined three-dimensional structure, and as such might exhibit ambiguous, dynamic behaviour that is not evident from static structure representations, nor from molecular dynamics simulations using these structures. MAIN: We present a website ( https://bio2byte.be/sars2/ ) that provides protein sequence-based predictions of the backbone and side-chain dynamics and conformational propensities of these proteins, as well as derived early folding, disorder, β-sheet aggregation, protein-protein interaction and epitope propensities. These predictions attempt to capture the inherent biophysical propensities encoded in the sequence, rather than context-dependent behaviour such as the final folded state. In addition, we provide the biophysical variation that is observed in homologous proteins, which gives an indication of the limits of their functionally relevant biophysical behaviour.
    Conclusion: The https://bio2byte.be/sars2/ website provides a range of protein sequence-based predictions for 27 SARS-CoV-2 proteins, enabling researchers to form hypotheses about their possible functional modes of action.
    MeSH term(s) Databases, Protein ; Humans ; Internet Access ; SARS-CoV-2/chemistry ; Sequence Alignment ; Sequence Analysis, Protein ; Software ; Viral Proteins/chemistry ; Viral Proteins/metabolism
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2021-04-23
    Publishing country England
    Document type Journal Article
    ISSN 2661-8850
    ISSN (online) 2661-8850
    DOI 10.1186/s12860-021-00362-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  5. Article ; Online: LaSOM 335, active against bladder cancer cells, interferes with Let-60 (hRas) and reduces CD73 expression/activity.

    Kagami, Luciano Porto / Gonçalves, Itamar Luís / da Silva, Álisson Coldebella / Silva, Aline Castro / das Neves, Gustavo Machado / Göethel, Gabriela / Spillere, Adriano / Dos Santos, Maitê Roxo / Figueiró, Fabrício / Garcia, Solange Cristina / Ávila, Daiana Silva / Battastini, Ana Maria Oliveira / Eifler-Lima, Vera Lucia

    Chemical biology & drug design

    2023  Volume 102, Issue 3, Page(s) 536–546

    Abstract: Bladder cancer is the fourth most common malignancy in men. It can present along the entire continuum of severity, from mild to well-differentiated disease to extremely malignant tumors with low survival rates. Human RAS genes are the most frequently ... ...

    Abstract Bladder cancer is the fourth most common malignancy in men. It can present along the entire continuum of severity, from mild to well-differentiated disease to extremely malignant tumors with low survival rates. Human RAS genes are the most frequently mutated oncogenes in human cancers, and the critical role of aberrant Ras protein function in carcinogenesis is well established. Therefore, considerable efforts have been devoted to the development of anti-Ras inhibitors for cancer treatment. This study presents the biphenyl dihydropyrimidinone LaSOM 335 with high activity against T24 bladder cancer cells (IC
    MeSH term(s) Male ; Animals ; Humans ; Genes, ras ; Caenorhabditis elegans/genetics ; Caenorhabditis elegans/metabolism ; Cell Line, Tumor ; Urinary Bladder Neoplasms/drug therapy ; Urinary Bladder Neoplasms/metabolism ; 5'-Nucleotidase/genetics ; 5'-Nucleotidase/metabolism ; Mammals/genetics ; Mammals/metabolism
    Chemical Substances diphenyl (2L9GJK6MGN) ; 5'-Nucleotidase (EC 3.1.3.5)
    Language English
    Publishing date 2023-06-05
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2216600-2
    ISSN 1747-0285 ; 1747-0277
    ISSN (online) 1747-0285
    ISSN 1747-0277
    DOI 10.1111/cbdd.14273
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  6. Article ; Online: Targeting pteridine reductase 1 and dihydrofolate reductase: the old is a new trend for leishmaniasis drug discovery.

    das Neves, Gustavo Machado / Kagami, Luciano P / Gonçalves, Itamar L / Eifler-Lima, Vera L

    Future medicinal chemistry

    2019  Volume 11, Issue 16, Page(s) 2107–2130

    Abstract: Leishmaniasis is one of the major neglected tropical diseases in the world and it is considered endemic in 88 countries. This disease is transmitted by ... ...

