Volume 43; Issue W1

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Nucleic Acids Research
Volume 43; Issue W1

Nucleic Acids Research

Volume 43; Issue W1

1

The EMBL-EBI bioinformatics web and programmatic tools framework

Li, Weizhong, Cowley, Andrew, Uludag, Mahmut, Gur, Tamer, McWilliam, Hamish, Squizzato, Silvano, Park, Young Mi, Buso, Nicola, Lopez, Rodrigo

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.19 MB

english, 2015

2

The EBI Search engine: providing search and retrieval functionality for biological data from EMBL-EBI

Squizzato, Silvano, Park, Young Mi, Buso, Nicola, Gur, Tamer, Cowley, Andrew, Li, Weizhong, Uludag, Mahmut, Pundir, Sangya, Cham, Jennifer A., McWilliam, Hamish, Lopez, Rodrigo

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 81 KB

english, 2015

3

RNAPattMatch: a web server for RNA sequence/structure motif detection based on pattern matching with flexible gaps

Drory Retwitzer, Matan, Polishchuk, Maya, Churkin, Elena, Kifer, Ilona, Yakhini, Zohar, Barash, Danny

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.95 MB

english, 2015

4

The iceLogo web server and SOAP service for determining protein consensus sequences

Maddelein, Davy, Colaert, Niklaas, Buchanan, Iain, Hulstaert, Niels, Gevaert, Kris, Martens, Lennart

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 990 KB

english, 2015

5

PrionW: a server to identify proteins containing glutamine/asparagine rich prion-like domains and their amyloid cores

Zambrano, Rafael, Conchillo-Sole, Oscar, Iglesias, Valentin, Illa, Ricard, Rousseau, Frederic, Schymkowitz, Joost, Sabate, Raimon, Daura, Xavier, Ventura, Salvador

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.84 MB

english, 2015

6

TFmiR: a web server for constructing and analyzing disease-specific transcription factor and miRNA co-regulatory networks

Hamed, Mohamed, Spaniol, Christian, Nazarieh, Maryam, Helms, Volkhard

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 589 KB

english, 2015

7

OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

Wang, Yi, Coleman-Derr, Devin, Chen, Guoping, Gu, Yong Q.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.79 MB

english, 2015

8

The MEME Suite

Bailey, Timothy L., Johnson, James, Grant, Charles E., Noble, William S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.86 MB

english, 2015

9

HMMER web server: 2015 update

Finn, Robert D., Clements, Jody, Arndt, William, Miller, Benjamin L., Wheeler, Travis J., Schreiber, Fabian, Bateman, Alex, Eddy, Sean R.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.84 MB

english, 2015

10

SIFTER search: a web server for accurate phylogeny-based protein function prediction

Sahraeian, Sayed M., Luo, Kevin R., Brenner, Steven E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.81 MB

english, 2015

11

PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more

Liu, Yifeng, Liang, Yongjie, Wishart, David

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.68 MB

english, 2015

12

MetaboAnalyst 3.0—making metabolomics more meaningful

Xia, Jianguo, Sinelnikov, Igor V., Han, Beomsoo, Wishart, David S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.74 MB

english, 2015

13

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

Kurcinski, Mateusz, Jamroz, Michal, Blaszczyk, Maciej, Kolinski, Andrzej, Kmiecik, Sebastian

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.57 MB

english, 2015

14

Galahad: a web server for drug effect analysis from gene expression

Laenen, Griet, Ardeshirdavani, Amin, Moreau, Yves, Thorrez, Lieven

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 290 KB

english, 2015

15

SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets

Petsalaki, Evangelia, Helbig, Andreas O., Gopal, Anjali, Pasculescu, Adrian, Roth, Frederick P., Pawson, Tony

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.14 MB

english, 2015

16

MapMyFlu: visualizing spatio-temporal relationships between related influenza sequences

Nolte, Nicholas, Kurzawa, Nils, Eils, Roland, Herrmann, Carl

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.13 MB

english, 2015

17

NFFinder: an online bioinformatics tool for searching similar transcriptomics experiments in the context of drug repositioning

Setoain, Javier, Franch, Mònica, Martínez, Marta, Tabas-Madrid, Daniel, Sorzano, Carlos O. S., Bakker, Annette, Gonzalez-Couto, Eduardo, Elvira, Juan, Pascual-Montano, Alberto

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.33 MB

english, 2015

18

CCTOP: a Consensus Constrained TOPology prediction web server

Dobson, László, Reményi, István, Tusnády, Gábor E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.14 MB

english, 2015

19

PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins

Hussein, Hiba Abi, Borrel, Alexandre, Geneix, Colette, Petitjean, Michel, Regad, Leslie, Camproux, Anne-Claude

