skip to main content
Visitante
Meu Espaço
Minha Conta
Sair
Identificação
This feature requires javascript
Tags
Revistas Eletrônicas (eJournals)
Livros Eletrônicos (eBooks)
Bases de Dados
Bibliotecas USP
Ajuda
Ajuda
Idioma:
Inglês
Espanhol
Português
This feature required javascript
This feature requires javascript
Primo Search
Busca Geral
Busca Geral
Acervo Físico
Acervo Físico
Produção Intelectual da USP
Produção USP
Search For:
Clear Search Box
Search in:
Busca Geral
Or select another collection:
Search in:
Busca Geral
Busca Avançada
Busca por Índices
This feature requires javascript
This feature requires javascript
Proteome-scale Structure Prediction Data - Pseudodesulfovibrio mercurii
Davidson, Russell B ; Coletti, Mark ; Gao, Mu ; Parks, Jerry M ; Sedova, Ada
United States 2022
Sem texto completo
Citações
Citado por
Serviços
Detalhes
Resenhas & Tags
Nº de Citações
This feature requires javascript
Enviar para
Adicionar ao Meu Espaço
Remover do Meu Espaço
E-mail (máximo 30 registros por vez)
Imprimir
Link permanente
Referência
EasyBib
EndNote
RefWorks
del.icio.us
Exportar RIS
Exportar BibTeX
This feature requires javascript
Título:
Proteome-scale Structure Prediction Data - Pseudodesulfovibrio mercurii
Autor:
Davidson, Russell B
;
Coletti, Mark
;
Gao, Mu
;
Parks, Jerry M
;
Sedova, Ada
Assuntos:
BASIC BIOLOGICAL SCIENCES
;
CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS
;
GENERAL AND MISCELLANEOUS
;
Structural Proteomics, AlphaFold, APoc
Notas:
Office of Science (SC), Advanced Scientific Computing Research (ASCR) (SC-21)
Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
DE-AC05-00OR22725
USDOE Office of Science (SC)
Descrição:
The number of proteins predicted for Pseudodesulfovibrio mercurii is 3,446, each of which have five predicted structures from an AlphaFold run, as well as structural alignment results using the TMscore-based structural alignment method within the APoc program. Specifically, AlphaFold outputs the atoms and coordinates of the protein model in human-readable PDB files and quantitative prediction metrics in Python PICKLE files. The 5 models have been ranked based on the predicted TM-score (pTMS), a quantitative confidence metric output by AlphaFold that reports on protein model quality. The top ranked model has undergone an energy minimization calculation to relax and remove any potential clashes in the atomic coordinates. Structural alignment results are stored in two files for each protein; the top ranked model (as discussed above) is used for all alignment analyses. Both are compressed gzip files that, once unpacked, are human readable. The first file is the TMalign score results and contains the quantitative metrics for the top alignments between the predicted structure and experimental structures from the PDB70, a curated non-redundant database of about 80,000 experimental structures developed by the Soding lab. Each data point in this file is directly associated with one experimental structure; PDB ID and brief meta-data about the protein taken from the PDB70 file are reported alongside the quantitative metrics. The second results file contains the raw results associated with each alignment reported in the score results file. Specifically, the translation and rotation arrays for each alignment are provided so that the structural alignment can be recreated. Additionally, residue-level scores are reported to quantify the closeness of the aligned residues between the predicted and experimental models.
Editor:
United States
Data de criação/publicação:
2022
Idioma:
Inglês
Links
View this record in Osti.gov
This feature requires javascript
This feature requires javascript
Voltar para lista de resultados
This feature requires javascript
This feature requires javascript
Buscando em bases de dados remotas. Favor aguardar.
Buscando por
em
scope:(USP_PRODUCAO),scope:(USP_EBOOKS),scope:("PRIMO"),scope:(USP),scope:(USP_EREVISTAS),scope:(USP_FISICO),primo_central_multiple_fe
Mostrar o que foi encontrado até o momento
This feature requires javascript
This feature requires javascript