An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Autor: Chen Keasar, Liam J. McGuffin, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, Leandro Oliveira Bortot, Renzhi Cao, B. K. Dhanasekaran, Itzhel Dimas, Rodrigo Antonio Faccioli, Eshel Faraggi, Robert Ganzynkowicz, Sambit Ghosh, Soma Ghosh, Artur Giełdoń, Lukasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George A. Khoury, Chris Kieslich, David E. Kim, Pawel Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka Lipska, Adam Liwo, Ali Hassan A. Maghrabi, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, Sergey Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, Adam K. Sieradzan, Magdalena Ślusarz, Rafal Ślusarz, James Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yanping Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popović, Bartlomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre Cláudio Botazzo Delbem, Christodoulos Floudas, Andrzej Kloczkowski, Stanislaw Ołdziej, Michael Levitt, Harold Scheraga, Chaok Seok, Johannes Söding, Saraswathi Vishveshwara, Dong Xu, Foldit Players consortium, Silvia N. Crivelli

Publikováno v: Scientific Reports, Vol 8, Iss 1, Pp 1-18 (2018)

Abstract Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field

Externí odkaz: https://doaj.org/article/b0b847aec1154062a3c86bac14d94e55

Large-scale determination of previously unsolved protein structures using evolutionary information

Autor: Sergey Ovchinnikov, Lisa Kinch, Hahnbeom Park, Yuxing Liao, Jimin Pei, David E Kim, Hetunandan Kamisetty, Nick V Grishin, David Baker

Publikováno v: eLife, Vol 4 (2015)

The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind struc

Externí odkaz: https://doaj.org/article/bf36d51e866a428788292677ef37e206

Genomic language model predicts protein co-regulation and function

Autor: Yunha Hwang, Andre L. Cornman, Elizabeth H. Kellogg, Sergey Ovchinnikov, Peter R. Girguis

Publikováno v: Nature Communications, Vol 15, Iss 1, Pp 1-13 (2024)

Abstract Deciphering the relationship between a gene and its genomic context is fundamental to understanding and engineering biological systems. Machine learning has shown promise in learning latent relationships underlying the sequence-structure-fun

Externí odkaz: https://doaj.org/article/e89d2e92e119410faf6ff04cf3e744c7

Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters

Autor: Fotis A. Baltoumas, Evangelos Karatzas, David Paez-Espino, Nefeli K. Venetsianou, Eleni Aplakidou, Anastasis Oulas, Robert D. Finn, Sergey Ovchinnikov, Evangelos Pafilis, Nikos C. Kyrpides, Georgios A. Pavlopoulos

Publikováno v: Frontiers in Bioinformatics, Vol 3 (2023)

Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several meth

Externí odkaz: https://doaj.org/article/f02d335b56704ff4a762c935e45990f2