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.22 MB

english, 2015

20

pyDockSAXS: protein–protein complex structure by SAXS and computational docking

Jiménez-García, Brian, Pons, Carles, Svergun, Dmitri I., Bernadó, Pau, Fernández-Recio, Juan

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.18 MB

english, 2015

21

PLIP: fully automated protein–ligand interaction profiler

Salentin, Sebastian, Schreiber, Sven, Haupt, V. Joachim, Adasme, Melissa F., Schroeder, Michael

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.85 MB

english, 2015

22

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

Weber, Tilmann, Blin, Kai, Duddela, Srikanth, Krug, Daniel, Kim, Hyun Uk, Bruccoleri, Robert, Lee, Sang Yup, Fischbach, Michael A., Müller, Rolf, Wohlleben, Wolfgang, Breitling, Rainer, Takano, Eriko,

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.15 MB

english, 2015

23

(PS) 2 : protein structure prediction server version 3.0

Huang, Tsun-Tsao, Hwang, Jenn-Kang, Chen, Chu-Huang, Chu, Chih-Sheng, Lee, Chi-Wen, Chen, Chih-Chieh

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.07 MB

english, 2015

24

I-TASSER server: new development for protein structure and function predictions

Yang, Jianyi, Zhang, Yang

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.87 MB

english, 2015

25

MTiOpenScreen: a web server for structure-based virtual screening

Labbé, Céline M., Rey, Julien, Lagorce, David, Vavruša, Marek, Becot, Jérome, Sperandio, Olivier, Villoutreix, Bruno O., Tufféry, Pierre, Miteva, Maria A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.29 MB

english, 2015

26

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

Liu, Bin, Liu, Fule, Wang, Xiaolong, Chen, Junjie, Fang, Longyun, Chou, Kuo-Chen

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.69 MB

english, 2015

27

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity

Piovesan, Damiano, Giollo, Manuel, Leonardi, Emanuela, Ferrari, Carlo, Tosatto, Silvio C.E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

28

ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap

Metsalu, Tauno, Vilo, Jaak

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 170 KB

english, 2015

29

Web-Beagle: a web server for the alignment of RNA secondary structures: Figure 1.

Mattei, Eugenio, Pietrosanto, Marco, Ferrè, Fabrizio, Helmer-Citterich, Manuela

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 995 KB

english, 2015

30

sRNAtoolbox: an integrated collection of small RNA research tools

Rueda, Antonio, Barturen, Guillermo, Lebrón, Ricardo, Gómez-Martín, Cristina, Alganza, Ángel, Oliver, José L., Hackenberg, Michael

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.95 MB

english, 2015

31

NPDock: a web server for protein–nucleic acid docking

Tuszynska, Irina, Magnus, Marcin, Jonak, Katarzyna, Dawson, Wayne, Bujnicki, Janusz M.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 903 KB

english, 2015

32

QmRLFS-finder: a model, web server and stand-alone tool for prediction and analysis of R-loop forming sequences

Jenjaroenpun, Piroon, Wongsurawat, Thidathip, Yenamandra, Surya Pavan, Kuznetsov, Vladimir A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.68 MB

english, 2015

33

NGL Viewer: a web application for molecular visualization

Rose, Alexander S., Hildebrand, Peter W.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.11 MB

english, 2015

34

LYRA, a webserver for lymphocyte receptor structural modeling

Klausen, Michael Schantz, Anderson, Mads Valdemar, Jespersen, Martin Closter, Nielsen, Morten, Marcatili, Paolo

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.34 MB

english, 2015

35

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

Sela, Itamar, Ashkenazy, Haim, Katoh, Kazutaka, Pupko, Tal

Journal:

Nucleic Acids Research

Year:

2015

File:

PDF, 1.14 MB

2015

36

IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks

Wong, Aaron K., Krishnan, Arjun, Yao, Victoria, Tadych, Alicja, Troyanskaya, Olga G.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.57 MB

english, 2015

37

SANSparallel: interactive homology search against Uniprot

Somervuo, Panu, Holm, Liisa

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.65 MB

english, 2015

38

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

Sela, Itamar, Ashkenazy, Haim, Katoh, Kazutaka, Pupko, Tal

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.14 MB

english, 2015

39

RiceNet v2: an improved network prioritization server for rice genes

Lee, Tak, Oh, Taeyun, Yang, Sunmo, Shin, Junha, Hwang, Sohyun, Kim, Chan Yeong, Kim, Hyojin, Shim, Hongseok, Shim, Jung Eun, Ronald, Pamela C., Lee, Insuk

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 808 KB

english, 2015

40

CATNAP: a tool to compile, analyze and tally neutralizing antibody panels

Yoon, Hyejin, Macke, Jennifer, West, Anthony P., Foley, Brian, Bjorkman, Pamela J., Korber, Bette, Yusim, Karina

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.57 MB

english, 2015

41

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

Imrichová, Hana, Hulselmans, Gert, Kalender Atak, Zeynep, Potier, Delphine, Aerts, Stein

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.62 MB

english, 2015

42

IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis: Figure 1.

