Works matching IS 03051048 AND DT 2011 AND VI 39 AND IP suppl_2

Results: 96

MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W167, doi. 10.1093/nar/gkr490

By:

Tjioe, Elina;
Lasker, Keren;
Webb, Ben;
Wolfson, Haim J.;
Sali, Andrej

Publication type:

Article

The RNAmute web server for the mutational analysis of RNA secondary structures.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W92, doi. 10.1093/nar/gkr207

By:

Churkin, Alexander;
Gabdank, Idan;
Barash, Danny

Publication type:

Article

BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W462, doi. 10.1093/nar/gkr285

By:

Sen Sarma, Moushumi;
Arcoleo, David;
Khetani, Radhika S.;
Chee, Brant;
Ling, Xu;
He, Xin;
Jiang, Jing;
Mei, Qiaozhu;
Zhai, ChengXiang;
Schatz, Bruce

Publication type:

Article

ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W430, doi. 10.1093/nar/gkr332

By:

Qin, Jing;
Li, Mulin Jun;
Wang, Panwen;
Zhang, Michael Q.;
Wang, Junwen

Publication type:

Article

ARISTO: ontological classification of small molecules by electron ionization-mass spectrometry.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W505, doi. 10.1093/nar/gkr403

By:

Askenazi, Manor;
Linial, Michal

Publication type:

Article

PHAST: A Fast Phage Search Tool.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W347, doi. 10.1093/nar/gkr485

By:

Zhou, You;
Liang, Yongjie;
Lynch, Karlene H.;
Dennis, Jonathan J.;
Wishart, David S.

Publication type:

Article

NRPSpredictor2—a web server for predicting NRPS adenylation domain specificity.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W362, doi. 10.1093/nar/gkr323

By:

Röttig, Marc;
Medema, Marnix H.;
Blin, Kai;
Weber, Tilmann;
Rausch, Christian;
Kohlbacher, Oliver

Publication type:

Article

GPU.proton.DOCK: Genuine Protein Ultrafast proton equilibria consistent DOCKing.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W223, doi. 10.1093/nar/gkr412

By:

Kantardjiev, Alexander A.

Publication type:

Article

MetalDetector v2.0: predicting the geometry of metal binding sites from protein sequence.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W288, doi. 10.1093/nar/gkr365

By:

Passerini, Andrea;
Lippi, Marco;
Frasconi, Paolo

Publication type:

Article

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W112, doi. 10.1093/nar/gkr357

By:

Fasold, Mario;
Langenberger, David;
Binder, Hans;
Stadler, Peter F.;
Hoffmann, Steve

Publication type:

Article

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W524, doi. 10.1093/nar/gkr373

By:

Muiño, Jose M.;
Hoogstraat, Marlous;
van Ham, Roeland C. H. J.;
van Dijk, Aalt D. J.

Publication type:

Article

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W511, doi. 10.1093/nar/gkr288

By:

Vanquelef, Enguerran;
Simon, Sabrina;
Marquant, Gaelle;
Garcia, Elodie;
Klimerak, Geoffroy;
Delepine, Jean Charles;
Cieplak, Piotr;
Dupradeau, François-Yves

Publication type:

Article

ncFANs: a web server for functional annotation of long non-coding RNAs.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W118, doi. 10.1093/nar/gkr432

By:

Liao, Qi;
Xiao, Hui;
Bu, Dechao;
Xie, Chaoyong;
Miao, Ruoyu;
Luo, Haitao;
Zhao, Guoguang;
Yu, Kuntao;
Zhao, Haitao;
Skogerbø, Geir;
Chen, Runsheng;
Wu, Zhongdao;
Liu, Changning;
Zhao, Yi

Publication type:

Article

AnnotQTL: a new tool to gather functional and comparative information on a genomic region.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W328, doi. 10.1093/nar/gkr361

By:

Lecerf, F.;
Bretaudeau, A.;
Sallou, O.;
Desert, C.;
Blum, Y.;
Lagarrigue, S.;
Demeure, O.

Publication type:

Article

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W278, doi. 10.1093/nar/gkr389

By:

Parca, Luca;
Mangone, Iolanda;
Gherardini, Pier Federico;
Ausiello, Gabriele;
Helmer-Citterich, Manuela

Publication type:

Article

Update of PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W385, doi. 10.1093/nar/gkr284

By:

Rao, H. B.;
Zhu, F.;
Yang, G. B.;
Li, Z. R.;
Chen, Y. Z.

