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YASARA View—molecular graphics for all devices—from smartphones to workstations

Elmar Krieger, Gert Vriend
2014 Computer applications in the biosciences : CABIOS  
Availability and implementation: YASARA View, a molecular modeling program built around the visualization algorithm described here, is freely available (including commercial use) for Linux, MacOS, Windows  ...  Today's graphics processing units (GPUs) compose the scene from individual triangles.  ...  ACKNOWLEDGEMENT The authors thank the YASARA users for their invaluable feedback and financial support.  ... 
doi:10.1093/bioinformatics/btu426 pmid:24996895 pmcid:PMC4184264 fatcat:doragtpjmjd5rergcurrccypsm

A Novel Computer Vision Methodology for Intelligent Molecular Modeling and Simulation

Belal Medhat, Ahmed Shawish
2018 Proceedings of the 11th International Joint Conference on Biomedical Engineering Systems and Technologies  
Molecular modeling and simulation tools are used to study the structure of the molecules for the purpose of understanding and creating a new generation of technology that works on the nano-scale.  ...  This paper represents a novel computer vision method for molecular modeling and simulation that gives the computer the ability to see and understand the structure of molecules just like the human eyes,  ...  The YASARA tool has the advantage of working on molecules anywhere and on any type of computers from workstations to smartphones. however, this tool pays much attention to rendering and rotating the molecules  ... 
doi:10.5220/0006576100970104 dblp:conf/biostec/MedhatS18 fatcat:gxdxdfn44nhrpn5ljksawcnwzi

Molmil: a molecular viewer for the PDB and beyond

Gert-Jan Bekker, Haruki Nakamura, Akira R. Kinjo
2016 Journal of Cheminformatics  
Molmil is available for all platforms supporting WebGL (e.g. Windows, Linux, iOS, Android) from  ...  Furthermore, the viewer can be used to load files in various formats from the user's local hard drive without uploading the data to a server.  ...  These controls are reminiscent from Yasara [11] , which uses a similar hierarchical structures menu and context menu to modify the display and colour modes of the loaded structures.  ... 
doi:10.1186/s13321-016-0155-1 pmid:27570544 pmcid:PMC5002144 fatcat:3gxi2nv6lbeyhosnwgydm52k7u

Mutational effects on carbapenem hydrolysis of YEM-1, a new sub-class B2 metallo-β-lactamase from Yersinia mollaretii [article]

Paola Sandra Mercuri, Roberto Esposito, Sylvie Bletard, Stefano Di Costanzo, Maria Grazia Perilli, Frederic Kerff, Moreno Galleni
2020 bioRxiv   pre-print
We showed that the substitution of Y67 broadened the activity profile of the enzyme for all carbapenems but still displayed a poor activity toward the other β-lactam classes.  ...  Compared to the known subclass B2 metallo-β-lactamase, YEM-1 displayed a narrowest substrate profile since it is only able to hydrolyse imipenem with a high catalytic efficiency but not all the other carbapenems  ...  of YEM-1 was obtained with the Yasara software (Krieger, E., and G. Vriend. YASARA 273 View -molecular graphics for all device -from smartphones to workstations.  ... 
doi:10.1101/2020.01.29.926220 fatcat:uxveo74wwba2hnjlvygfepeapq

Revisiting the interaction of heme with hemopexin: Recommendations for the responsible use of an emerging drug [article]

Milena S. Detzel, Benjamin F. Syllwasschy, Francèl Steinbock, Anuradha Ramoji, Marie-Thérèse Hopp, Ajay A. Paul George, Ute Neugebauer, Diana Imhof
2020 bioRxiv   pre-print
In addition, in silico molecular modelling with a newly created homology model of human hemopexin allowed us to propose a recruiting mechanism by which heme consecutively binds to several histidine residues  ...  Hemopexin is the major protective factor against heme toxicity in human blood and currently considered for therapeutic use.  ...  Acknowledgements 640 The authors would like to thank Sabrina Linden (University of Bonn, Germany) for technical 641 assistance.  ... 
doi:10.1101/2020.04.16.044321 fatcat:dd3oeecw3bgqxahaqvqyfjrkau

Two Tau binding sites on tubulin revealed by thiol-disulfide exchanges

Marlène Martinho, Diane Allegro, Isabelle Huvent, Charlotte Chabaud, Emilien Etienne, Hervé Kovacic, Bruno Guigliarelli, Vincent Peyrot, Isabelle Landrieu, Valérie Belle, Pascale Barbier
2018 Scientific Reports  
The Microtubules binding region of Tau has been determined for a long time but where and how Tau binds to its partner still remain a topic of debate.  ...  More interestingly, using labels linked by a disulfide bridge, we evidenced for the first time thiol disulfide exchanges between αβ-tubulin or MTs and Tau.  ...  Mansuelle from the Proteomic center, Institut de Microbiologie de la Mediteŕraneé and C. Villard from the Institut de Neurophysiopathologie, for the help in protein mass analyses.  ... 
doi:10.1038/s41598-018-32096-9 pmid:30218010 pmcid:PMC6138654 fatcat:djkehtuldnh3lbo5ix5g4zbhoq

A Glycoengineered Interferon-β Mutein (R27T) Generates Prolonged Signaling by an Altered Receptor-Binding Kinetics