Dhillon, Bhavjinder K., Laird, Matthew R., Shay, Julie A., Winsor, Geoffrey L., Lo, Raymond, Nizam, Fazmin, Pereira, Sheldon K., Waglechner, Nicholas, McArthur, Andrew G., Langille, Morgan G.I., Brink

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 998 KB

english, 2015

43

MS 2 PIP prediction server: compute and visualize MS 2 peak intensity predictions for CID and HCD fragmentation

Degroeve, Sven, Maddelein, Davy, Martens, Lennart

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 818 KB

english, 2015

44

IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences: Figure 1.

McGuffin, Liam J., Atkins, Jennifer D., Salehe, Bajuna R., Shuid, Ahmad N., Roche, Daniel B.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 3.28 MB

english, 2015

45

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics

Knight, Christopher J., Hub, Jochen S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.87 MB

english, 2015

46

Stock-based detection of protein oligomeric states in jsPISA

Krissinel, Eugene

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.44 MB

english, 2015

47

The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community

Darde, Thomas A., Sallou, Olivier, Becker, Emmanuelle, Evrard, Bertrand, Monjeaud, Cyril, Le Bras, Yvan, Jégou, Bernard, Collin, Olivier, Rolland, Antoine D., Chalmel, Frédéric

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.27 MB

english, 2015

48

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL

May, Ali, Abeln, Sanne, Buijs, Mark J., Heringa, Jaap, Crielaard, Wim, Brandt, Bernd W.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 643 KB

english, 2015

49

PheNetic: network-based interpretation of molecular profiling data

De Maeyer, Dries, Weytjens, Bram, Renkens, Joris, De Raedt, Luc, Marchal, Kathleen

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.50 MB

english, 2015

50

Assessing the impact of mutations found in next generation sequencing data over human signaling pathways

Hernansaiz-Ballesteros, Rosa D., Salavert, Francisco, Sebastián-León, Patricia, Alemán, Alejandro, Medina, Ignacio, Dopazo, Joaquín

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 742 KB

english, 2015

51

The BioMart community portal: an innovative alternative to large, centralized data repositories

Smedley, Damian, Haider, Syed, Durinck, Steffen, Pandini, Luca, Provero, Paolo, Allen, James, Arnaiz, Olivier, Awedh, Mohammad Hamza, Baldock, Richard, Barbiera, Giulia, Bardou, Philippe, Beck, Tim, B

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.34 MB

english, 2015

52

FAF-Drugs3: a web server for compound property calculation and chemical library design

Lagorce, David, Sperandio, Olivier, Baell, Jonathan B., Miteva, Maria A., Villoutreix, Bruno O.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.05 MB

english, 2015

53

CellWhere: graphical display of interaction networks organized on subcellular localizations

Zhu, Lu, Malatras, Apostolos, Thorley, Matthew, Aghoghogbe, Idonnya, Mer, Arvind, Duguez, Stéphanie, Butler-Browne, Gillian, Voit, Thomas, Duddy, William

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.32 MB

english, 2015

54

BetaCavityWeb: a webserver for molecular voids and channels

Kim, Jae-Kwan, Cho, Youngsong, Lee, Mokwon, Laskowski, Roman A., Ryu, Seong Eon, Sugihara, Kokichi, Kim, Deok-Soo

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.47 MB

english, 2015

55

miRiadne: a web tool for consistent integration of miRNA nomenclature

Bonnal, Raoul J. P., Rossi, Riccardo L., Carpi, Donatella, Ranzani, Valeria, Abrignani, Sergio, Pagani, Massimiliano

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.10 MB

english, 2015

56

Babelomics 5.0: functional interpretation for new generations of genomic data

Alonso, Roberto, Salavert, Francisco, Garcia-Garcia, Francisco, Carbonell-Caballero, Jose, Bleda, Marta, Garcia-Alonso, Luz, Sanchis-Juan, Alba, Perez-Gil, Daniel, Marin-Garcia, Pablo, Sanchez, Ruben,

