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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

TopoLink: evaluation of structural models using chemical crosslinking distance constraints

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Author(s):
Ferrari, Allan J. R. [1] ; Clasen, Milan A. [2] ; Kurt, Louise [2] ; Carvalho, Paulo C. [2] ; Gozzo, Fabio C. [1] ; Martinez, Leandro [1, 3]
Total Authors: 6
Affiliation:
[1] Univ Estadual Campinas, Inst Chem, Campinas, SP - Brazil
[2] Fiocruz MS, Carlos Chagas Inst, Rio De Janeiro, RJ - Brazil
[3] Univ Estadual Campinas, Ctr Comp Engn & Sci, Campinas, SP - Brazil
Total Affiliations: 3
Document type: Journal article
Source: Bioinformatics; v. 35, n. 17, p. 3169-3170, SEP 1 2019.
Web of Science Citations: 4
Abstract

The Summary: A software was developed to evaluate structural models using chemical crosslinking experiments. The user provides the types of linkers used and their reactivity, and the observed crosslinks and dead-ends. The software computes the minimum length of a physically inspired linker that connects the reactive atoms of interest, and reports the consistency of each distance with the experimental observation. Statistics on model consistency with the links are provided. Tools to evaluate the correlation of crosslinks in ensembles of models were developed. TopoLink was used to evaluate the potential crosslinks of all structures of the CATH database. The number of crosslinks expected as a function of protein size and linker length can be used as guide for experimental design. (AU)

FAPESP's process: 13/05475-7 - Computational methods in optimization
Grantee:Sandra Augusta Santos
Support type: Research Projects - Thematic Grants
FAPESP's process: 18/14274-9 - Protein structure determination from distance constraints derived from chemical cross-linking: computational methods and applications
Grantee:Leandro Martinez
Support type: Regular Research Grants
FAPESP's process: 10/16947-9 - Correlations between dynamics, structure and function in protein: computer simulations and algorithms
Grantee:Leandro Martinez
Support type: Regular Research Grants
FAPESP's process: 16/13195-2 - Modeling of protein structure and protein complexes using mass spectrometry data
Grantee:Allan Jhonathan Ramos Ferrari
Support type: Scholarships in Brazil - Doctorate
FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
Grantee:Munir Salomao Skaf
Support type: Research Grants - Research, Innovation and Dissemination Centers - RIDC