Local function conservation in sequence and structure space.

Autor: Nils Weinhold, Oliver Sander, Francisco S Domingues, Thomas Lengauer, Ingolf Sommer

Publikováno v: PLoS Computational Biology, Vol 4, Iss 7, p e1000105 (2008)

We assess the variability of protein function in protein sequence and structure space. Various regions in this space exhibit considerable difference in the local conservation of molecular function. We analyze and capture local function conservation b

Externí odkaz: https://doaj.org/article/a8d845fa6d63435bbce472f3970461a5

Moment invariants as shape recognition technique for comparing protein binding sites

Autor: Joachim Weickert, Ingolf Sommer, Oliver Müller, Francisco S. Domingues, Oliver Sander, Thomas Lengauer

Publikováno v: Bioinformatics. 23:3139-3146

Motivation: An approach for identifying similarities of protein–protein binding sites is presented. The geometric shape of a binding site is described by computing a feature vector based on moment invariants. In order to search for similarities, fe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9904ee88e0c4e827103ec0d04160101e
https://doi.org/10.1093/bioinformatics/btm503

Three-Dimensional Organization of the Bacterial Ribosome and Its Subunits: Transition from Low-Resolution Models to High-Resolution Structures

Autor: Richard Brimacombe, Jutta Rinke-Appel, Barbara Greuer, Ingolf Sommer, Florian Mueller, Monika Osswald

Publikováno v: The Ribosome

The structure of the bacterial ribosome, in particular that of Escherichia coli, has been studied over a period of several decades with the help of a wide variety of biochemical and biophysical techniques. This chapter summarizes briefly how the 70S

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::4885cb6f96e181157c4e3bcab5f5ec4d
https://doi.org/10.1128/9781555818142.ch14

A large-scale evaluation of computational protein function prediction

Autor: Christine A. Orengo, Liang Lan, Daniel W. A. Buchan, Jeffrey M. Yunes, Alberto Paccanaro, Yannick Mahlich, Enrico Lavezzo, Patricia C. Babbitt, Domenico Cozzetto, Cedric Landerer, Jari Björne, Esmeralda Vicedo, Robert Rentzsch, Rajendra Joshi, Hagit Shatkay, Nives Škunca, Zheng Wang, Tal Ronnen Oron, Ingolf Sommer, Amos Marc Bairoch, Mark Heron, Panče Panov, Daisuke Kihara, Wyatt T. Clark, Michael J.E. Sternberg, Steven E. Brenner, Sašo Džeroski, Burkhard Rost, Christian Schaefer, Karin Verspoor, Harshal Inamdar, Tapio Salakoski, Meghana Chitale, Alfonso E. Romero, Julian Gough, Fran Supek, Olivier Lichtarge, Dominik Achten, Serkan Erdin, Michael Kiening, Petri Törönen, Avik Datta, Iddo Friedberg, Thomas A. Hopf, Liisa Holm, Rita Casadio, Asa Ben-Hur, Tatjana Braun, Sean D. Mooney, Marco Falda, Kiley Graim, Michal Linial, Alexandra M. Schnoes, Christopher S. Funk, Rebecca Kaßner, Patrik Koskinen, Nemanja Djuric, Paolo Fontana, Predrag Radivojac, Tobias Wittkop, Kevin Bryson, Maximilian Hecht, Susanna Repo, Haixuan Yang, Artem Sokolov, Prajwal Bhat, Tobias Hamp, Jianlin Cheng, Mark N. Wass, Gaurav Pandey, Michael L Souza, Damiano Piovesan, Ameet Talwalkar, Stefan Seemayer, Eric Venner, Sunitha K Manjari, Fanny Gatzmann, Aalt D. J. van Dijk, Manfred Roos, Tomislav Šmuc, David T. Jones, Peter Hönigschmid, Ariane Boehm, Florian Auer, Jussi Nokso-Koivisto, Stefano Toppo, Slobodan Vucetic, Denis Krompass, Qingtian Gong, Cajo J. F. ter Braak, Andrew Wong, Barbara Di Camillo, Yiannis A. I. Kourmpetis, Andreas Martin Lisewski, Matko Bošnjak, Bhakti Limaye, Weidong Tian, Yuhong Guo, Xinran Dong, Hai Fang, Yuanpeng Zhou, Stefanie Kaufmann

Publikováno v: Nature Methods
Nature methods
Nature Methods : techniques for life scientists and chemists 10 (2013)
Nature Methods : techniques for life scientists and chemists, 10, 221-227
Nature Methods, Vol. 10, No 3 (2013) pp. 221-7

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c19e166af084819ee544097527791f10
http://hdl.handle.net/10449/22010

Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage

Autor: Francisco S. Domingues, Peter K. Cheung, P. Richard Harrigan, Thomas Lengauer, Ingolf Sommer, Oliver Sander, Andrew J. Low, Tobias Sing

Publikováno v: PLoS Computational Biology, Vol 3, Iss 3, p e58 (2007)
PLoS Computational Biology

HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as for supporting therapy with the novel drug class o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2ed5a404990e028d7654da4d942d1bb7
http://europepmc.org/articles/PMC1848001?pdf=render