Publication type:

Article

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W8, doi. 10.1093/nar/gkr244

By:

Sahraeian, Sayed Mohammad Ebrahim;
Yoon, Byung-Jun

Publication type:

Article

DEPTH: a web server to compute depth and predict small-molecule binding cavities in proteins.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W242, doi. 10.1093/nar/gkr356

By:

Tan, Kuan Pern;
Varadarajan, Raghavan;
Madhusudhan, M. S.

Publication type:

Article

PredUs: a web server for predicting protein interfaces using structural neighbors.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W283, doi. 10.1093/nar/gkr311

By:

Zhang, Qiangfeng Cliff;
Deng, Lei;
Fisher, Markus;
Guan, Jihong;
Honig, Barry;
Petrey, Donald

Publication type:

Article

GCView: the genomic context viewer for protein homology searches.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W353, doi. 10.1093/nar/gkr364

By:

Grin, Iwan;
Linke, Dirk

Publication type:

Article

Nucleic Acids Research.

Published in:: Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. ii, doi. 10.1093/nar/gkr569
Publication type:: Article

CLICK—topology-independent comparison of biomolecular 3D structures.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W24, doi. 10.1093/nar/gkr393

By:

Nguyen, M. N.;
Tan, K. P.;
Madhusudhan, M. S.

Publication type:

Article

The University of Minnesota Pathway Prediction System: multi-level prediction and visualization.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W406, doi. 10.1093/nar/gkr200

By:

Gao, Junfeng;
Ellis, Lynda B. M.;
Wackett, Lawrence P.

Publication type:

Article

KINARI-Web: a server for protein rigidity analysis.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W177, doi. 10.1093/nar/gkr482

By:

Fox, Naomi;
Jagodzinski, Filip;
Li, Yang;
Streinu, Ileana

Publication type:

Article

PRUNE and PROBE—two modular web services for protein–protein docking.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W229, doi. 10.1093/nar/gkr317

By:

Mitra, Pralay;
Pal, Debnath

Publication type:

Article

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W541, doi. 10.1093/nar/gkr469

By:

Whetzel, Patricia L.;
Noy, Natalya F.;
Shah, Nigam H.;
Alexander, Paul R.;
Nyulas, Csongor;
Tudorache, Tania;
Musen, Mark A.

Publication type:

Article

SwissDock, a protein-small molecule docking web service based on EADock DSS.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W270, doi. 10.1093/nar/gkr366

By:

Grosdidier, Aurélien;
Zoete, Vincent;
Michielin, Olivier

Publication type:

Article

R3D-BLAST: a search tool for similar RNA 3D substructures.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W45, doi. 10.1093/nar/gkr379

By:

Liu, Yun-Chen;
Yang, Chung-Han;
Chen, Kun-Tze;
Wang, Jyun-Rong;
Cheng, Mei-Ling;
Chung, Jen-Chun;
Chiu, Hsien-Tai;
Lu, Chin Lung

Publication type:

Article

The 2011 bioinformatics links directory update: more resources, tools and databases and features to empower the bioinformatics community.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W3, doi. 10.1093/nar/gkr514

By:

Brazas, Michelle D.;
Yim, David S.;
Yamada, Joseph T.;
Ouellette, B. F. Francis

Publication type:

Article

PepServe: a web server for peptide analysis, clustering and visualization.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W381, doi. 10.1093/nar/gkr318

By:

Alexandridou, Anastasia;
Dovrolis, Nikolas;
Tsangaris, George Th.;
Nikita, Konstantina;
Spyrou, George

Publication type:

Article

Detecting selection in immunoglobulin sequences.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W499, doi. 10.1093/nar/gkr413

By:

Uduman, Mohamed;
Yaari, Gur;
Hershberg, Uri;
Stern, Jacob A.;
Shlomchik, Mark J.;
Kleinstein, Steven H.

Publication type:

Article

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W13, doi. 10.1093/nar/gkr245

By:

Di Tommaso, Paolo;
Moretti, Sebastien;
Xenarios, Ioannis;
Orobitg, Miquel;
Montanyola, Alberto;
Chang, Jia-Ming;
Taly, Jean-François;
Notredame, Cedric

Publication type:

Article

CENTDIST: discovery of co-associated factors by motif distribution.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W391, doi. 10.1093/nar/gkr387

By:

Zhang, Zhizhuo;
Chang, Cheng Wei;
Goh, Wan Ling;
Sung, Wing-Kin;
Cheung, Edwin

Publication type:

Article

RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W293, doi. 10.1093/nar/gkr507

By:

Gruca, Aleksandra;
Sikora, Marek;
Polanski, Andrzej

Publication type:

Article

SNPsyn: detection and exploration of SNP–SNP interactions.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W444, doi. 10.1093/nar/gkr321

By:

Curk, Tomaz;
Rot, Gregor;
Zupan, Blaz

Publication type:

