List of works - Arne Elofsson

A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder

scientific article published on 09 April 2020

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

scientific article published on 22 April 2020

A comparison of sequence and structure protein domain families as a basis for structural genomics.

scientific article published in June 1999

A guideline to proteome-wide α-helical membrane protein topology predictions

scientific article

A structural biology community assessment of AlphaFold 2 applications

A structural biology community assessment of AlphaFold2 applications

scientific article published in 2022

A study of quality measures for protein threading models

scientific article

A study of the membrane-water interface region of membrane proteins.

scientific article

A study on protein sequence alignment quality

scholarly article by Arne Elofsson published in January 2002

Accurate contact predictions for thousands of protein families using PconsC3

All are not equal: a benchmark of different homology modeling programs

scientific article

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

scientific article (publication date: 28 April 2015)

An intrinsically disordered proteins community for ELIXIR

scientific article published on 15 October 2019

An introduction to membrane proteins

scientific article published on August 2011

Arrangements in the modular evolution of proteins.

scientific article

Assessment of global and local model quality in CASP8 using Pcons and ProQ

article

Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller

scientific article published on 01 January 2003

BOCTOPUS: improved topology prediction of transmembrane β barrel proteins

scientific article

Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information

scientific article published in July 2004

Bioinformatics: From nucleic acids and proteins to cell metabolism

scholarly article by Arne Elofsson published in June 1996

CAFASP2: the second critical assessment of fully automated structure prediction methods

scientific article published on January 2001

CAFASP3: The third critical assessment of fully automated structure prediction methods

scholarly article by Daniel Fischer published in January 2003

Can correct protein models be identified? ⬇️

scientific article published on May 1, 2003

Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion.

scientific article published on 7 December 2012

Coils in the Membrane Core Are Conserved and Functionally Important

Detecting sequence signals in targeting peptides using deep learning

scientific article published on 30 September 2019

Determining receptor-ligand interaction of human galanin receptor type 3

scientific article

Domain rearrangements in protein evolution

scientific article published on 21 September 2005

Estimating the length of transmembrane helices using Z-coordinate predictions

scientific article published on 20 December 2007

Estimation of model accuracy in CASP13

scientific article published on 16 July 2019

Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia

scientific article published on January 2007

Expansion of protein domain repeats

scientific article

Expansion of protein domain repeats

Folding of Aquaporin 1: Multiple evidence that helix 3 can shift out of the membrane core

article

Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core

scientific article published on 14 May 2014

Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants

scientific article

Helix-helix packing in a membrane-like environment ⬇️

scientific article published on October 3, 1997

Hidden Markov models that use predicted secondary structures for fold recognition

scientific article published on 01 July 1999

High GC content causes orphan proteins to be intrinsically disordered.

scientific article

How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin.

scientific article published on October 1993

Identification of correct regions in protein models using structural, alignment, and consensus information

scientific article published on 7 March 2006

Identification of related proteins on family, superfamily and fold level

scientific article published in January 2000

Identifying and Quantifying Orphan Protein Sequences in Fungi

Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps.

scientific article

Improved detection of homologous membrane proteins by inclusion of information from topology predictions.

scientific article

Improved prediction of protein-protein interactions using AlphaFold2

scientific article published on 10 March 2022

Improved predictions by Pcons.net using multiple templates

scientific article

Improved protein model quality assessments by changing the target function.

scientific article published on 9 March 2018

In silico prediction of the peroxisomal proteome in fungi, plants and animals.

scientific article

Interaction of mitochondrial presequences with DnaK and mitochondrial hsp70.

scientific article published in April 1999

Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare

scientific article

KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2.

scientific article published on 19 April 2011

LiveBench-1: continuous benchmarking of protein structure prediction servers

scientific article

LiveBench-6: large-scale automated evaluation of protein structure prediction servers.

scientific article

Local moves: an efficient algorithm for simulation of protein folding

scientific article published in September 1995

Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins

scientific article published on 17 January 2013

M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings

scientific article published in 2024

MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane

scientific article

Manipulating the genetic code for membrane protein production: what have we learnt so far?