    Abstract Leishmaniasis is one of the major neglected tropical diseases in the world and it is considered endemic in 88 countries. This disease is transmitted by a
    MeSH term(s) Animals ; Antiprotozoal Agents/chemistry ; Antiprotozoal Agents/pharmacology ; Antiprotozoal Agents/therapeutic use ; Drug Discovery ; Folic Acid Antagonists/chemistry ; Folic Acid Antagonists/pharmacology ; Folic Acid Antagonists/therapeutic use ; Humans ; Leishmania/drug effects ; Leishmania/enzymology ; Leishmania/metabolism ; Leishmaniasis/drug therapy ; Leishmaniasis/parasitology ; Molecular Targeted Therapy ; Multienzyme Complexes/antagonists & inhibitors ; Multienzyme Complexes/metabolism ; Oxidoreductases/antagonists & inhibitors ; Oxidoreductases/metabolism ; Tetrahydrofolate Dehydrogenase/metabolism ; Thymidylate Synthase/antagonists & inhibitors ; Thymidylate Synthase/metabolism
    Chemical Substances Antiprotozoal Agents ; Folic Acid Antagonists ; Multienzyme Complexes ; thymidylate synthase-dihydrofolate reductase ; Oxidoreductases (EC 1.-) ; pteridine reductase (EC 1.1.1.33) ; Tetrahydrofolate Dehydrogenase (EC 1.5.1.3) ; Thymidylate Synthase (EC 2.1.1.45)
    Language English
    Publishing date 2019-08-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 1756-8927
    ISSN (online) 1756-8927
    DOI 10.4155/fmc-2018-0512
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  7. Article ; Online: Geo-Measures: A PyMOL plugin for protein structure ensembles analysis.

    Kagami, Luciano Porto / das Neves, Gustavo Machado / Timmers, Luís Fernando Saraiva Macedo / Caceres, Rafael Andrade / Eifler-Lima, Vera Lucia

    Computational biology and chemistry

    2020  Volume 87, Page(s) 107322

    Abstract: Although molecular dynamics encompasses several applications, studies focusing on biomolecular systems are central issues of this research area. Such simulations require the generation of trajectory files, which provide a path for the analysis and ... ...

    Abstract Although molecular dynamics encompasses several applications, studies focusing on biomolecular systems are central issues of this research area. Such simulations require the generation of trajectory files, which provide a path for the analysis and interpretation of results with biological significance. However, although several programs have been developed in Python language for the analyses of molecular dynamics (MD) trajectories, they usually require some knowledge of programming languages in order to write or run the scripts using command lines, which certainly hinders the access of MD simulations to many scientists with the necessary biological background to interpret their results. To ease the access to Python packages focusing on MD trajectory analyses, we built a user-friendly and easy-to-install graphical PyMOL interface. Geo-Measures integrates the PyMOL functionalities with MDTraj, a powerful library of trajectory analyses, allowing the users to access up to 14 different types of analyses. Two sample cases are reported here to demonstrate the use of Geo-Measures. In the first example, which involves the use a MD trajectory file of hemoglobin from the MoDEL MD bank, we exemplified the analyses of the following variables: root mean square deviation, radius of gyration, free energy landscape and principal component analysis. In the second case, we built a trajectory file for the ecto-5'-nucleotidase using the LiGRO program to study the carbon alpha pincer angles, to define the secondary structure of the proteins and to analyze the Modevectors. This user-friendly graphical PyMOL plugin, which can be used to generate several descriptive analyses for protein structures, is open source and can be downloaded at: https://pymolwiki.org/index.php/Geo_Measures_Plugin.
    Language English
    Publishing date 2020-06-24
    Publishing country England
    Document type Journal Article
    ISSN 1476-928X
    ISSN (online) 1476-928X
    DOI 10.1016/j.compbiolchem.2020.107322
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

  8. Article ; Online: Discovery, development, chemical diversity and design of isoxazoline-based insecticides.

    Gonçalves, Itamar Luís / Machado das Neves, Gustavo / Porto Kagami, Luciano / Eifler-Lima, Vera Lucia / Merlo, Aloir Antonio

    Bioorganic & medicinal chemistry

    2020  Volume 30, Page(s) 115934

    Abstract: Isoxazoline is a 5-membered heterocycle present in the active compounds of many commercial veterinary anti-ectoparasitic products. The molecular target of isoxazolines is the inhibition of GABA-gated chloride channels in insects. These facts have ... ...

