TopoLink: evaluation of structural models using chemical crosslinking distance constraints

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]}

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

• 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: 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
• 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: 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