Application of parameter optimization to molecular comparison (2008)
C. Lemmen, A. Zien, R. Zimmer, T. Lengauer
problems
Bioinformatical Recognition Of, B. Heil, J. Ludwig, H. Lichtenberg, T. Lengauer
Figure 3: The amino acids were coded as unique 23-bit strings. Each string encodes the properties of five different categories.
A. Zien, G. Rätsch, S. Mika, B. Schölkopf, T. Lengauer
Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called...
Summary: The Helmholtz Network for Bioinformatics (HNB) (2008)
T. Crass, I. Antes, R. Basekow, P. Bork, C. Buning, M. Christensen, ...
EMC-Driven Midway Routing on PCBs (2007)
H. Schmidt, D. Theune, R. Thiele, T. Lengauer
Phenomena of electromagnetic compatibility (EMC) have to be considered during layout synthesis of printedcircuit boards (PCBs), in order to design failsafe and highperformance systems. In this paper...
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. (2006)
Tameling, W.I.L., Vossen, J.H., Albrecht, M., Lengauer, T., Berden, J.A., Haring, M.A., ...
Resistance (R) proteins in plants confer specificity to the innate immune system. Most R proteins have a centrally located NBARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4)...
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. (2006)
Tameling, W.I.L., Vossen, J.H., Albrecht, M., Lengauer, T., Berden, J.A., Haring, M.A., ...
Arevir: a secure platform for designing personalized antiretroviral therapies against HIV (2006)
Roomp, K., Beerenwinkel, N., Sing, T., Schuelter, E., Buech, J., Sierra-Aragon, S., ...
Beerenwinkel, N., Sing, T., Lengauer, T., Rahnenfuhrer, J., Roomp, K., Savenkov, I., ...
The development of drug resistance is a major obstacle to successful treatment of HIV infection. The extraordinary replication dynamics of HIV facilitates its escape from selective pressure exerted...
Estimating HIV evolutionary pathways and the genetic barrier to drug resistance (2005)
Beerenwinkel, N., Daumer, M., Sing, T., Rahnenfuhrer, J., Lengauer, T., Selbig, J., ...
Background. The evolution of drug-resistant viruses challenges the management of human immunodeficiency virus (HIV) infections. Understanding this evolutionary process is important for the design of...
Mtreemix: a software package for learning and using mixture models of mutagenetic trees (2005)
Beerenwinkel, N., Rahnenfuhrer, J., Kaiser, R., Hoffmann, D., Selbig, J., Lengauer, T.
Mixture models of mutagenetic trees constitute a class of probabilistic models for describing evolutionary processes that are characterized by the accumulation of permanent genetic changes. They have...
Multiple-ligand-based virtual screening: Methods and applications of the MTree approach (2005)
Hessler, G., Zimmermann, M., Matter, H., Evers, A., Naumann, T., Lengauer, T., ...
We present a novel approach for ligand-based virtual screening by combining query molecules into a multiple feature tree model called MTree. All molecules are described by the established...
Crass,T., Antes,I., Basekow,R., Bork,P., Buning,C., Christensen,M., ...
The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...
Crass,T., Antes,I., Basekow,R., Bork,P., Buning,C., Christensen,M., ...
The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...
Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., ...
The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...
Modelling amorphous Si3B3N7: Structure and elastic properties (2004)
Hannemann, A., Schön, J. C., Jansen, M., Putz, H., Lengauer, T.
Modelling amorphous Si3B3N7: Structure and elastic properties (2004)
Hannemann, A., Schön, J. C., Jansen, M., Putz, H., Lengauer, T.
Novel technologies for virtual screening (2004)
Lengauer, T., Lemmen, C., Rarey, M., Zimmermann, M.
There are several methods for virtual screening of databases of small organic compounds to find tight binders to a given protein target. Recent reviews in Drug Discovery Today have concentrated on...
Öhsen, N. Von, Sommer, I., Zimmer, R., Lengauer, T.
Motivation: Arby is a new server for protein structure prediction that combines several homology-based methods for predicting the three-dimensional structure of a protein, given its sequence. The...
Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., ...
The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...
Learning multiple evolutionary pathways from cross-sectional data (2004)
Beerenwinkel, N., Rahnenführer, J., Daeumer, M., Hoffmann, D., Kaiser, R., Selbig, J., ...
Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., ...
Summary: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a...