Saehyung Lee, Woo Sung Son, Ho Bin Yang, Nirmal Rajasekaran, Sung-Su Kim, Sungyoul Hong, Joon-Seok Choi, Jun Young Choi, Kyoung Song, Young Kee Shin
2019 Frontiers in Pharmacology  
The glycoengineering approach is used to improve biophysical properties of protein-based drugs, but its direct impact on binding affinity and kinetic properties for the glycoengineered protein and its  ...  Thus, we believe that R27T may be clinically beneficial for patients with multiple sclerosis.  ...  YASARA viewmolecular graphics for all devicesfrom smartphones to workstations.  ... 
doi:10.3389/fphar.2018.01568 pmid:30733680 pmcid:PMC6353837 fatcat:3v3tiiig4jcb7lx6lvk3x3zkna

The ancillary N-terminal region of the yeast AP-1 transcription factor Yap8 contributes to its DNA binding specificity [article]

Ewa Maciaszczyk-Dziubinska, Anna Reymer, Nallani Vijay Kumar, Wojciech Białek, Katarzyna Mizio, Markus J Tamas, Robert Wysocki
2019 bioRxiv   pre-print
In this work, we use molecular and biochemical analysis combined with computer-based structural design and molecular dynamics simulations of Yap8-DNA interactions to better understand the structural basis  ...  In contrast to the other members of the Yap family, which preferentially bind to short (7-8 bp) DNA motifs, Yap8 binds to an unusually long DNA motif (13 bp).  ...  Krieger,E. and Vriend,G. (2014) YASARA View -molecular graphics for all devices -from smartphones to workstations.  ... 
doi:10.1101/614503 fatcat:kikgcv7bdjh4fcqmc2dnobzchq

The anti-parasitic drug suramin potently inhibits formation of seminal amyloid fibrils and their interaction with HIV-1

Suiyi Tan, Jin-Qing Li, Hongyan Cheng, Zhaofeng Li, Yan Lan, Ting-Ting Zhang, Zi-Chao Yang, Wenjuan Li, Tao Qi, Yu-Rong Qiu, Zhipeng Chen, Lin Li (+1 others)
2019 Journal of Biological Chemistry  
Collectively, suramin has great potential for further development as a combination microbicide to reduce the spread of the AIDS pandemic by targeting both viral and host factors involved in HIV-1 sexual  ...  Suramin also displayed a good safety profile for vaginal application.  ...  Journal of the American Chemical Society 131, E., and Vriend, G. (2014) YASARA View -molecular graphics for all devices -from smartphones to workstations. Bioinformatics 30, 2981-2982 40.  ... 
doi:10.1074/jbc.ra118.006797 pmid:31346035 pmcid:PMC6746445 fatcat:frhum7kmwvaxhoeotjj6x3oy34

Structure and Mechanism of Dimer–Monomer Transition of a Plant Poly(A)-Binding Protein upon RNA Interaction: Insights into Its Poly(A) Tail Assembly

Mariane Noronha Domingues, Mauricio Luis Sforça, Adriana Santos Soprano, Jack Lee, Tatiana de Arruda Campos Brasil de Souza, Alexandre Cassago, Rodrigo Villares Portugal, Ana Carolina de Mattos Zeri, Mario Tyago Murakami, Ari Sadanandom, Paulo Sergio Lopes de Oliveira, Celso Eduardo Benedetti
2015 Journal of Molecular Biology  
YASARA View -molecular graphics for all devices -from smartphones to workstations.  ...  All these tasks were performed with YASARA [63] .  ...  Moreover, T138, which corresponds to S47 in HnRNP C (panel 'a'), also interacts with an adenine base. (c) Structural alignment between PABPC and HnRNP C bound to poly(A) and poly(U), respectively.  ... 
doi:10.1016/j.jmb.2015.05.017 pmid:26013164 fatcat:3yeyg5dqmfg2nidqrwsv3ylmra

Structure of the essential peptidoglycan amidotransferase MurT/GatD complex from Streptococcus pneumoniae

Cécile Morlot, Daniel Straume, Katharina Peters, Olav A. Hegnar, Nolwenn Simon, Anne-Marie Villard, Carlos Contreras-Martel, Francisco Leisico, Eefjan Breukink, Christine Gravier-Pelletier, Laurent Le Corre, Waldemar Vollmer (+3 others)
2018 Nature Communications  
The structure and assay presented here constitute a knowledge base for future drug development studies.  ...  MurT has central and C-terminal domains similar to Mur ligases with a cysteine-rich insertion, which probably binds zinc, contributing to the interface with GatD.  ...  YASARA View -molecular graphics for all devices-from smartphones to workstations. Bioinformatics 30, 2981-2982 (2014). 48. Berg, K. H., Biørnstad, T. J., Straume, D. & Håvarstein, L. S.  ... 
doi:10.1038/s41467-018-05602-w pmid:30093673 pmcid:PMC6085368 fatcat:yhju6nksbvgwjo7342xmlqxeqa

Virtual reality computer program for biomolecule structure determination [article]

Hamish Todd, University Of Edinburgh, Andrew Goryachev, Taku Komura
We have created a computer program for performing this task in virtual reality, which allows structural biologists to build models using their hands.  ...  Some portion of time spent creating these models must be spent manually modifying the model in order to make it line up with the data; this is difficult and time consuming, in part because the data is  ...  They are also, from the point of view of computer graphics, an unusual sort of shape.  ... 
doi:10.7488/era/540 fatcat:arfhhfnkyfdjjhetbsxa5bbvma