Works matching IS 03051048 AND DT 2016 AND VI 44 AND IP W1

Results: 95

InterEvDock: a docking server to predict the structure of protein--protein interactions using evolutionary information.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W542, doi. 10.1093/nar/gkw340

By:

Yu, Jinchao;
Vavrusa, Marek;
Andreani, Jessica;
Rey, Julien;
Tufféry, Pierre;
Guerois, Raphaël

Publication type:

Article

Candidate gene prioritization with Endeavour.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W117, doi. 10.1093/nar/gkw365

By:

Tranchevent, Léon-Charles;
Ardeshirdavani, Amin;
ElShal, Sarah;
Alcaide, Daniel;
Aerts, Jan;
Auboeuf, Didier;
Moreau, Yves

Publication type:

Article

tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W185, doi. 10.1093/nar/gkw414

By:

Ling-Ling Zheng;
Wei-Lin Xu;
Shun Liu;
Wen-Ju Sun;
Jun-Hao Li;
Jie Wu;
Jian-Hua Yang;
Liang-Hu Qu

Publication type:

Article

DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W166, doi. 10.1093/nar/gkw427

By:

Yuanwei Zhang;
Qiguang Zang;
Huan Zhang;
Rongjun Ban;
Yifan Yang;
Furhan Iqbal;
Ao Li;
Qinghua Shi

Publication type:

Article

GeNemo: a search engine for web-based functional genomic data.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W122, doi. 10.1093/nar/gkw299

By:

Yongqing Zhang;
Xiaoyi Caof;
Sheng Zhong

Publication type:

Article

iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W328, doi. 10.1093/nar/gkw412

By:

Chung-Han Yang;
Cheng-Ting Shih;
Kun-Tze Chen;
Po-Han Lee;
Ping-Han Tsai;
Jian-Cheng Lin;
Ching-Yu Yen;
Tiao-Yin Lin;
Chin Lung Lu

Publication type:

Article

CTLPScanner: a web server for chromothripsis-like pattern detection.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W252, doi. 10.1093/nar/gkw434

By:

Jian Yang;
Jixiang Liu;
Liang Ouyang;
Yi Chen;
Bo Liu;
Haoyang Cai

Publication type:

Article

RNAex: an RNA secondary structure prediction server enhanced by high-throughput structure-probing data.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W294, doi. 10.1093/nar/gkw362

By:

Yang Wuf;
Rihao Quf;
Yiming Huang;
Binbin Shi;
Mengrong Liu;
Yang Li;
Zhi John Lu

Publication type:

Article

mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W64, doi. 10.1093/nar/gkw247

By:

Weissensteiner, Hansi;
Forer, Lukas;
Fuchsberger, Christian;
Schöpf, Bernd;
Kloss-Brandstätter, Anita;
Specht, Gunther;
Kronenberg, Florian;
Schönherr, Sebastian

Publication type:

Article

HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W58, doi. 10.1093/nar/gkw233

By:

Weissensteiner, Hansi;
Pacher, Dominic;
Kloss-Brandstätter, Anita;
Forer, Lukas;
Specht, Gunther;
Bandelt, Hans-Jürgen;
Kronenberg, Florian;
Salas, Antonio;
Schönherr, Sebastian

Publication type:

Article

RaptorX-Property: a web server for protein structure property prediction.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W430, doi. 10.1093/nar/gkw306

By:

Sheng Wang;
Wei Li;
Shiwang Liu;
Jinbo Xu

Publication type:

Article

CoinFold: a web server for protein contact prediction and contact-assisted protein folding.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W361, doi. 10.1093/nar/gkw307

By:

Sheng Wang;
Wei Li;
Renyu Zhang;
Shiwang Liu;
Jinbo Xu

Publication type:

Article

Editorial: Nucleic Acids Research annual Web Server Issue in 2016.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W1, doi. 10.1093/nar/gkw460

By:

Benson, Gary

Publication type:

Article

DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W128, doi. 10.1093/nar/gkw455

By:

Vlachos, Ioannis S.;
Vergoulis, Thanasis;
Paraskevopoulou, Maria D.;
Lykokanellos, Filopoimin;
Georgakilas, Georgios;
Georgiou, Penny;
Chatzopoulos, Serafeim;
Karagkouni, Dimitra;
Christodoulou, Foteini;
Dalamagas, Theodore;
Hatzigeorgiou, Artemis G.

