BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btt005 Structural bioinformatics Advance Access publication January 10, 2013

On the upper bound of the prediction accuracy of residue contacts in proteins with correlated mutations: the case study of the similarity matrices

P. Di Lena
P. Fariselli
L. Margara
M. Vassura
R. Casadio

January 2009

Correlated mutations in proteins are believed to occur in order to preserve the protein functional f...

Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations

Fariselli, Piero
Olmea, O
Valencia, A
Casadio, R.

January 2001

This article presents recent progress in predicting inter-residue contacts of proteins with a neural...

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btl677 Sequence analysis

David T. Jones

August 2015

Improving the accuracy of transmembrane protein topology prediction using evolutionary informatio

Structural bioinformatics Advance Access publication January 10, 2013

Nikolas S. Burkoff
David L. Wild
Anna Tramontano

January 2013

Predicting protein b-sheet contacts using a maximum entropy-based correlated mutation measur

BIOINFORMATICS Pages 1–8 Predicting

Nikolas S Burkoff
David L. Wild

October 2016

protein β-sheet contacts using a maximum entropy based correlated mutation measur

Predicting protein : sheet contacts using a maximum entropy-based correlated mutation measure

Burkoff, Nikolas S.
Várnai, Csilla
Wild, David L.

Motivation: The problem of ab initio protein folding is one of the most difficult in modern computat...

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btt691 Structural bioinformatics Advance Access publication November 26, 2013

Douglas E. V. Pires
David B. Ascher
Tom L. Blundell

January 2013

mCSM: predicting the effects of mutations in proteins using graph-based signature

Reaction system reconstruction and protein contact prediction.

Richard R. Stein (496395)
Debora S. Marks (193565)
Chris Sander (1345)

July 2015

<p>Association results of correlation-based and maximum-entropy methods on biological data from an <...

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm604 Sequence analysis Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction

S. D. Dunn
L. M. Wahl
G. B. Gloor

October 2016

Motivation: Compensating alterations during the evolution of protein families give rise to coevolvin...

Improved inference of intermolecular contacts through protein–protein interaction prediction using coevolutionary analysis

Correa Marrero, M.
Immink, G.H.
de Ridder, D.
van Dijk, A.D.J.

January 2019

Motivation: Predicting residue–residue contacts between interacting proteins is an important problem...

Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?

July 2015

none5Correlated mutations in proteins are believed to occur in order to preserve the protein functio...

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm637 Sequence analysis

Rotem Rubinstein
Andras Fiser

July 2015

Predicting disulfide bond connectivity in proteins by correlated mutations analysi

Prediction of protein residue contacts with a PDB-derived likelihood matrix.

Singer, M.S.
Vriend, G.
Bywater, R.P.

January 2002

Item does not contain fulltextProteins with similar folds often display common patterns of residue v...

Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs

Várnai, Csilla
Burkoff, Nikolas S.
Wild, David L.

February 2017

Evolutionary information stored in multiple sequence alignments (MSAs) has been used to identify the...

Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs.

Csilla Várnai
Nikolas S Burkoff
David L Wild

January 2017

Evolutionary information stored in multiple sequence alignments (MSAs) has been used to identify the...

On the upper bound of the prediction accuracy of residue contacts in proteins with correlated mutations: the case study of the similarity matrices

P. Di Lena
P. Fariselli
L. Margara
M. Vassura
R. Casadio

January 2009

Correlated mutations in proteins are believed to occur in order to preserve the protein functional f...

Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations

Fariselli, Piero
Olmea, O
Valencia, A
Casadio, R.

January 2001

This article presents recent progress in predicting inter-residue contacts of proteins with a neural...

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btl677 Sequence analysis

David T. Jones

August 2015

Improving the accuracy of transmembrane protein topology prediction using evolutionary informatio

Structural bioinformatics Advance Access publication January 10, 2013

Nikolas S. Burkoff
David L. Wild
Anna Tramontano

January 2013

Predicting protein b-sheet contacts using a maximum entropy-based correlated mutation measur

BIOINFORMATICS Pages 1–8 Predicting

Nikolas S Burkoff
David L. Wild

October 2016

protein β-sheet contacts using a maximum entropy based correlated mutation measur

Predicting protein : sheet contacts using a maximum entropy-based correlated mutation measure

Burkoff, Nikolas S.
Várnai, Csilla
Wild, David L.

Motivation: The problem of ab initio protein folding is one of the most difficult in modern computat...

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btt691 Structural bioinformatics Advance Access publication November 26, 2013

Douglas E. V. Pires
David B. Ascher
Tom L. Blundell

January 2013

mCSM: predicting the effects of mutations in proteins using graph-based signature

Reaction system reconstruction and protein contact prediction.

Richard R. Stein (496395)
Debora S. Marks (193565)
Chris Sander (1345)

July 2015

<p>Association results of correlation-based and maximum-entropy methods on biological data from an <...

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm604 Sequence analysis Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction

S. D. Dunn
L. M. Wahl
G. B. Gloor

October 2016

Motivation: Compensating alterations during the evolution of protein families give rise to coevolvin...

Improved inference of intermolecular contacts through protein–protein interaction prediction using coevolutionary analysis

Correa Marrero, M.
Immink, G.H.
de Ridder, D.
van Dijk, A.D.J.

January 2019

Motivation: Predicting residue–residue contacts between interacting proteins is an important problem...

Is There an Optimal Substitution Matrix for Contact Prediction with Correlated Mutations?

July 2015

none5Correlated mutations in proteins are believed to occur in order to preserve the protein functio...

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm637 Sequence analysis

Rotem Rubinstein
Andras Fiser

July 2015

Predicting disulfide bond connectivity in proteins by correlated mutations analysi

Prediction of protein residue contacts with a PDB-derived likelihood matrix.

Singer, M.S.
Vriend, G.
Bywater, R.P.

January 2002

Item does not contain fulltextProteins with similar folds often display common patterns of residue v...

Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs

Várnai, Csilla
Burkoff, Nikolas S.
Wild, David L.

February 2017

Evolutionary information stored in multiple sequence alignments (MSAs) has been used to identify the...

Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs.

Csilla Várnai
Nikolas S Burkoff
David L Wild

January 2017

Evolutionary information stored in multiple sequence alignments (MSAs) has been used to identify the...

On the upper bound of the prediction accuracy of residue contacts in proteins with correlated mutations: the case study of the similarity matrices

P. Di Lena
P. Fariselli
L. Margara
M. Vassura
R. Casadio

January 2009

Correlated mutations in proteins are believed to occur in order to preserve the protein functional f...

Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations

Fariselli, Piero
Olmea, O
Valencia, A
Casadio, R.

January 2001

This article presents recent progress in predicting inter-residue contacts of proteins with a neural...

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btl677 Sequence analysis

David T. Jones

August 2015

Improving the accuracy of transmembrane protein topology prediction using evolutionary informatio

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btt005 Structural bioinformatics Advance Access publication January 10, 2013

Abstract

Extracted data

BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btt005 Structural bioinformatics Advance Access publication January 10, 2013

Abstract

Extracted data

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