Welsch, Christoph, Domingues, Francisco S, Susser, Simone, Antes, Iris, Hartmann, Christoph, Mayr, Gabriele, ...
Abstract Background The inhibitor telaprevir (VX-950) of the hepatitis C virus (HCV) protease NS3-4A has been tested in a recent phase 1b clinical trial in patients infected with HCV genotype 1. This...
Comparative Analysis of Protein Structure Alignments (2007)
Mayr, Gabriele, Domingues, Francisco S, Lackner, Peter
Abstract Background Several methods are currently available for the comparison of protein structures. These methods have been analysed regarding the performance in the identification of...
GOTax: investigating biological processes and biochemical activities along the taxonomic tree (2007)
Schlicker, Andreas, Rahnenführer, Jörg, Albrecht, Mario, Lengauer, Thomas, Domingues, Francisco S
Abstract We describe GOTax, a comparative genomics platform that integrates protein annotation with protein family classification and taxonomy. User-defined sets of proteins, protein families,...
GOTax: investigating biological processes and biochemical activities along the taxonomic tree (2007)
Schlicker, Andreas, Rahnenführer, Jörg, Albrecht, Mario, Lengauer, Thomas, Domingues, Francisco S
Abstract We describe GOTax, a comparative genomics platform that integrates protein annotation with protein family classification and taxonomy. User-defined sets of proteins, protein families,...
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage (2007)
Oliver Sander, Tobias Sing, Ingolf Sommer, Andrew J. Low, Peter K. Cheung, P. Richard Harrigan, ...
HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as...
A new measure for functional similarity of gene products based on Gene Ontology (2006)
Schlicker, Andreas, Domingues, Francisco S, Rahnenführer, Jörg, Lengauer, Thomas
Abstract Background Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare...
NOXclass: prediction of protein-protein interaction types (2006)
Zhu, Hongbo, Domingues, Francisco S, Sommer, Lngolf, Lengauer, Thomas
Abstract Background Structural models determined by X-ray crystallography play a central role in understanding protein-protein interactions at the molecular level. Interpretation of these models...
Rahnenführer, Jörg, Domingues, Francisco S, Maydt, Jochen, Lengauer, Thomas
We present a statistical approach to scoring changes in activity of metabolic pathways from gene expression data. The method identifies the biologically relevant pathways with corresponding...
Rahnenführer, Jörg, Domingues, Francisco S, Maydt, Jochen, Lengauer, Thomas
We present a statistical approach to scoring changes in activity of metabolic pathways from gene expression data. The method identifies the biologically relevant pathways with corresponding...
Rahnenführer, Jörg, Domingues, Francisco S, Maydt, Jochen, Lengauer, Thomas
We present a statistical approach to scoring changes in activity of metabolic pathways from gene expression data. The method identifies the biologically relevant pathways with corresponding...
Rahnenführer, Jörg, Domingues, Francisco S, Maydt, Jochen, Lengauer, Thomas
We present a statistical approach to scoring changes in activity of metabolic pathways from gene expression data. The method identifies the biologically relevant pathways with corresponding...
WILMA-automated annotation of protein sequences (2004)
Prlic,Andreas, Domingues,Francisco S., Lackner,Peter, Sippl,Manfred J.
Predicting Protein Structure Classes from Function Predictions (2004)
Sommer,Ingolf, Rahnenführer,Jörg, Domingues,Francisco S., De Lichtenberg,Ulrik, Lengauer,Thomas
WILMA-automated annotation of protein sequences (2004)
Prlic, Andreas, Domingues, Francisco S., Lackner, Peter, Sippl, Manfred J.
Predicting Protein Structure Classes from Function Predictions (2004)
Sommer, Ingolf, Rahnenführer, Jörg, Domingues, Francisco S., De Lichtenberg, Ulrik, Lengauer, Thomas
Automated clustering of ensembles of alternative models in protein structure databases (2004)
Domingues, Francisco S., Rahnenführer, Jörg, Lengauer, Thomas
Protein Structure Prediction and Databases (2004)
Domingues, Francisco S., Lengauer, Thomas, Sommer, Ingolf, Cooper, David
Identification of mammalian orthologs associates PYPAF5 with distinct functional roles (2003)
Albrecht,Mario, Domingues,Francisco S., Schreiber,Stefan, Lengauer,Thomas
Identification of mammalian orthologs associates PYPAF5 with distinct functional roles (2003)
Albrecht, Mario, Domingues, Francisco S., Schreiber, Stefan, Lengauer, Thomas
Assessment of the CASP4 Fold Recognition Category (2002)
Peter Lackner, Francisco S. Domingues, Andreas Prli, Rainer Malik, Antonina Andreeva, Markus Wiederstein
We present the assessment of the CASP4 fold recognition category. The tasks we had to execute include the splitting of multidomain targets into single domains, the classification of target domains in...