Publication type:

Article

SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W41, doi. 10.1093/nar/gkw330

By:

Veltri, Daniel;
Wight, Martha Malapi;
Crouch, Jo Anne

Publication type:

Article

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W232, doi. 10.1093/nar/gkw256

By:

Trifinopoulos, Jana;
Lam-Tung Nguyen;
von Haeseler, Arndt;
Bui Quang Minh

Publication type:

Article

miRNAFold: a web server for fast miRNA precursor prediction in genomes.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W181, doi. 10.1093/nar/gkw459

By:

Tav, Christophe;
Tempel, Sébastien;
Poligny, Laurent;
Tahi, Fariza

Publication type:

Article

MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein-ligand fragment interaction, pathways and SNPs.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W514, doi. 10.1093/nar/gkw314

By:

Duangrudee Tanramluk;
Lalita Narupiyakul;
Ruj Akavipat;
Sungsam Gong;
Varodom Charoensawan

Publication type:

Article

3D-GNOME: an integrated web service for structural modeling of the 3D genome.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W288, doi. 10.1093/nar/gkw437

By:

Szalaj, Przemyslaw;
Michalski, Paul J.;
Wróblewski, Przemys-law;
Zhonghui Tang;
Kadlof, Michal;
Mazzocco, Giovanni;
Yijun Ruan;
Plewczynski, Dariusz

Publication type:

Article

Pharmit: interactive exploration of chemical space.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W442, doi. 10.1093/nar/gkw287

By:

Sunseri, Jocelyn;
Koes, David Ryan

Publication type:

Article

Companion: a web server for annotation and analysis of parasite genomes.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W29, doi. 10.1093/nar/gkw292

By:

Steinbiss, Sascha;
Silva-Franco, Fatima;
Brunk, Brian;
Foth, Bernardo;
Hertz-Fowler, Christiane;
Berriman, Matthew;
Otto, Thomas D.

Publication type:

Article

PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W205, doi. 10.1093/nar/gkw415

By:

Sriyudthsak, Kansuporn;
Mejia, Ramon Francisco;
Arita, Masanori;
Masami Yokota Hirai

Publication type:

Article

GAM: a web-service for integrated transcriptional and metabolic network analysis.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W194, doi. 10.1093/nar/gkw266

By:

Sergushichev, Alexey A.;
Loboda, Alexander A.;
Jha, Abhishek K.;
Vincent, Emma E.;
Driggers, Edward M.;
Jones, Russell G.;
Pearce, Edward J.;
Artyomov, Maxim N.

Publication type:

Article

Peptiderive server: derive peptide inhibitors from protein-protein interactions.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W536, doi. 10.1093/nar/gkw385

By:

Sedan, Yuval;
Marcu, Orly;
Lyskov, Sergey;
Schueler-Furman, Ora

Publication type:

Article

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W424, doi. 10.1093/nar/gkw389

By:

Schneidman-Duhovny, Dina;
Hammel, Michal;
Tainer, John A.;
Sali, Andrej

Publication type:

Article

Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W212, doi. 10.1093/nar/gkw369

By:

Salavert, Francisco;
Hidago, Marta R.;
Amadoz, Alicia;
Çubuk, Cankut;
Medina, Ignacio;
Crespo, Daniel;
Carbonell-Caballero, Jose;
Dopazo, Joaquín

Publication type:

Article

BetaSCPWeb: side-chain prediction for protein structures using Voronoi diagrams and geometry prioritization.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W416, doi. 10.1093/nar/gkw368

By:

Joonghyun Ryu;
Mokwon Lee;
Jehyun Cha;
Laskowski, Roman A.;
Seong Eon Ryu;
Deok-Soo Kim

Publication type:

Article

JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W320, doi. 10.1093/nar/gkw453

By:

Roll, James;
Zirbel, Craig L.;
Sweeney, Blake;
Petrov, Anton I.;
Leontis, Neocles

Publication type:

Article

GIANT API: an application programming interface for functional genomics.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W587, doi. 10.1093/nar/gkw289

By:

Roberts, Andrew M.;
Wong, Aaron K.;
Fisk, Ian;
Troyanskaya, Olga G.

Publication type:

Article

PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W246, doi. 10.1093/nar/gkw359

By:

Ribeiro-Gonçalves, Bruno;
Francisco, Alexandre P.;
Vaz, Cátia;
Ramirez, Mário;
Carriço, João André

Publication type:

Article

g:Profiler--a web server for functional interpretation of gene lists (2016 update).