    Abstract Isoxazoline is a 5-membered heterocycle present in the active compounds of many commercial veterinary anti-ectoparasitic products. The molecular target of isoxazolines is the inhibition of GABA-gated chloride channels in insects. These facts have inspired the use of the isoxazoline scaffold in the design of novel insecticide compounds. The main strategies used for isoxazoline synthesis are either the 1,3-dipolar cycloaddition between a nitrile oxide and an alkene or the reaction between hydroxylamine and an α,β-unsaturated carbonyl compound. This review highlights the utilization of isoxazoline as insecticide: its mode of action, its commercial preparations and its consideration in the design of novel insecticides. Similarity analyses were performed with 235 isoxazoline derivatives in three different cheminformatic approaches - chemical property correlations, similarity network and compound clustering. The cheminformatic methodologies are interesting tools to use in evaluating the similarity between commercial isoxazolines and to clarify the main features explored within their derivatives.
    MeSH term(s) Animals ; Drug Development ; Insecta/drug effects ; Insecticides/chemical synthesis ; Insecticides/chemistry ; Insecticides/pharmacology ; Isoxazoles/chemical synthesis ; Isoxazoles/chemistry ; Isoxazoles/pharmacology ; Molecular Structure ; Receptors, GABA/metabolism
    Chemical Substances Insecticides ; Isoxazoles ; Receptors, GABA
    Language English
    Publishing date 2020-12-09
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 1161284-8
    ISSN 1464-3391 ; 0968-0896
    ISSN (online) 1464-3391
    ISSN 0968-0896
    DOI 10.1016/j.bmc.2020.115934
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 3815: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  9. Article ; Online: Trans-acting genetic variants causing multilocus imprinting disturbance (MLID): common mechanisms and consequences.

    Eggermann, Thomas / Yapici, Elzem / Bliek, Jet / Pereda, Arrate / Begemann, Matthias / Russo, Silvia / Tannorella, Pierpaola / Calzari, Luciano / de Nanclares, Guiomar Perez / Lombardi, Paola / Temple, I Karen / Mackay, Deborah / Riccio, Andrea / Kagami, Masayo / Ogata, Tsutomu / Lapunzina, Pablo / Monk, David / Maher, Eamonn R / Tümer, Zeynep

    Clinical epigenetics

    2022  Volume 14, Issue 1, Page(s) 41

    Abstract: Background: Imprinting disorders are a group of congenital diseases which are characterized by molecular alterations affecting differentially methylated regions (DMRs). To date, at least twelve imprinting disorders have been defined with overlapping but ...

