Logo
Logo

Universität zu KölnFachgruppe PhysikTheoretische PhysikAG PortoMarkus Porto

Reconstruction of protein structures from a vectorial representation

The source of the reconstruction algorithm discussed in

(R35)
Reconstruction of protein structures from a vectorial representation
M. Porto, U. Bastolla, H.E. Roman, and M. Vendruscolo, Phys. Rev. Lett. 92, 218101 (2004) (4 pages).

can be obtained here. When using this code or referring to it, please cite the above article.

Publications discussing the application of the vectorial representation of protein structures are

(R36)
Principal eigenvector of contact matrices and hydrophobicity profiles in proteins
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, Proteins 58, 22-30 (2005).

(R37)
Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences
M. Porto, H.E. Roman, M. Vendruscolo, and U. Bastolla, Mol. Biol. Evol. 22, 630-638 (2005).

(R39)
A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, BMC Evol. Biol. 6, 43 (2006) (21 pages).

(P13)
Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, Gene 347, 219-230 (2005).
(International Conference `Structural approaches to sequence evolution: Molecules, networks, populations´, Dresden, Germany, July 4 to 10, 2003)

(C4)
The structurally constrained neutral model of protein evolution
U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, in Structural approaches to sequence evolution: Molecules, networks, populations, edited by U. Bastolla, M. Porto, H.E. Roman, and M. Vendruscolo, Springer, Berlin, 2007, pp. 75-113.

A generalization of the vectorial representation applicable to single- and multi-domain folds is discussed in the following publication

(R42)
Vectorial representation of single- and multi-domain protein folds
F. Teichert and M. Porto, Eur. Phys. J. B 54, 131-136 (2006).

A generalization of the vectorial representation applicable to single- and multi-domain folds focusing on the relationship between protein structures and sequences is discussed in the following publication

(R54)
Effective connectivity profile: A structural representation that evidences the relationship between protein structures and sequences
U. Bastolla, A.R. Ortiz, M. Porto, and F. Teichert, Proteins 73, 872-888 (2008).

A generalization of the vectorial representation applicable to single- and multi-domain folds and explicitly including the energetics of secondary structure is discussed in the following publication

(R48)
Local interactions in protein folding determined through an inverse folding model
U. Bastolla, M. Porto, and A.R. Ortiz, Proteins 71, 278-299 (2008).

An application of the vectorial representation to structural alignment is discussed in the following publication

(R45)
SABERTOOTH: Protein structural alignment based on a vectorial structure representation
F. Teichert, U. Bastolla, and M. Porto, BMC Bioinformatics 8, 425 (2007) (17 pages).

An application of the vectorial representation to sequence alignment is discussed in the following publication

(R61)
High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABERTOOTH
F. Teichert, J. Minning, U. Bastolla, and M. Porto, BMC Bioinformatics 11, 251 (2010) (14 pages).

An application of the vectorial representation to protein folding is discussed in the following publications

(R55)
Stochastic reconstruction of protein structures from effective connectivity profiles
K. Wolff, M. Vendruscolo, and M. Porto, PMC Biophys. 1, 5 (2008) (13 pages).
(R63)
Asymmetric folding pathways and transient misfolding in a coarse-grained model of proteins
K. Wolff, M. Vendruscolo, and M. Porto, EPL 94, 48005 (2011) (5 pages)
(R64)
Coarse-grained model for protein folding based on structural profiles
K. Wolff, M. Vendruscolo, and M. Porto, Phys. Rev. E 84, 041934 (2011) (7 pages).

An application of the vectorial representation to ab initio protein structure predicion is discussed in the following publication

(R59)
Efficient identification of near-native conformations in ab initio protein structure prediction using structural profiles
K. Wolff, M. Vendruscolo, and M. Porto, Proteins 78, 249-258 (2010).

You might also be interested to have a look on the list of publications related to molecular biology and structural bioinformatics.