Predicting protein structure classes from function predictions (2004)
Sommer, I., Rahnenführer, J., Domingues, F. S., De Lichtenberg, U., Lengauer, T.
Motivation: We introduce a new approach to using the information contained in sequence-to-function prediction data in order to recognize protein template classes, a critical step in predicting...
Predicting protein structure classes from function predictions (2004)
Sommer, I., Rahnenführer, J., Domingues, F.S., De Lichtenberg, U., Lengauer, T.
Motivation: We introduce a new approach to using the information contained in sequence-to-function prediction data in order to recognize protein template classes, a critical step in predicting...
Predicting protein structure classes from function predictions (2004)
Sommer, I., Rahnenführer, J., Domingues, F. S., De Lichtenberg, U., Lengauer, T.
Motivation: We introduce a new approach to using the information contained in sequence-to-function prediction data in order to recognize protein template classes, a critical step in predicting...
Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes (2003)
Beerenwinkel, N., Daumer, M., Oette, M., Korn, K., Hoffmann, D., Kaiser, R., ...
Therapeutic success of anti-HIV therapies is limited by the development of drug resistant viruses. These genetic variants display complex mutational patterns in their pol gene, which codes for...
Methods for optimizing antiviral combination therapies. (2003)
Beerenwinkel, N., Lengauer, T., Däumer, M., Kaiser, R., Walter, H., Korn, K., ...
Tenofovir resistance and resensitization (2003)
Wolf, K., Walter, H., Beerenwinkel, N., Keulen, W., Kaiser, R., Hoffmann, D., ...
Human immunodeficiency viruses in 321 samples from tenofovir-naive patients were retrospectively evaluated for resistance to this nucleotide analogue. All virus strains with insertions between amino...
Microarrays: How Many Do You Need? (2003)
Zien, A., Fluck, J., Zimmer, R., Lengauer, T.
We estimate the number of microarrays that is required in order to gain reliable results from a common type of study: the pairwise comparison of different classes of samples. We show that current...
Structural modeling of ataxin-3 reveals distant homology to adaptins (2003)
Albrecht, M., Hoffmann, D., Evert, B.O., Schmitt, I., Wüllner, U., Lengauer, T.
Spinocerebellar ataxia type 3 (SCA3) is a polyglutamine disorder caused by a CAG repeat expansion in the coding region of a gene encoding ataxin-3, a protein of yet unknown function. Based on a...
The Arby automated protein structure prediction server (2003)
Sommer, I., Öhsen, N. Von, Mevissen, T., Albrecht, M., Zimmer, R., Lengauer, T.
Beerenwinkel, N., Schmidt, B., Walter, H., Kaiser, R., Lengauer, T., Hoffmann, D., ...
Drug resistance testing has been shown to be beneficial for clinical management of HIV type 1 infected patients. Whereas phenotypic assays directly measure drug resistance, the commonly used...
Quantitative phenotype prediction by support vector machines (2002)
Beerenwinkel, N., Schmidt, B., Walter, H., Kaiser, R., Lengauer, T., Hoffmann, D., ...
Geno2pheno is predictive of short-term virological response (2002)
Beerenwinkel, N., Daumer, M., Sierra, S., Schmidt, B., Walter, H., Korn, K., ...
Freudenberg, J., Hanisch, D., Zimmer, R., Lengauer, T.
Classification of proteins is a major challenge in bioinformatics. Here an approach is presented, that unifies different existing classifications of protein structures and sequences. Protein...
Bioinformatics - from genomes to drugs. Vol.2: Applications (2002)
Die Bioinformatik verspricht die medizinisch-pharmazeutische Forschung zu revolutionieren. Dieses hochaktuelle Buch liefert das notwendige Hintergrundwissen, um das Potential der Bioinformatik...
Bioinformatics - from genomes to drugs. Vol.1: Basic technologies (2002)
Die Bioinformatik verspricht die medizinisch-pharmazeutische Forschung zu revolutionieren. Dieses hochaktuelle Buch liefert das notwendige Hintergrundwissen, um das Potential der Bioinformatik...
Confidence measures for protein fold recognition (2002)
Sommer, I., Zien, A., Öhsen, N. Von, Zimmer, R., Lengauer, T.
Motivation: We present an extensive evaluation of different methods and criteria to detect remote homologs of a given protein sequence. We investigate two associated problems: first, to develop a...
