Volume 34; Issue Web Server

Nucleic Acids Research

Volume 34; Issue Web Server
4

MEME: discovering and analyzing DNA and protein sequence motifs

Bailey, T. L., Williams, N., Misleh, C., Li, W. W.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 221 KB
english, 2006
5

APID: Agile Protein Interaction DataAnalyzer

Prieto, C., De Las Rivas, J.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 535 KB
english, 2006
6

GRAMM-X public web server for protein-protein docking

Tovchigrechko, A., Vakser, I. A.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 732 KB
english, 2006
9

MeMo: a web tool for prediction of protein methylation modifications

Chen, H., Xue, Y., Huang, N., Yao, X., Sun, Z.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 145 KB
english, 2006
16

Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases

Mandell, J. G., Barbas, C. F.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 3.03 MB
english, 2006
19

sgTarget: a target selection resource for structural genomics

Rodrigues, A. P. C., Grant, B. J., Hubbard, R. E.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.31 MB
english, 2006
24

DILIMOT: discovery of linear motifs in proteins

Neduva, V., Russell, R. B.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.42 MB
english, 2006
25

RosettaDesign server for protein design

Liu, Y., Kuhlman, B.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 494 KB
english, 2006
26

CAPweb: a bioinformatics CGH array Analysis Platform

Liva, S., Hupe, P., Neuvial, P., Brito, I., Viara, E., Rosa, P. L., Barillot, E.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 415 KB
english, 2006
28

DyNAVacS: an integrative tool for optimized DNA vaccine design

Harish, N., Gupta, R., Agarwal, P., Scaria, V., Pillai, B.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 842 KB
english, 2006
29

CUPSAT: prediction of protein stability upon point mutations

Parthiban, V., Gromiha, M. M., Schomburg, D.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 87 KB
english, 2006
33

BLAST: improvements for better sequence analysis

Ye, J., McGinnis, S., Madden, T. L.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 513 KB
english, 2006
36

BiologicalNetworks: visualization and analysis tool for systems biology

Baitaluk, M., Sedova, M., Ray, A., Gupta, A.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 2.72 MB
english, 2006
37

WEGO: a web tool for plotting GO annotations

Ye, J., Fang, L., Zheng, H., Zhang, Y., Chen, J., Zhang, Z., Wang, J., Li, S., Li, R., Bolund, L., Wang, J.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.78 MB
english, 2006
39

RNAhybrid: microRNA target prediction easy, fast and flexible

Kruger, J., Rehmsmeier, M.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 76 KB
english, 2006
45

KOBAS server: a web-based platform for automated annotation and pathway identification

Wu, J., Mao, X., Cai, T., Luo, J., Wei, L.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 252 KB
english, 2006
48

The MPI Bioinformatics Toolkit for protein sequence analysis

Biegert, A., Mayer, C., Remmert, M., Soding, J., Lupas, A. N.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.78 MB
english, 2006
49

BAGEL: a web-based bacteriocin genome mining tool

de Jong, A., van Hijum, S. A. F. T., Bijlsma, J. J. E., Kok, J., Kuipers, O. P.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 503 KB
english, 2006
50

pTARGET: a web server for predicting protein subcellular localization

Guda, C.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 365 KB
english, 2006
52

ArchPRED: a template based loop structure prediction server

Fernandez-Fuentes, N., Zhai, J., Fiser, A.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 466 KB
english, 2006
59

BTW: a web server for Boltzmann time warping of gene expression time series

Ferre, F., Clote, P.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 589 KB
english, 2006
61

3dSS: 3D structural superposition

Sumathi, K., Ananthalakshmi, P., Roshan, M. N. A. Md., Sekar, K.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 3.45 MB
english, 2006
62

HubMed: a web-based biomedical literature search interface

Eaton, A. D.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 237 KB
english, 2006
63

FOLD-RATE: prediction of protein folding rates from amino acid sequence

Gromiha, M. M., Thangakani, A. M., Selvaraj, S.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 494 KB
english, 2006
64

JAFA: a protein function annotation meta-server

Friedberg, I., Harder, T., Godzik, A.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 94 KB
english, 2006
66

GEPS: the Gene Expression Pattern Scanner

Wang, Y.-P., Liang, L., Han, B.-C., Quan, Y., Wang, X., Tao, T., Ji, Z.-L.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.05 MB
english, 2006
67

MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes

Neph, S., Tompa, M.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 49 KB
english, 2006
72

FootPrinter3: phylogenetic footprinting in partially alignable sequences

Fang, F., Blanchette, M.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 2.21 MB
english, 2006
73

SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes

Andreson, R., Puurand, T., Remm, M.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 2.21 MB
english, 2006
77

PHEPS: web-based pH-dependent Protein Electrostatics Server

Kantardjiev, A. A., Atanasov, B. P.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 93 KB
english, 2006
78