J. Phys. IV France 1 (2002) Pr1-1 c EDP Sciences, Les Ulis (2002)
Francisco S. Domingues, Peter Lackner, Antonina Andreeva, Proceryon Biosciences Gmbh, Jakob Haringer Strae
Developments in the protein structure prediction eld are reected in large scale prediction experiments (CASP) which take place every two years. Here we look at the results of the previous CASP...
Assessment of the CASP4 Fold Recognition Category (2001)
Peter Lackner, Francisco S. Domingues, Rainer Malik, Antonina Andreeva, Markus Wiederstein, Proceryon Biosciences Gmbh, ...
respective target structures than any of the known folds in PDB. The CASP4 assessment included the automated servers of the parallel CAFASP experiment. With respect to the total score the highest...
The Role of Protein Structure in Genomics (2000)
Francisco S. Domingues, Proceryon Biosciences Gmbh, Jakob Haringer Strae
The genome projects produce an enormous amount of sequence data that needs to be annotated in terms of molecular structure and biological function. These tasks have triggered additional initiatives...
Structure Based Evaluation of Sequence Comparison and Fold Recognition Alignment Accuracy (2000)
Francisco S. Domingues, Peter Lackner, Antonina Andreeva
this paper we focus on alignment accuracy and derive a standard set of alignments that can be used to benchmark sequence based or fold recognition search techniques. The benchmark consists of a set...
Structure Based Evaluation of Sequence Comparison and Fold Recognition Alignment Accuracy (1999)
Francisco S. Domingues, Peter Lackner
this paper we focus on alignment accuracy and derive a standard set of alignments that can be used to benchmark sequence based or fold recognition search techniques. The benchmark consists of a set...
Sustained Performance of Knowledge Based Potentials in Fold Recognition (1999)
Francisco S. Domingues, Markus Jaritz, Christian Weichenberger, Markus Wiederstein, Hannes Floeckner, Jakob Haringer Str
We describe the results obtained in our third participation in the CASP experiment using fold recognition techniques. The approach relies on knowledge based potentials for alignment production and...
An attempt to analyse progress in fold recognition from CASP1 to CASP3. (1999)
Peter Lackner, Francisco S. Domingues, Walter A
The CASP experiment has been conducted for the third time. An obvious question is whether there has been progress from CASP1 to CASP3. An analysis depends on many variables, including prediction...
NOXclass: prediction of protein-protein interaction types
Zhu, Hongbo, Domingues, Francisco S, Sommer, Lngolf, Lengauer, Thomas
A new measure for functional similarity of gene products based on Gene Ontology
Schlicker, Andreas, Domingues, Francisco S, Rahnenführer, Jörg, Lengauer, Thomas
NOXclass: prediction of protein-protein interaction types
Zhu, Hongbo, Domingues, Francisco S, Sommer, Lngolf, Lengauer, Thomas
A new measure for functional similarity of gene products based on Gene Ontology
Schlicker, Andreas, Domingues, Francisco S, Rahnenführer, Jörg, Lengauer, Thomas
Structural Descriptors of gp120 V3 Loop for the Prediction of HIV-1 Coreceptor Usage
Sander, Oliver, Sing, Tobias, Sommer, Ingolf, Low, Andrew J, Cheung, Peter K, Harrigan, P. Richard, ...
HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as...
GOTax: investigating biological processes and biochemical activities along the taxonomic tree
Schlicker, Andreas, Rahnenführer, Jörg, Albrecht, Mario, Lengauer, Thomas, Domingues, Francisco S
GOTax, a novel web-based platform that integrates protein annotation with protein family classification and taxonomy, allows for an extensive assessment of functional similarity between proteins and...
Alignment of Non-Covalent Interactions at Protein-Protein Interfaces
Zhu, Hongbo, Sommer, Ingolf, Lengauer, Thomas, Domingues, Francisco S.
Welsch, Christoph, Domingues, Francisco S, Susser, Simone, Antes, Iris, Hartmann, Christoph, Mayr, Gabriele, ...
Structural analysis of the inhibitor Telaprevir (VX-950) of the hepatitis C virus (HCV) protease NS3-4A shows that mutations at V36 and/or T54 result in impaired interaction with VX-950, explaining...
Local Function Conservation in Sequence and Structure Space
Weinhold, Nils, Sander, Oliver, Domingues, Francisco S., Lengauer, Thomas, Sommer, Ingolf
We assess the variability of protein function in protein sequence and structure space. Various regions in this space exhibit considerable difference in the local conservation of molecular function....