Beerenwinkel, N., Schmidt, B., Walter, H., Kaiser, R., Lengauer, T., Hoffmann, D., ...
Drug resistance testing has been shown to be beneficial for clinical management of HIV type 1 infected patients. Whereas phenotypic assays directly measure drug resistance, the commonly used...
Flexible docking under pharmacophore type constraints (2002)
Hindle, S.A., Rarey, M., Buning, C., Lengauer, T.
FlexX-Pharm, an extended version of the flexible docking tool FlexX, allows the incorporation of information about important characteristics of protein-ligand binding modes into a docking...
Computational biology at the beginning of the post-genomic era (2001)
The year 2000 will be remembered in history as the year in which the human genome has been sequenced. This marks the end of the pre-genomic era which was characterized by strong world-wide efforts to...
Derivation of a scoring function for crystal structure prediction (2001)
Apostolakis, J., Hofmann, D.W.M., Lengauer, T.
The ever increasing number of experimentally resolved crystal structures supports the possibility of fully empirical crystal structure prediction for small organic molecules. Empirical methods...
Geno2pheno: Interpreting genotypic HIV drug resistance tests (2001)
Beerenwinkel, N., Lengauer, T., Selbig, J., Schmidt, B., Walter, H., Korn, K., ...
This intelligent system uses information encoded in the HIV genomic sequence to predict the virus's resistance or susceptibility to drugs. To make predictions, geno2pheno employs decision tree...
Identification of Drug Target Proteins (2000)
Zien, A., Küffner, R., Mevissen, T., Zimmer, R., Lengauer, T.
A recursive algorithm for efficient combinatorial library docking (2000)
Due to the rapid development of combinatorial chemistry and high throughputscreening, a new virtual screening scenario emerged. While previously the focus was on analyzing large collections of...
Engineering support vector machine kernels that recognize translation initiation sites (2000)
Zien, A., Rätsch, G., Mika, S., Schölkopf, B., Lengauer, T.
Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called...
Computational methods for the structural alignment of molecules (2000)
In drug design, often enough, no structural information on a particular receptor protein is available. However, frequently a considerable number of different ligands is known together with their...
Multiple molecular superpositioning as an effective tool for virtual database screening (2000)
Lemmen, C., Zimmermann, M., Lengauer, T.
Molecular superpositioning is an important task in rational drug design. Usually it is the key step in a comparative analysis of molecules by 3D QSAR methods. Also it is helpful for the elucidation...
Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites (2000)
A. Zien, G. Rätsch, S. Mika, B. Schölkopf, T. Lengauer
Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called...
Engineering support vector machine kernels that recognize translation initiation sites (2000)
Zien, A., Rätsch, G., Mika, S., Schölkopf, B., Lengauer, T.
Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called...
Zien, A., Rätsch, G., Mika, S., Schölkopf, B., Lemmen, C., Smola, A.J., ...
Rarey, M., Kramer, B., Lengauer, T.
Water is known to play a significant role in the formation of protein-ligand complexes. In this paper, we focus on the influence of water molecules on the structure of protein-ligand complexes. We...
Robust Methods for EMC-Driven Routing (1994)
D. Theune, R. Thiele, W. John, T. Lengauer
Due to the application of fast device technologies and the increasing complexity of printed-- circuit boards, electromagnetic phenomena, e.g., reflections and crosstalk, gain more and more importance...
Robust and accurate hierarchical floorplanning with integrated global wiring (1993)
Many popular floorplanning methods are based on circuit partitioning. Besides effectiveness, their main advantages are the easy handling of flexible cells and the ability to incorporate global wiring...
Integer programming formulation of global routing and placement problems (1993)
Global routing is an essential phase during the process of physical design of integrated circuits. Combinatorially, this problem amounts to a set of interdependent Steiner tree problems. Several...
HERO: Hierarchical EMC-Constrained Routing (1992)
D. Theune, R. Thiele, T. Lengauer, A. Feldmann, Nixdorf Informationssysteme Ag
Due to the increasing significance of fast component technologies and the increasing complexity of printed circuit boards, electromagnetic phenomena, e.g. reflections and crosstalk, gain more and...
Integer Program Formulations of Global Routing and Placement Problems (1991)
Global routing is an essential phase during the process of physical design of integrated circuits. Combinatorially, this problem amounts to a set of interdependent Steiner tree problems. Several...