MutScreener: primer design tool for PCR-direct sequencing

Yao, F., Zhang, R., Zhu, Z., Xia, K., Liu, C.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 205 KB
english, 2006
82

DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification

Ferre, F., Clote, P.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 406 KB
english, 2006
83

Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment

Lassmann, T., Sonnhammer, E. L. L.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.10 MB
english, 2006
84

pKD: re-designing protein pKa values

Tynan-Connolly, B. M., Nielsen, J. E.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 160 KB
english, 2006
87

HHsenser: exhaustive transitive profile search using HMM-HMM comparison

Soding, J., Remmert, M., Biegert, A., Lupas, A. N.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 502 KB
english, 2006
89

AUGUSTUS: ab initio prediction of alternative transcripts

Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., Morgenstern, B.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 254 KB
english, 2006
93

SUMOsp: a web server for sumoylation site prediction

Xue, Y., Zhou, F., Fu, C., Xu, Y., Yao, X.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 135 KB
english, 2006
95

kinDOCK: a tool for comparative docking of protein kinase ligands

Martin, L., Catherinot, V., Labesse, G.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.74 MB
english, 2006
98

ProSAT2--Protein Structure Annotation Server

Gabdoulline, R. R., Ulbrich, S., Richter, S., Wade, R. C.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 662 KB
english, 2006
100

Stubb: a program for discovery and analysis of cis-regulatory modules

Sinha, S., Liang, Y., Siggia, E.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 872 KB
english, 2006
106

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

Rampp, M., Soddemann, T., Lederer, H.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 2.18 MB
english, 2006
108

PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins

Bigelow, H., Rost, B.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 496 KB
english, 2006
111

ASGS: an alternative splicing graph web service

Bollina, D., Lee, B. T. K., Tan, T. W., Ranganathan, S.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 76 KB
english, 2006
112

PAST: fast structure-based searching in the PDB

Taubig, H., Buchner, A., Griebsch, J.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 605 KB
english, 2006
115

SVMHC: a server for prediction of MHC-binding peptides

Donnes, P., Kohlbacher, O.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 442 KB
english, 2006
117

AliWABA: alignment on the web through an A-Bruijn approach

Jones, N. C., Zhi, D., Raphael, B. J.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 110 KB
english, 2006
122

The ARTS web server for aligning RNA tertiary structures

Dror, O., Nussinov, R., Wolfson, H. J.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.13 MB
english, 2006
123

HARMONY: a server for the assessment of protein structures

Pugalenthi, G., Shameer, K., Srinivasan, N., Sowdhamini, R.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.59 MB
english, 2006
125

CEAS: cis-regulatory element annotation system

Ji, X., Li, W., Song, J., Wei, L., Liu, X. S.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.83 MB
english, 2006
129

KemaDom: a web server for domain prediction using kernel machine with local context

Chen, L., Wang, W., Ling, S., Jia, C., Wang, F.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 603 KB
english, 2006
132

PREDITOR: a web server for predicting protein torsion angle restraints

Berjanskii, M. V., Neal, S., Wishart, D. S.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.37 MB
english, 2006
134

AlgPred: prediction of allergenic proteins and mapping of IgE epitopes

Saha, S., Raghava, G. P. S.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 201 KB
english, 2006
135

(PS)2: protein structure prediction server

Chen, C.-C., Hwang, J.-K., Yang, J.-M.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 614 KB
english, 2006
136

CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments

Bindewald, E., Schneider, T. D., Shapiro, B. A.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 3.55 MB
english, 2006
139

HHrep: de novo protein repeat detection and the origin of TIM barrels

Soding, J., Remmert, M., Biegert, A.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 3.64 MB
english, 2006
140

VIRGO: computational prediction of gene functions

Massjouni, N., Rivera, C. G., Murali, T. M.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 908 KB
english, 2006
144

GenDecoder: genetic code prediction for metazoan mitochondria

Abascal, F., Zardoya, R., Posada, D.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 108 KB
english, 2006
145

jPREdictor: a versatile tool for the prediction of cis-regulatory elements

Fiedler, T., Rehmsmeier, M.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1008 KB
english, 2006
147

CorGen--measuring and generating long-range correlations for DNA sequence analysis

Messer, P. W., Arndt, P. F.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.55 MB
english, 2006
148

EDITORIAL

Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 24 KB
english, 2006
149

PreBI: prediction of biological interfaces of proteins in crystals

Tsuchiya, Y., Kinoshita, K., Ito, N., Nakamura, H.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 1.77 MB
english, 2006
152

The Path-A metabolic pathway prediction web server

Pireddu, L., Szafron, D., Lu, P., Greiner, R.
Journal:
Nucleic Acids Research
Year:
2006
Language:
english
File:
PDF, 904 KB
english, 2006