scientific article published on 22 August 2011

Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones

scientific article published in 2022

Membrane Insertion of Marginally Hydrophobic Transmembrane Helices Depends on Sequence Context

article published in 2010

Membrane protein structure: prediction versus reality.

scientific article

Methods for estimation of model accuracy in CASP12.

scientific article published on 4 October 2017

Molecular recognition of a single sphingolipid species by a protein's transmembrane domain

scientific article published on 9 January 2012

Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions.

scientific article

Nebulin: a study of protein repeat evolution

scientific article

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

scientific article published on 12 May 2008

Orphans and new gene origination, a structural and evolutionary perspective

scientific article

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

scientific article published on July 2006

Pcons.net: protein structure prediction meta server.

scientific article

Pcons5: combining consensus, structural evaluation and fold recognition scores.

scientific article

Pcons: a neural-network-based consensus predictor that improves fold recognition.

scientific article

Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search

scientific article published in 2022

Prediction of MHC class I binding peptides, using SVMHC

scientific article

Prediction of global and local model quality in CASP7 using Pcons and ProQ.

scientific article

Prediction of membrane-protein topology from first principles

scholarly article

Preferential attachment in the evolution of metabolic networks

scientific article

ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins

scientific article

Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods

scholarly article by Tomas Ohlson published in May 2004

Quantification of the Elevated Rate of Domain Rearrangements in Metazoa

scientific article published on 15 June 2007

Quantitative assessment of the structural bias in protein-protein interaction assays

article

Ranking models of transmembrane β-barrel proteins using Z-coordinate predictions

scientific article published in June 2012

Rapid membrane protein topology prediction

scientific article published on May 2011

Remote homology detection of integral membrane proteins using conserved sequence features

scientific article published in May 2008

Repositioning of transmembrane alpha-helices during membrane protein folding

scientific article published on 25 January 2010

SPOCTOPUS: a combined predictor of signal peptides and membrane protein topology.

scientific article

Site specific point mutation changes specificity: A molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions

scholarly article by Arne Elofsson published in October 1993

Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes.

scientific article

Structure is three to ten times more conserved than sequence-A study of structural response in protein cores

article

Study of the electrostatics treatment in molecular dynamics simulations

scientific article published in November 1999

TOPCONS: consensus prediction of membrane protein topology

scientific article published on 8 May 2009

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

scientific article published in January 2019

Tertiary Windowing to Detect Positive Diversifying Selection

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

scientific article published on 13 September 2017

The Use of Phylogenetic Profiles for Gene Predictions

article

The Use of Phylogenetic Profiles for Gene Predictions Revisited

scholarly article by Asa Bjorklund et al published 1 April 2006 in Current Genomics

The complement regulator CD46 is bactericidal to Helicobacter pylori and blocks urease activity

scientific article published on 18 May 2011

The evolution of filamin-a protein domain repeat perspective

scientific article

The evolutionary history of topological variations in the CPA/AT transporters

scientific article published on 17 August 2021

The interface of protein structure, protein biophysics, and molecular evolution

scientific article

The positive inside rule is stronger when followed by a transmembrane helix

The relationship between ageing and changes in the human blood and brain methylomes

scientific article published on 02 February 2022

The salmon genome (and other issues in bioinformatics)

scientific article

Turns in transmembrane helices: determination of the minimal length of a “helical hairpin” and derivation of a fine-grained turn propensity scale 1 1Edited by F. E. Cohen

Using Micro- and Macro-Level Network Metrics Unveils Top Communicative Gene Modules in Psoriasis

scientific article published on 10 August 2020

Using evolutionary information for the query and target improves fold recognition.

scientific article published in February 2004

Using multiple templates to improve quality of homology models in automated homology modeling.

scientific article published on 25 April 2008

What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?

scientific article published on January 2006

Why are polar residues within the membrane core evolutionary conserved?

scientific article

Why do eukaryotic proteins contain more intrinsically disordered regions?

scientific article published on 22 July 2019

ZPRED: predicting the distance to the membrane center for residues in alpha-helical membrane proteins

scientific article published in July 2006

List of works by Arne Elofsson

A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

A comparison of sequence and structure protein domain families as a basis for structural genomics.