Article

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W533, doi. 10.1093/nar/gkr353

By:

Kobayashi, Norio;
Ishii, Manabu;
Takahashi, Satoshi;
Mochizuki, Yoshiki;
Matsushima, Akihiro;
Toyoda, Tetsuro

Publication type:

Article

HapEdit: an accuracy assessment viewer for haplotype assembly using massively parallel DNA-sequencing technologies.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W557, doi. 10.1093/nar/gkr354

By:

Kim, Jong Hyun;
Kim, Woo-Cheol;
Li, Lei M.;
Park, Sanghyun

Publication type:

Article

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W339, doi. 10.1093/nar/gkr466

By:

Medema, Marnix H.;
Blin, Kai;
Cimermancic, Peter;
de Jager, Victor;
Zakrzewski, Piotr;
Fischbach, Michael A.;
Weber, Tilmann;
Takano, Eriko;
Breitling, Rainer

Publication type:

Article

PHUSER (Primer Help for USER): a novel tool for USER fusion primer design.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W61, doi. 10.1093/nar/gkr394

By:

Olsen, Lars Rønn;
Hansen, Niels Bjørn;
Bonde, Mads Tvillinggaard;
Genee, Hans Jasper;
Holm, Dorte Koefoed;
Carlsen, Simon;
Hansen, Bjarne Gram;
Patil, Kiran Raosaheb;
Mortensen, Uffe Hasbro;
Wernersson, Rasmus

Publication type:

Article

CURVES+ web server for analyzing and visualizing the helical, backbone and groove parameters of nucleic acid structures.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W68, doi. 10.1093/nar/gkr316

By:

Blanchet, Christophe;
Pasi, Marco;
Zakrzewska, Krystyna;
Lavery, Richard

Publication type:

Article

The FALC-Loop web server for protein loop modeling.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W210

By:

Ko, Junsu;
Lee, Dongseon;
Park, Hahnbeom;
Coutsias, Evangelos A.;
Lee, Julian;
Seok, Chaok

Publication type:

Article

firestar—advances in the prediction of functionally important residues.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W235, doi. 10.1093/nar/gkr437

By:

Lopez, Gonzalo;
Maietta, Paolo;
Rodriguez, Jose Manuel;
Valencia, Alfonso;
Tress, Michael L.

Publication type:

Article

iPBA: a tool for protein structure comparison using sequence alignment strategies.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W18, doi. 10.1093/nar/gkr333

By:

Gelly, Jean-Christophe;
Joseph, Agnel Praveen;
Srinivasan, Narayanaswamy;
de Brevern, Alexandre G.

Publication type:

Article

BioProfiling.de: analytical web portal for high-throughput cell biology.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W323, doi. 10.1093/nar/gkr372

By:

Antonov, Alexey V.

Publication type:

Article

The PETfold and PETcofold web servers for intra- and intermolecular structures of multiple RNA sequences.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W107, doi. 10.1093/nar/gkr248

By:

Seemann, Stefan E.;
Menzel, Peter;
Backofen, Rolf;
Gorodkin, Jan

Publication type:

Article

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W316, doi. 10.1093/nar/gkr483

By:

Xie, Chen;
Mao, Xizeng;
Huang, Jiaju;
Ding, Yang;
Wu, Jianmin;
Dong, Shan;
Kong, Lei;
Gao, Ge;
Li, Chuan-Yun;
Wei, Liping

Publication type:

Article

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W100, doi. 10.1093/nar/gkr290

By:

Hamada, Michiaki;
Yamada, Koichiro;
Sato, Kengo;
Frith, Martin C.;
Asai, Kiyoshi

Publication type:

Article

RSAT 2011: regulatory sequence analysis tools.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W86, doi. 10.1093/nar/gkr377

By:

Thomas-Chollier, Morgane;
Defrance, Matthieu;
Medina-Rivera, Alejandra;
Sand, Olivier;
Herrmann, Carl;
Thieffry, Denis;
van Helden, Jacques

Publication type:

Article

Swimming into peptidomimetic chemical space using pepMMsMIMIC.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W261, doi. 10.1093/nar/gkr287

By:

Floris, Matteo;
Masciocchi, Joel;
Fanton, Marco;
Moro, Stefano

Publication type:

Article

MarkUs: a server to navigate sequence–structure–function space.

Published in:

Nucleic Acids Research, 2011, v. 39, n. suppl_2, p. W357, doi. 10.1093/nar/gkr468

By:

Fischer, Markus;
Zhang, Qiangfeng Cliff;
Dey, Fabian;
Chen, Brian Y.;
Honig, Barry;
Petrey, Donald

Publication type:

Article