List of works - Torsten Schwede

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

scientific article published in 2022

A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0.

scientific article published on 21 July 2020

A computational protocol to evaluate the effects of protein mutants in the kinase gatekeeper position on the binding of ATP substrate analogues

scientific article published on 20 February 2017

Anna Tramontano 1957-2017.

scientific article published in May 2017

Asp1424Asn MYH9 mutation results in an unstable protein responsible for the phenotypes in May-Hegglin anomaly/Fechtner syndrome

scientific article

Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane).

scientific article published on September 2014

Assessment of CASP7 predictions for template-based modeling targets

scientific article

Assessment of disorder predictions in CASP7.

scientific article

Assessment of ligand binding site predictions in CASP10

scientific article

Assessment of ligand-binding residue predictions in CASP9.

scientific article published on 11 October 2011

Assessment of protein assembly prediction in CASP12.

scientific article published on 26 October 2017

Assessment of template based protein structure predictions in CASP9.

scientific article

Assessment of the assessment: evaluation of the model quality estimates in CASP10

scientific article (publication date: February 2014)

Author Correction: High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

scientific article published on 12 November 2020

Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective.

scientific article

Automated protein structure homology modeling: a progress report.

scientific article

Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal

scientific article

Automated server predictions in CASP7

scientific article

CASP9 target classification

scientific article

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

scientific article

Cohesive Properties of the Caulobacter crescentus Holdfast Adhesin Are Regulated by a Novel c-di-GMP Effector Protein

scientific article

Computational analysis of methyl transfer reactions in dengue virus methyltransferase

scientific article published on 21 May 2014

Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92

scientific article (publication date: May 2003)

Critical assessment of methods of protein structure prediction (CASP)--round x

scientific article (publication date: February 2014)

Critical assessment of methods of protein structure prediction (CASP)-Round XII.

scientific article published on 30 October 2017

Critical assessment of methods of protein structure prediction (CASP)-Round XIII

scientific article published on 23 October 2019

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.

scientific article

Crystal structure of urease from Yersinia enterocolitica

Data to knowledge: how to get meaning from your result.

scientific article

Domain definition and target classification for CASP7

scholarly article by Neil D. Clarke published in January 2007

Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public

article by Antoine Daina et al published 27 February 2017 in Journal of Chemical Education

Dual activities of odorants on olfactory and nuclear hormone receptors.: TABLE 1

scientific article published in Journal of Biological Chemistry

ECCB 2012: The 11th European Conference on Computational Biology.

scientific article

Estimation of model accuracy in CASP13

scientific article published on 16 July 2019

Evaluation of the template-based modeling in CASP12.

scientific article

Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

scientific article published on 25 November 2019

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

scientific article

GA4GH: International policies and standards for data sharing across genomic research and healthcare

scientific article published on 10 November 2021

Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust.

scientific article

High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

scientific article published on 09 October 2020

Homogenization and crystallization of histidine ammonia-lyase by exchange of a surface cysteine residue

scientific article published on 01 February 1999

How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding.

scientific article

How to use the PSI Structural Genomics Knowledgebase to Enable Research

Improving your target-template alignment with MODalign

scientific article (publication date: April 2012)

Increased efficiency of Campylobacter jejuni N-oligosaccharyltransferase PglB by structure-guided engineering

scientific article published on April 2015

Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)

scientific article published on 16 October 2019

LIGATE - LIgand Generator and portable drug discovery platform AT Exascale

scientific article published on 01 July 2024

Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking

Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11

scientific article

Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology

scientific article

Modelling three-dimensional protein structures for applications in drug design.

scientific article

Mutations in the Sec61p Channel Affecting Signal Sequence Recognition and Membrane Protein Topology

scientific article published in Journal of Biological Chemistry

Mutations in the TMPRSS3 gene are a rare cause of childhood nonsyndromic deafness in Caucasian patients

scientific article (publication date: February 2002)

Novel cargo-binding site in the beta and delta subunits of coatomer

scientific article

Novel inhibitors of dengue virus methyltransferase: discovery by in vitro-driven virtual screening on a desktop computer grid

scientific article

Novel missense mutations of TMPRSS3 in two consanguineous Tunisian families with non-syndromic autosomal recessive deafness

scientific article (publication date: August 2001)

OpenStructure: a flexible software framework for computational structural biology

scientific article

OpenStructure: an integrated software framework for computational structural biology

scientific article

Outcome of a workshop on applications of protein models in biomedical research

scientific article (publication date: 13 February 2009)

Outcome of a workshop on archiving structural models of biological macromolecules

scientific article

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

scientific article published on 18 June 2015

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

scientific article

Plasmid-mediated colistin resistance in a patient infected with Klebsiella pneumoniae.

scientific article

ProMod3-A versatile homology modelling toolbox

scientific article published on 28 January 2021

Protein Tertiary Structure Modeling

scientific article published on 01 May 2001

Protein modeling: what happened to the "protein structure gap"?

scientific article

Protein structure computing in the genomic era.

scientific article

Protein structure homology modeling using SWISS-MODEL workspace.

scientific article

QMEAN server for protein model quality estimation

scientific article

QMEANDisCo-distance constraints applied on model quality estimation

scientific article published on 01 March 2020

QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information.

scientific article

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

scientific article

SWISS-MODEL: An automated protein homology-modeling server

scientific article

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

scientific article (publication date: July 2014)

Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression

scientific article published on January 2009

Sulfonylureas and Glinides Exhibit Peroxisome Proliferator-Activated Receptor Activity: A Combined Virtual Screening and Biological Assay Approach

Tandem mass spectrometry protein identification on a PC grid

scientific article published on January 2007

Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016).

scientific article published on 28 September 2017

Target highlights in CASP13: Experimental target structures through the eyes of their authors

scientific article published on 09 September 2019

Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction

scientific article

The Protein Model Portal

scientific article

The Protein Model Portal--a comprehensive resource for protein structure and model information

scientific article

The SWISS-MODEL Repository and associated resources

scientific article

The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models

scientific article

The SWISS-MODEL Repository-new features and functionality

scientific article

The SWISS-MODEL Repository: new features and functionalities

scientific article

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

scientific article (publication date: 15 January 2006)

The Structural Biology Knowledgebase - search Online for Protein Sequences, Structures, Functions, Methods and More

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

scientific article

The mouse eugenol odorant receptor: structural and functional plasticity of a broadly tuned odorant binding pocket

scientific article

The plug domain of yeast Sec61p is important for efficient protein translocation, but is not essential for cell viability

scientific article

The protein structure initiative structural genomics knowledgebase.

scientific article

Toward the estimation of the absolute quality of individual protein structure models

scientific article

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale

scientific article published on 04 August 2023

Uncovering new families and folds in the natural protein universe

scientific article published on 13 September 2023

What is hidden in the darkness? Deep-learning assisted large-scale protein family curation uncovers novel protein families and folds

Zinc-selective inhibition of the promiscuous bacterial amide-hydrolase DapE: implications of metal heterogeneity for evolution and antibiotic drug design

scientific article published on January 2014

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests.

scientific article

List of works by Torsten Schwede

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0.

A computational protocol to evaluate the effects of protein mutants in the kinase gatekeeper position on the binding of ATP substrate analogues

Anna Tramontano 1957-2017.

Asp1424Asn MYH9 mutation results in an unstable protein responsible for the phenotypes in May-Hegglin anomaly/Fechtner syndrome

Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane).

Assessment of CASP7 predictions for template-based modeling targets

Assessment of disorder predictions in CASP7.

Assessment of ligand binding site predictions in CASP10

Assessment of ligand-binding residue predictions in CASP9.

Assessment of protein assembly prediction in CASP12.

Assessment of template based protein structure predictions in CASP9.

Assessment of the assessment: evaluation of the model quality estimates in CASP10

Author Correction: High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective.

Automated protein structure homology modeling: a progress report.

Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal

Automated server predictions in CASP7

CASP9 target classification

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

Cohesive Properties of the Caulobacter crescentus Holdfast Adhesin Are Regulated by a Novel c-di-GMP Effector Protein

Computational analysis of methyl transfer reactions in dengue virus methyltransferase

Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92

Critical assessment of methods of protein structure prediction (CASP)--round x

Critical assessment of methods of protein structure prediction (CASP)-Round XII.

Critical assessment of methods of protein structure prediction (CASP)-Round XIII

Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.

Crystal structure of urease from Yersinia enterocolitica

Data to knowledge: how to get meaning from your result.

Domain definition and target classification for CASP7

Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public

Dual activities of odorants on olfactory and nuclear hormone receptors.: TABLE 1

ECCB 2012: The 11th European Conference on Computational Biology.

Estimation of model accuracy in CASP13

Evaluation of the template-based modeling in CASP12.

Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust.

High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica

Homogenization and crystallization of histidine ammonia-lyase by exchange of a surface cysteine residue

How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding.

How to use the PSI Structural Genomics Knowledgebase to Enable Research

Improving your target-template alignment with MODalign

Increased efficiency of Campylobacter jejuni N-oligosaccharyltransferase PglB by structure-guided engineering

Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)

LIGATE - LIgand Generator and portable drug discovery platform AT Exascale

Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking

Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11

Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology

Modelling three-dimensional protein structures for applications in drug design.

Mutations in the Sec61p Channel Affecting Signal Sequence Recognition and Membrane Protein Topology

Mutations in the TMPRSS3 gene are a rare cause of childhood nonsyndromic deafness in Caucasian patients

Novel cargo-binding site in the beta and delta subunits of coatomer

Novel inhibitors of dengue virus methyltransferase: discovery by in vitro-driven virtual screening on a desktop computer grid

Novel missense mutations of TMPRSS3 in two consanguineous Tunisian families with non-syndromic autosomal recessive deafness

OpenStructure: a flexible software framework for computational structural biology

OpenStructure: an integrated software framework for computational structural biology

Outcome of a workshop on applications of protein models in biomedical research

Outcome of a workshop on archiving structural models of biological macromolecules

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

Plasmid-mediated colistin resistance in a patient infected with Klebsiella pneumoniae.

ProMod3-A versatile homology modelling toolbox

Protein Tertiary Structure Modeling

Protein modeling: what happened to the "protein structure gap"?

Protein structure computing in the genomic era.

Protein structure homology modeling using SWISS-MODEL workspace.

QMEAN server for protein model quality estimation

QMEANDisCo-distance constraints applied on model quality estimation

QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information.

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

SWISS-MODEL: An automated protein homology-modeling server

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression

Sulfonylureas and Glinides Exhibit Peroxisome Proliferator-Activated Receptor Activity: A Combined Virtual Screening and Biological Assay Approach

Tandem mass spectrometry protein identification on a PC grid

Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016).