Results 51 to 60 of about 15,507,347 (338)

AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

Nucleic Acids Res., 2021
The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions.
M. Váradi, S. Anyango, M. Deshpande, S. Nair, Cindy Natassia, Galabina Yordanova, D. Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Žídek, Tim Green, Kathryn Tunyasuvunakool, Stig Petersen, J. Jumper, Ellen Clancy, Richard Green, Ankur Vora, Mira Lutfi, Michael Figurnov, A. Cowie, Nicole Hobbs, Pushmeet Kohli, G. Kleywegt, E. Birney, D. Hassabis, S. Velankar   +26 more
semanticscholar   +1 more source

Conservation and specialization in PAS domain dynamics [PDF]

, 2005
The PAS (Per-ARNT-Sim) superfamily is presented as a well-suited study case to demonstrate how comparison of functional motions among distant homologous proteins with conserved fold characteristics may give insight into their functional specialization ...
Bonati, L, Pandini, A
core   +2 more sources

Comparative Protein Structure Modeling Using MODELLER

Current Protocols in Bioinformatics, 2016
Comparative protein structure modeling predicts the three‐dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates).
Ben M. Webb, A. Sali
semanticscholar   +1 more source

A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing

Nature, 2020
A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals
D. Gordon, Gwendolyn M. Jang, Mehdi Bouhaddou, Jiewei Xu, K. Obernier, K. White, Matthew J. O’Meara, V. Rezelj, Jeffrey Z. Guo, D. Swaney, Tia A. Tummino, Ruth Hüttenhain, Robyn M. Kaake, Alicia L. Richards, B. Tutuncuoglu, Helene Foussard, J. Batra, Kelsey M. Haas, Mayank Modak, Minkyu Kim, Paige Haas, Benjamin J. Polacco, Hannes Braberg, Jacqueline M. Fabius, Manon Eckhardt, Margaret Soucheray, M. J. Bennett, Merve Cakir, Michael J. McGregor, Qiongyu Li, Bjoern Meyer, F. Roesch, T. Vallet, Alice Mac Kain, Lisa Miorin, Elena Moreno, Zun Zar Chi Naing, Yuan Zhou, S. Peng, Ying Shi, Ziyang Zhang, W. Shen, I. T. Kirby, James E. Melnyk, John S. Chorba, Kevin Lou, Shizhong A. Dai, Inigo Barrio-Hernandez, D. Memon, Claudia Hernandez-Armenta, Jiankun Lyu, Christopher J. P. Mathy, Tina Perica, K. B. Pilla, Sai J. Ganesan, Daniel J. Saltzberg, R. Rakesh, Xi Liu, S. Rosenthal, Lorenzo Calviello, S. Venkataramanan, José M Liboy-Lugo, Yizhu Lin, Xi-Ping Huang, Yongfeng Liu, S. Wankowicz, M. Bohn, M. Safari, Fatima S. Ugur, C. Koh, Nastaran Sadat Savar, Q. D. Tran, Djoshkun Shengjuler, S. Fletcher, M. C. O’Neal, Yiming Cai, Jason C. J. Chang, D. Broadhurst, Saker Klippsten, P. P. Sharp, Nicole A. Wenzell, Duygu Kuzuoglu-Ozturk, Hao-Yuan Wang, R. Trenker, Janet M. Young, D. A. Cavero, J. Hiatt, Theodore L. Roth, Ujjwal Rathore, Advait Subramanian, Julia Noack, Mathieu Hubert, R. Stroud, A. Frankel, O. Rosenberg, K. Verba, D. Agard, M. Ott, M. Emerman, N. Jura, M. von Zastrow, E. Verdin, A. Ashworth, O. Schwartz, C. d’Enfert, Shaeri Mukherjee, Matt Jacobson, Harmit S. Malik, D. Fujimori, T. Ideker, C. Craik, S. Floor, J. Fraser, J. Gross, A. Sali, B. Roth, D. Ruggero, J. Taunton, T. Kortemme, P. Beltrão, M. Vignuzzi, A. García-Sastre, K. Shokat, B. Shoichet, N. Krogan   +124 more
semanticscholar   +1 more source

Multiple structural alignment for distantly related all b structures using TOPS pattern discovery and simulated annealing [PDF]

, 2003
Topsalign is a method that will structurally align diverse protein structures, for example, structural alignment of protein superfolds. All proteins within a superfold share the same fold but often have very low sequence identity and different biological
Gilbert, D, Westhead, DR, Williams, A
core   +1 more source

UniProt: a worldwide hub of protein knowledge

Nucleic Acids Res., 2018
The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a million of these ...
Tunca Dogan
semanticscholar   +1 more source

Structures of the wild-type MexAB–OprM tripartite pump reveal its complex formation and drug efflux mechanism

Nature Communications, 2019
In Pseudomonas aeruginosa, MexAB–OprM plays a central role in multidrug resistance by ejecting various drug compounds. Here the authors present the structure of wild-type MexAB–OprM in the presence or absence of drugs and propose mechanisms for complex ...
Kenta Tsutsumi, Ryo Yonehara, Etsuko Ishizaka-Ikeda, Naoyuki Miyazaki, Shintaro Maeda, Kenji Iwasaki, Atsushi Nakagawa, Eiki Yamashita   +7 more
doaj   +1 more source

A Novel Sequence-Based Antigenic Distance Measure for H1N1, with Application to Vaccine Effectiveness and the Selection of Vaccine Strains [PDF]

, 2011
H1N1 influenza causes substantial seasonal illness and was the subtype of the 2009 influenza pandemic. Precise measures of antigenic distance between the vaccine and circulating virus strains help researchers design influenza vaccines with high vaccine ...
Brown, Caton, Daniels, Deem, Donatelli, Ferguson, K. C. Subieta, K. Pan, KEITEL, Lee, M. W. Deem, Nobusawa, Pan, Rambaut, Smith, Wiley, Zaraket   +16 more
core   +3 more sources

Analysis of protein-coding genetic variation in 60,706 humans

Nature, 2015
Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. Here we describe the aggregation and analysis of high-quality exome (protein-coding region) DNA sequence data ...
James Y. Zou
semanticscholar   +1 more source

Time-resolved spectroscopic and electrophysiological data reveal insights in the gating mechanism of anion channelrhodopsin

Communications Biology, 2021
Dreier et al. reports that the anion channelrhodopsin GtACR1 does not undergo a syn-cycle (light adapted ground state) and thus has a more efficient channel behaviour than CrChR2.
Max-Aylmer Dreier, Philipp Althoff, Mohamad Javad Norahan, Stefan Alexander Tennigkeit, Samir F. El-Mashtoly, Mathias Lübben, Carsten Kötting, Till Rudack, Klaus Gerwert   +8 more
doaj   +1 more source