A guideline to proteome-wide α-helical membrane protein topology predictions

A structural biology community assessment of AlphaFold 2 applications

A structural biology community assessment of AlphaFold2 applications

A study of quality measures for protein threading models

A study of the membrane-water interface region of membrane proteins.

A study on protein sequence alignment quality

Accurate contact predictions for thousands of protein families using PconsC3

All are not equal: a benchmark of different homology modeling programs

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

An intrinsically disordered proteins community for ELIXIR

An introduction to membrane proteins

Arrangements in the modular evolution of proteins.

Assessment of global and local model quality in CASP8 using Pcons and ProQ

Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller

BOCTOPUS: improved topology prediction of transmembrane β barrel proteins

Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information

Bioinformatics: From nucleic acids and proteins to cell metabolism

CAFASP2: the second critical assessment of fully automated structure prediction methods

CAFASP3: The third critical assessment of fully automated structure prediction methods

Can correct protein models be identified? ⬇️

Charge pair interactions in transmembrane helices and turn propensity of the connecting sequence promote helical hairpin insertion.

Coils in the Membrane Core Are Conserved and Functionally Important

Detecting sequence signals in targeting peptides using deep learning

Determining receptor-ligand interaction of human galanin receptor type 3

Domain rearrangements in protein evolution

Estimating the length of transmembrane helices using Z-coordinate predictions

Estimation of model accuracy in CASP13

Evaluating dosage compensation as a cause of duplicate gene retention in Paramecium tetraurelia

Expansion of protein domain repeats

Expansion of protein domain repeats

Folding of Aquaporin 1: Multiple evidence that helix 3 can shift out of the membrane core

Folding of Aquaporin 1: multiple evidence that helix 3 can shift out of the membrane core

Genomic evolution and complexity of the Anaphase-promoting Complex (APC) in land plants

Helix-helix packing in a membrane-like environment ⬇️

Hidden Markov models that use predicted secondary structures for fold recognition

High GC content causes orphan proteins to be intrinsically disordered.

How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin.

Identification of correct regions in protein models using structural, alignment, and consensus information

Identification of related proteins on family, superfamily and fold level

Identifying and Quantifying Orphan Protein Sequences in Fungi

Improved alignment quality by combining evolutionary information, predicted secondary structure and self-organizing maps.

Improved detection of homologous membrane proteins by inclusion of information from topology predictions.

Improved prediction of protein-protein interactions using AlphaFold2

Improved predictions by Pcons.net using multiple templates

Improved protein model quality assessments by changing the target function.

In silico prediction of the peroxisomal proteome in fungi, plants and animals.

Interaction of mitochondrial presequences with DnaK and mitochondrial hsp70.

Internal duplications in α-helical membrane protein topologies are common but the nonduplicated forms are rare

KalignP: improved multiple sequence alignments using position specific gap penalties in Kalign2.

LiveBench-1: continuous benchmarking of protein structure prediction servers

LiveBench-6: large-scale automated evaluation of protein structure prediction servers.

Local moves: an efficient algorithm for simulation of protein folding

Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins

M-Ionic: prediction of metal-ion-binding sites from sequence using residue embeddings

MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane

Manipulating the genetic code for membrane protein production: what have we learnt so far?

Mass Spectrometry and Machine Learning Reveal Determinants of Client Recognition by Antiamyloid Chaperones

Membrane Insertion of Marginally Hydrophobic Transmembrane Helices Depends on Sequence Context

Membrane protein structure: prediction versus reality.

Methods for estimation of model accuracy in CASP12.

Molecular recognition of a single sphingolipid species by a protein's transmembrane domain

Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions.

Nebulin: a study of protein repeat evolution

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

Orphans and new gene origination, a structural and evolutionary perspective

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

Pcons.net: protein structure prediction meta server.

Pcons5: combining consensus, structural evaluation and fold recognition scores.

Pcons: a neural-network-based consensus predictor that improves fold recognition.

Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search

Prediction of MHC class I binding peptides, using SVMHC

Prediction of global and local model quality in CASP7 using Pcons and ProQ.

Prediction of membrane-protein topology from first principles

Preferential attachment in the evolution of metabolic networks

ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins

Profile-profile methods provide improved fold-recognition: A study of different profile-profile alignment methods