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 105 KB

english, 2015

57

PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem

Kim, Sunghwan, Thiessen, Paul A., Bolton, Evan E., Bryant, Stephen H.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.04 MB

english, 2015

58

ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks

Wang, Panwen, Qin, Jing, Qin, Yiming, Zhu, Yun, Wang, Lily Yan, Li, Mulin Jun, Zhang, Michael Q., Wang, Junwen

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.76 MB

english, 2015

59

DIANA-miRPath v3.0: deciphering microRNA function with experimental support

Vlachos, Ioannis S., Zagganas, Konstantinos, Paraskevopoulou, Maria D., Georgakilas, Georgios, Karagkouni, Dimitra, Vergoulis, Thanasis, Dalamagas, Theodore, Hatzigeorgiou, Artemis G.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.02 MB

english, 2015

60

FNTM: a server for predicting functional networks of tissues in mouse

Goya, Jonathan, Wong, Aaron K., Yao, Victoria, Krishnan, Arjun, Homilius, Max, Troyanskaya, Olga G.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.53 MB

english, 2015

61

SCUDO: a tool for signature-based clustering of expression profiles

Lauria, Mario, Moyseos, Petros, Priami, Corrado

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.30 MB

english, 2015

62

NaviCell Web Service for network-based data visualization

Bonnet, Eric, Viara, Eric, Kuperstein, Inna, Calzone, Laurence, Cohen, David P. A., Barillot, Emmanuel, Zinovyev, Andrei

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 6.30 MB

english, 2015

63

PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles

Sadreyev, Ilyas R., Ji, Fei, Cohen, Emiliano, Ruvkun, Gary, Tabach, Yuval

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 4.27 MB

english, 2015

64

PACCMIT/PACCMIT-CDS: identifying microRNA targets in 3′ UTRs and coding sequences

Šulc, Miroslav, Marín, Ray M., Robins, Harlan S., Vaníček, Jiří

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.84 MB

english, 2015

65

RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules

Garcia-Martin, Juan Antonio, Dotu, Ivan, Clote, Peter

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.03 MB

english, 2015

66

RNA-Redesign: a web server for fixed-backbone 3D design of RNA: Figure 1.

Yesselman, Joseph D., Das, Rhiju

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.90 MB

english, 2015

67

ZCURVE 3.0: identify prokaryotic genes with higher accuracy as well as automatically and accurately select essential genes

Hua, Zhi-Gang, Lin, Yan, Yuan, Ya-Zhou, Yang, De-Chang, Wei, Wen, Guo, Feng-Biao

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.25 MB

english, 2015

68

BCSearch: fast structural fragment mining over large collections of protein structures

Guyon, Frédéric, Martz, François, Vavrusa, Marek, Bécot, Jérôme, Rey, Julien, Tufféry, Pierre

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.19 MB

english, 2015

69

GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization

Lee, Hasup, Heo, Lim, Lee, Myeong Sup, Seok, Chaok

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 939 KB

english, 2015

70

Multidimensional gene search with Genehopper

Munz, Matthias, Tönnies, Sascha, Balke, Wolf-Tilo, Simon, Eric

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.01 MB

english, 2015

71

APPRIS WebServer and WebServices

Rodriguez, Jose Manuel, Carro, Angel, Valencia, Alfonso, Tress, Michael L.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.51 MB

english, 2015

72

MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts

Basha, Omer, Flom, Dvir, Barshir, Ruth, Smoly, Ilan, Tirman, Shoval, Yeger-Lotem, Esti

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 484 KB

english, 2015

73

Primerize: automated primer assembly for transcribing non-coding RNA domains

Tian, Siqi, Yesselman, Joseph D., Cordero, Pablo, Das, Rhiju

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.91 MB

english, 2015

74

R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server

Cannone, Jamie J., Sweeney, Blake A., Petrov, Anton I., Gutell, Robin R., Zirbel, Craig L., Leontis, Neocles

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.78 MB

english, 2015

75

RNAssess—a web server for quality assessment of RNA 3D structures

Lukasiak, Piotr, Antczak, Maciej, Ratajczak, Tomasz, Szachniuk, Marta, Popenda, Mariusz, Adamiak, Ryszard W., Blazewicz, Jacek

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.43 MB

english, 2015

76

Editorial: Nucleic Acids Research annual Web Server Issue in 2015: Figure 1.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 579 KB

english, 2015

77

StemChecker: a web-based tool to discover and explore stemness signatures in gene sets

