Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12thCritical Assessment of protein Structure Prediction experiment

Autor: Matteo Dal Peraro, Luciano A. Abriata, Giulia Fonti, Giorgio E. Tamò

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 86:215-227

Integrative modeling approaches attempt to combine experiments and computation to derive structure-function relationships in complex molecular assemblies. Despite their importance for the advancement of life sciences, benchmarking of existing methodo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::5080eae4be9e4860ba70d4c88b7eea79
https://doi.org/10.1002/prot.25442

A further leap of improvement in tertiary structure prediction in CASP13 prompts new routes for future assessments

Autor: Matteo Dal Peraro, Giorgio E. Tamò, Luciano A. Abriata

Publikováno v: ProteinsREFERENCES. 87(12)

We present our assessment of tertiary structure predictions for hard targets in Critical Assessment of Structure Prediction round 13 (CASP13). The analysis includes (a) assignment and discussion of best models through scores-aided visual inspection o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::41dab0d3db558f5dc020039254dcd34a
https://pubmed.ncbi.nlm.nih.gov/31344267

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment-based contact prediction methods

Autor: Giorgio E. Tamò, Bohdan Monastyrskyy, Andriy Kryshtafovych, Matteo Dal Peraro, Luciano A. Abriata

Publikováno v: Proteins. 86

We present our assessment of CASP12 modeling efforts for targets with no obvious templates of high sequence/structure similarity in the PDB, that is for evaluation units of the free modeling (FM) and free modeling/template-based modeling (FM/TBM) cat

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aa0351806d24195f08dbf743373d41cc
https://pubmed.ncbi.nlm.nih.gov/29139163

CorNet: Assigning function to networks of co-evolving residues by automated literature mining

Autor: Tom Desmet, Bas Vroling, Alberto Nobili, Peter J. Schaap, Tom van den Bergh, Uwe T. Bornscheuer, Yifeng Tao, Bernd Nidetzky, René M. de Jong, Gert Vriend, Kalyanasundaram Subramanian, Tianwei Tan, Henk-Jan Joosten, Remko Kuipers, Giorgio E. Tamò

Publikováno v: PLoS ONE 12 (2017) 5
PLoS One, 12
PLoS ONE
PLoS One, 12, 5
PLoS ONE, 12(5), e0176427-e0176427
PLOS ONE
PLoS ONE, Vol 12, Iss 5, p e0176427 (2017)

Contains fulltext : 174131.pdf (Publisher’s version ) (Open Access) CorNet is a web-based tool for the analysis of co-evolving residue positions in protein super-family sequence alignments. CorNet projects external information such as mutation data

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1ff783d1d1f0c9754ef6a56592178f85
https://research.wur.nl/en/publications/cornet-assigning-function-to-networks-of-co-evolving-residues-by-

Definition and classification of evaluation units for tertiary structure prediction in CASP12 facilitated through semi-automated metrics

Autor: Andriy Kryshtafovych, Giorgio E. Tamò, Lisa N. Kinch, Bohdan Monastyrskyy, Matteo Dal Peraro, Luciano A. Abriata

For assessment purposes, CASP targets are split into evaluation units. We herein present the official definition of CASP12 evaluation units (EUs) and their classification into difficulty categories. Each target can be evaluated as one EU (the whole t

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7609b141661b77754d141080a47d5e38
https://infoscience.epfl.ch/record/258639