    Abstract Background: Imprinting disorders are a group of congenital diseases which are characterized by molecular alterations affecting differentially methylated regions (DMRs). To date, at least twelve imprinting disorders have been defined with overlapping but variable clinical features including growth and metabolic disturbances, cognitive dysfunction, abdominal wall defects and asymmetry. In general, a single specific DMR is affected in an individual with a given imprinting disorder, but there are a growing number of reports on individuals with so-called multilocus imprinting disturbances (MLID), where aberrant imprinting marks (most commonly loss of methylation) occur at multiple DMRs. However, as the literature is fragmented, we reviewed the molecular and clinical data of 55 previously reported or newly identified MLID families with putative pathogenic variants in maternal effect genes (NLRP2, NLRP5, NLRP7, KHDC3L, OOEP, PADI6) and in other candidate genes (ZFP57, ARID4A, ZAR1, UHRF1, ZNF445).
    Results: In 55 families, a total of 68 different candidate pathogenic variants were identified (7 in NLRP2, 16 in NLRP5, 7 in NLRP7, 17 in PADI6, 15 in ZFP57, and a single variant in each of the genes ARID4A, ZAR1, OOEP, UHRF1, KHDC3L and ZNF445). Clinical diagnoses of affected offspring included Beckwith-Wiedemann syndrome spectrum, Silver-Russell syndrome spectrum, transient neonatal diabetes mellitus, or they were suspected for an imprinting disorder (undiagnosed). Some families had recurrent pregnancy loss.
    Conclusions: Genomic maternal effect and foetal variants causing MLID allow insights into the mechanisms behind the imprinting cycle of life, and the spatial and temporal function of the different factors involved in oocyte maturation and early development. Further basic research together with identification of new MLID families will enable a better understanding of the link between the different reproductive issues such as recurrent miscarriages and preeclampsia in maternal effect variant carriers/families and aneuploidy and the MLID observed in the offsprings. The current knowledge can already be employed in reproductive and genetic counselling in specific situations.
    MeSH term(s) Adaptor Proteins, Signal Transducing/genetics ; Beckwith-Wiedemann Syndrome/genetics ; CCAAT-Enhancer-Binding Proteins/genetics ; DNA Methylation ; Female ; Genomic Imprinting ; Humans ; Maternal Inheritance ; Pregnancy ; Silver-Russell Syndrome/diagnosis ; Silver-Russell Syndrome/genetics ; Ubiquitin-Protein Ligases/genetics
    Chemical Substances Adaptor Proteins, Signal Transducing ; CCAAT-Enhancer-Binding Proteins ; NLRP7 protein, human ; UHRF1 protein, human (EC 2.3.2.27) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Language English
    Publishing date 2022-03-16
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553921-8
    ISSN 1868-7083 ; 1868-7075
    ISSN (online) 1868-7083
    ISSN 1868-7075
    DOI 10.1186/s13148-022-01259-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

  10. Article ; Online: b2bTools: online predictions for protein biophysical features and their conservation.

    Kagami, Luciano Porto / Orlando, Gabriele / Raimondi, Daniele / Ancien, Francois / Dixit, Bhawna / Gavaldá-García, Jose / Ramasamy, Pathmanaban / Roca-Martínez, Joel / Tzavella, Konstantina / Vranken, Wim

    Nucleic acids research

    2021  Volume 49, Issue W1, Page(s) W52–W59

    Abstract: We provide integrated protein sequence-based predictions via https://bio2byte.be/b2btools/. The aim of our predictions is to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular ... ...

    Abstract We provide integrated protein sequence-based predictions via https://bio2byte.be/b2btools/. The aim of our predictions is to identify the biophysical behaviour or features of proteins that are not readily captured by structural biology and/or molecular dynamics approaches. Upload of a FASTA file or text input of a sequence provides integrated predictions from DynaMine backbone and side-chain dynamics, conformational propensities, and derived EFoldMine early folding, DisoMine disorder, and Agmata β-sheet aggregation. These predictions, several of which were previously not available online, capture 'emergent' properties of proteins, i.e. the inherent biophysical propensities encoded in their sequence, rather than context-dependent behaviour (e.g. final folded state). In addition, upload of a multiple sequence alignment (MSA) in a variety of formats enables exploration of the biophysical variation observed in homologous proteins. The associated plots indicate the biophysical limits of functionally relevant protein behaviour, with unusual residues flagged by a Gaussian mixture model analysis. The prediction results are available as JSON or CSV files and directly accessible via an API. Online visualisation is available as interactive plots, with brief explanations and tutorial pages included. The server and API employ an email-free token-based system that can be used to anonymously access previously generated results.
    MeSH term(s) Internet ; Proteins/chemistry ; Sequence Alignment ; Sequence Analysis, Protein/methods ; Software
    Chemical Substances Proteins
    Language English
    Publishing date 2021-05-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkab425
    Database MEDical Literature Analysis and Retrieval System OnLINE

    More links

    Kategorien

    In stock of ZB MED Cologne/Königswinter

    Zs.A 1067: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

    Order via subito

    This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

To top