The Buccaneer Software for Automated Model Building. 1. Tracing Protein Chains

Overview

Journal Acta Crystallogr D Biol Crystallogr

Specialty Chemistry

Date 2006 Aug 25

PMID 16929101

Citations 1194

Authors

Kevin Cowtan

Affiliations

Soon will be listed here.

Abstract

A new technique for the automated tracing of protein chains in experimental electron-density maps is described. The technique relies on the repeated application of an oriented electron-density likelihood target function to identify likely C(alpha) positions. This function is applied both in the location of a few promising ;seed' positions in the map and to grow those initial C(alpha) positions into extended chain fragments. Techniques for assembling the chain fragments into an initial chain trace are discussed.

Citing Articles

Flavin-containing siderophore-interacting protein of Shewanella putrefaciens DSM 9451 reveals common structural and functional aspects of ferric-siderophore reduction.

Trindade I, Fonseca B, Catarino T, Matias P, Moe E, Louro R J Biol Inorg Chem. 2025; .

PMID: 40080164 DOI: 10.1007/s00775-025-02106-z.

Expansion of the diversity of dispersin scaffolds.

Males A, Moroz O, Blagova E, Munch A, Hansen G, Johansen A Acta Crystallogr D Struct Biol. 2025; 81(Pt 3):130-146.

PMID: 40019001 PMC: 11883664. DOI: 10.1107/S205979832500110X.

Slice'N'Dice: maximizing the value of predicted models for structural biologists.

Simpkin A, Elliot L, Joseph A, Burnley T, Stevenson K, Sanchez Rodriguez F Acta Crystallogr D Struct Biol. 2025; 81(Pt 3):105-121.

PMID: 39976565 PMC: 11883665. DOI: 10.1107/S2059798325001251.

Structural analysis of extracellular ATP-independent chaperones of streptococcal species and protein substrate interactions.

Agbavor C, Torres M, Inniss N, Latimer S, Minasov G, Shuvalova L mSphere. 2025; 10(2):e0107824.

PMID: 39878509 PMC: 11853100. DOI: 10.1128/msphere.01078-24.

AI-based methods for biomolecular structure modeling for Cryo-EM.

Farheen F, Terashi G, Zhu H, Kihara D Curr Opin Struct Biol. 2025; 90:102989.

PMID: 39864242 PMC: 11793015. DOI: 10.1016/j.sbi.2025.102989.