Pinto, José P., Kalathur, Ravi K., Oliveira, Daniel V., Barata, Tânia, Machado, Rui S.R., Machado, Susana, Pacheco-Leyva, Ivette, Duarte, Isabel, Futschik, Matthias E.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.67 MB

english, 2015

78

JPred4: a protein secondary structure prediction server

Drozdetskiy, Alexey, Cole, Christian, Procter, James, Barton, Geoffrey J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 6.93 MB

english, 2015

79

RSAT 2015: Regulatory Sequence Analysis Tools

Medina-Rivera, Alejandra, Defrance, Matthieu, Sand, Olivier, Herrmann, Carl, Castro-Mondragon, Jaime A., Delerce, Jeremy, Jaeger, Sébastien, Blanchet, Christophe, Vincens, Pierre, Caron, Christophe, S

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 972 KB

english, 2015

80

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts

Hafsa, Noor E., Arndt, David, Wishart, David S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.85 MB

english, 2015

81

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction: Figure 1.

Chang, Jia-Ming, Di Tommaso, Paolo, Lefort, Vincent, Gascuel, Olivier, Notredame, Cedric

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.19 MB

english, 2015

82

xVis : a web server for the schematic visualization and interpretation of crosslink-derived spatial restraints

Grimm, Maximilian, Zimniak, Tomasz, Kahraman, Abdullah, Herzog, Franz

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.95 MB

english, 2015

83

Nucleic Acids Research

Journal:

Nucleic Acids Research

Year:

2015

File:

PDF, 1.49 MB

2015

84

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides

Tsirigos, Konstantinos D., Peters, Christoph, Shu, Nanjiang, Käll, Lukas, Elofsson, Arne

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 763 KB

english, 2015

85

Introducing the PRIDE Archive RESTful web services

Reisinger, Florian, del-Toro, Noemi, Ternent, Tobias, Hermjakob, Henning, Vizcaíno, Juan Antonio

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.75 MB

english, 2015

86

webSDA: a web server to simulate macromolecular diffusional association

Yu, Xiaofeng, Martinez, Michael, Gable, Annika L., Fuller, Jonathan C., Bruce, Neil J., Richter, Stefan, Wade, Rebecca C.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.84 MB

english, 2015

87

ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability

Frappier, Vincent, Chartier, Matthieu, Najmanovich, Rafael J.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.27 MB

english, 2015

88

SNiPlay3: a web-based application for exploration and large scale analyses of genomic variations

Dereeper, Alexis, Homa, Felix, Andres, Gwendoline, Sempere, Guilhem, Sarah, Gautier, Hueber, Yann, Dufayard, Jean-François, Ruiz, Manuel

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.97 MB

english, 2015

89

Localize.pytom: a modern webserver for cryo-electron tomography

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.35 MB

english, 2015

90

FlyNet: a versatile network prioritization server for the Drosophila community

Shin, Junha, Yang, Sunmo, Kim, Eiru, Kim, Chan Yeong, Shim, Hongseok, Cho, Ara, Kim, Hyojin, Hwang, Sohyun, Shim, Jung Eun, Lee, Insuk

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.29 MB

english, 2015

91

CATH FunFHMMer web server: protein functional annotations using functional family assignments

Das, Sayoni, Sillitoe, Ian, Lee, David, Lees, Jonathan G., Dawson, Natalie L., Ward, John, Orengo, Christine A.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.35 MB

english, 2015

92

I-COMS: Interprotein-COrrelated Mutations Server

Iserte, Javier, Simonetti, Franco L., Zea, Diego J., Teppa, Elin, Marino-Buslje, Cristina

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.79 MB

english, 2015

93

Nucleic Acids Research: Editorial Board

Journal:

Nucleic Acids Research

Year:

2015

File:

PDF, 1.61 MB

2015

94

Subscriptions

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 39 KB

english, 2015

95

RBO Aleph: leveraging novel information sources for protein structure prediction

Mabrouk, Mahmoud, Putz, Ines, Werner, Tim, Schneider, Michael, Neeb, Moritz, Bartels, Philipp, Brock, Oliver

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.88 MB

english, 2015

96

Pathways with PathWhiz

Pon, Allison, Jewison, Timothy, Su, Yilu, Liang, Yongjie, Knox, Craig, Maciejewski, Adam, Wilson, Michael, Wishart, David S.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.92 MB

english, 2015

97

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank

Sehnal, David, Pravda, Lukáš, Svobodová Vařeková, Radka, Ionescu, Crina-Maria, Koča, Jaroslav

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 1.09 MB

english, 2015

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