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W83, doi. 10.1093/nar/gkw199

By:

Reimand, Jüri;
Arak, Tambet;
Adler, Priit;
Kolberg, Liis;
Reisberg, Sulev;
Peterson, Hedi;
Vilo, Jaak

Publication type:

Article

deepTools2: a next generation web server for deep-sequencing data analysis.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W160, doi. 10.1093/nar/gkw257

By:

Ramírez, Fidel;
Ryan, Devon P.;
Grüning, Björn;
Bhardwaj, Vivek;
Kilpert, Fabian;
Richter, Andreas S.;
Heyne, Steffen;
Dündar, Friederike;
Manke, Thomas

Publication type:

Article

EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W142, doi. 10.1093/nar/gkw298

By:

Pulido-Tamayo, Sergio;
Duitama, Jorge;
Marchal, Kathleen

Publication type:

Article

CSM-lig: a web server for assessing and comparing protein-small molecule affinities.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W557, doi. 10.1093/nar/gkw390

By:

Pires, Douglas E. V.;
Ascher, David B.

Publication type:

Article

mCSM-AB: a web server for predicting antibody-antigen affinity changes upon mutation with graph-based signatures.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W469, doi. 10.1093/nar/gkw458

By:

Pires, Douglas E. V.;
Ascher, David B.

Publication type:

Article

The RING 2.0 web server for high quality residue interaction networks.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W367, doi. 10.1093/nar/gkw315

By:

Piovesan, Damiano;
Minervini, Giovanni;
Tosatto, Silvio C. E.

Publication type:

Article

BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W568, doi. 10.1093/nar/gkw454

By:

Paz, Inbal;
Kligun, Efrat;
Bengad, Barak;
Mandel-Gutfreund, Yael

Publication type:

Article

Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W256, doi. 10.1093/nar/gkw304

By:

Parra, R. Gonzalo;
Schafer, Nicholas P.;
Radusky, Leandro G.;
Min-Yeh Tsai;
Guzovsky, A. Brenda;
Wolynes, Peter G.;
Ferreiro, Diego U.

Publication type:

Article

rMAPS: RNA map analysis and plotting server for alternative exon regulation.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W333, doi. 10.1093/nar/gkw410

By:

Juw Won Park;
Sungbo Jung;
Rouchka, Eric C.;
Yu-Ting Tseng;
Yi Xing

Publication type:

Article

Breaking-Cas--interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W267, doi. 10.1093/nar/gkw407

By:

Oliveros, Juan C.;
Franch, Mònica;
Tabas-Madrid, Daniel;
San-León, David;
Montoliu, Lluis;
Cubas, Pilar;
Pazos, Florencio

Publication type:

Article

PathwAX: a web server for network crosstalk based pathway annotation.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W105, doi. 10.1093/nar/gkw356

By:

Ogris, Christoph;
Helleday, Thomas;
Sonnhammer, Erik L. L.

Publication type:

Article

PepComposer: computational design of peptides binding to a given protein surface.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W522, doi. 10.1093/nar/gkw366

By:

Obarska-Kosinska, Agnieszka;
Iacoangeli, Alfredo;
Lepore, Rosalba;
Tramontano, Anna

Publication type:

Article

RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W562, doi. 10.1093/nar/gkw251

By:

Zhichao Miao;
Westhof, Eric

Publication type:

Article

MoRFchibi SYSTEM: software tools for the identification of MoRFs in protein sequences.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W488, doi. 10.1093/nar/gkw409

By:

Malhis, Nawar;
Jacobson, Matthew;
Gsponer, Jörg

Publication type:

Article

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W315, doi. 10.1093/nar/gkw279

By:

Magnus, Marcin;
Boniecki, Michał J.;
Dawson, Wayne;
Bujnicki, Janusz M.

Publication type:

Article

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W54, doi. 10.1093/nar/gkw413

By:

Lowe, Todd M.;
Chan, Patricia P.

Publication type:

Article

MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W494, doi. 10.1093/nar/gkw374

By:

Minghui Li;
Simonetti, Franco L.;
Goncearenco, Alexander;
Panchenko, Anna R.

Publication type:

Article

USR-VS: a web server for large-scale prospective virtual screening using ultrafast shape recognition techniques.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W436, doi. 10.1093/nar/gkw320

By:

Hongjian Li;
Kwong-S. Leung;
Man-H. Wong;
Ballester, Pedro J.

Publication type:

Article

KeyPathwayMinerWeb: online multi-omics network enrichment.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W98, doi. 10.1093/nar/gkw373

By:

List, Markus;
Alcaraz, Nicolas;
Dissing-Hansen, Martin;
Ditzel, Henrik J.;
Mollenhauer, Jan;
Baumbach, Jan

Publication type:

Article

MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification.

Published in:

Nucleic Acids Research, 2016, v. 44, n. W1, p. W575, doi. 10.1093/nar/gkw254

By:

Lih, T. Mamie;
Wai-Kok Choong;
Chen-Chun Chen;
Cheng-Wei Cheng;
Hsin-Nan Lin;
Ching-Tai Chen;
Hui-Yin Chang;
Wen-Lian Hsu;
Ting-Yi Sung

Publication type:

Article