BA: CorreLogo: an online server for 3D sequence logos (2008)
Eckart Bindewald, Thomas D. Schneider, Bruce A. Shapiro
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
Bindewald, Eckart, Hayes, Robert, Yingling, Yaroslava G., Kasprzak, Wojciech, Shapiro, Bruce A.
We developed a database called RNAJunction that contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions....
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments (2006)
Bindewald, Eckart, Schneider, Thomas D., Shapiro, Bruce A.
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
The SSEA server for protein secondary structure alignment (2005)
Paolo Fontana, Eckart Bindewald, Riccardo Velasco, Giorgio Valle, Via E. Mach
The SSEA server for protein secondary structure alignment (2005)
Fontana, Paolo, Bindewald, Eckart, Toppo, Stefano, Velasco, Riccardo, Valle, Giorgio, Tosatto, Silvio C. E.
Summary: We present a web server that computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a...
Structural polymorphism of the HIV-1 leader region explored by computational methods (2005)
Kasprzak, Wojciech, Bindewald, Eckart, Shapiro, Bruce A.
Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5′-untranslated leader region (5′-UTR) can fold in vitro into two alternative conformations,...
The SSEA server for protein secondary structure alignment (2004)
Fontana, Paolo, Bindewald, Eckart, Toppo, Stefano, Velasco, Riccardo, Valle, Giorgio, Tosatto, Silvio C. E.
Summary: We present a web server which computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a...
The SSEA server for protein secondary structure alignment (2004)
Fontana, Paolo, Bindewald, Eckart, Toppo, Stefano, Velasco, Riccardo, Valle, Giorgio, Tosatto, Silvio C. E.
Summary: We present a web server which computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a...
A divide and conquer approach to fast loop modeling (2002)
Tosatto, Silvio C.E., Bindewald, Eckart, Hesser, Jürgen, Männer, Reinhard
We describe a fast ab initio method for modeling local segments in protein structures. The algorithm is based on a divide and conquer approach and uses a database of precalculated look-up tables,...
Structural polymorphism of the HIV-1 leader region explored by computational methods
Kasprzak, Wojciech, Bindewald, Eckart, Shapiro, Bruce A.
Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5′-untranslated leader region (5′-UTR) can fold in vitro into two alternative conformations,...
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
Bindewald, Eckart, Schneider, Thomas D., Shapiro, Bruce A.
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
BINDEWALD, ECKART, SHAPIRO, BRUCE A.
We present a machine learning method (a hierarchical network of k-nearest neighbor classifiers) that uses an RNA sequence alignment in order to predict a consensus RNA secondary structure. The input...
Structural polymorphism of the HIV-1 leader region explored by computational methods
Kasprzak, Wojciech, Bindewald, Eckart, Shapiro, Bruce A.
Experimental studies revealed that the elements of the human immunodeficiency virus type 1 (HIV-1) 5′-untranslated leader region (5′-UTR) can fold in vitro into two alternative conformations,...
BINDEWALD, ECKART, SHAPIRO, BRUCE A.
We present a machine learning method (a hierarchical network of k-nearest neighbor classifiers) that uses an RNA sequence alignment in order to predict a consensus RNA secondary structure. The input...
CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments
Bindewald, Eckart, Schneider, Thomas D., Shapiro, Bruce A.
We present an online server that generates a 3D representation of properties of user-submitted RNA or DNA alignments. The visualized properties are information of single alignment columns, mutual...
Bindewald, Eckart, Hayes, Robert, Yingling, Yaroslava G., Kasprzak, Wojciech, Shapiro, Bruce A.
We developed a database called RNAJunction that contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop–loop interactions....
Role of 3′UTRs in the Translation of mRNAs Regulated by Oncogenic eIF4E—A Computational Inference
Santhanam, Arti N., Bindewald, Eckart, Rajasekhar, Vinagolu K., Larsson, Ola, Sonenberg, Nahum, Colburn, Nancy H., ...
Eukaryotic cap-dependent mRNA translation is mediated by the initiation factor eIF4E, which binds mRNAs and stimulates efficient translation initiation. eIF4E is often overexpressed in human cancers....