Volume 42; Issue W1

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Nucleic Acids Research
Volume 42; Issue W1

Nucleic Acids Research

Volume 42; Issue W1

1

CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing

Montague, T. G., Cruz, J. M., Gagnon, J. A., Church, G. M., Valen, E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.49 MB

english, 2014

2

pocketZebra: a web-server for automated selection and classification of subfamily-specific binding sites by bioinformatic analysis of diverse protein families

Suplatov, D., Kirilin, E., Arbatsky, M., Takhaveev, V., vedas, V.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 839 KB

english, 2014

3

ProTox: a web server for the in silico prediction of rodent oral toxicity

Drwal, M. N., Banerjee, P., Dunkel, M., Wettig, M. R., Preissner, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.25 MB

english, 2014

4

DDI-CPI, a server that predicts drug-drug interactions through implementing the chemical-protein interactome

Luo, H., Zhang, P., Huang, H., Huang, J., Kao, E., Shi, L., He, L., Yang, L.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 873 KB

english, 2014

5

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T. G., Bertoni, M., Bordoli, L., Schwede, T.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.00 MB

english, 2014

6

PASTA 2.0: an improved server for protein aggregation prediction

Walsh, I., Seno, F., Tosatto, S. C. E., Trovato, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.59 MB

english, 2014

7

GalaxySite: ligand-binding-site prediction by using molecular docking

Heo, L., Shin, W.-H., Lee, M. S., Seok, C.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.56 MB

english, 2014

8

Enhancing UCSF Chimera through web services

Huang, C. C., Meng, E. C., Morris, J. H., Pettersen, E. F., Ferrin, T. E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.87 MB

english, 2014

9

PredictProtein--an open resource for online prediction of protein structural and functional features

Yachdav, G., Kloppmann, E., Kajan, L., Hecht, M., Goldberg, T., Hamp, T., Honigschmid, P., Schafferhans, A., Roos, M., Bernhofer, M., Richter, L., Ashkenazy, H., Punta, M., Schlessinger, A., Bromberg,

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 878 KB

english, 2014

10

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

Saladin, A., Rey, J., Thevenet, P., Zacharias, M., Moroy, G., Tuffery, P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.20 MB

english, 2014

11

DINIES: drug-target interaction network inference engine based on supervised analysis

Yamanishi, Y., Kotera, M., Moriya, Y., Sawada, R., Kanehisa, M., Goto, S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.18 MB

english, 2014

12

GeneGenie: optimized oligomer design for directed evolution

Swainston, N., Currin, A., Day, P. J., Kell, D. B.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.38 MB

english, 2014

13

ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context

Wu, C., Bardes, E. E., Jegga, A. G., Aronow, B. J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.91 MB

english, 2014

14

XTMS: pathway design in an eXTended metabolic space

Carbonell, P., Parutto, P., Herisson, J., Pandit, S. B., Faulon, J.-L.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 541 KB

english, 2014

15

PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties

Deng, L., Zhang, Q. C., Chen, Z., Meng, Y., Guan, J., Zhou, S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 924 KB

english, 2014

16

SuperPred: update on drug classification and target prediction

Nickel, J., Gohlke, B.-O., Erehman, J., Banerjee, P., Rong, W. W., Goede, A., Dunkel, M., Preissner, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 396 KB

english, 2014

17

SwissTargetPrediction: a web server for target prediction of bioactive small molecules

Gfeller, D., Grosdidier, A., Wirth, M., Daina, A., Michielin, O., Zoete, V.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.01 MB

english, 2014

18

Subscriptions

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 56 KB

english, 2014

19

WormNet v3: a network-assisted hypothesis-generating server for Caenorhabditis elegans

Cho, A., Shin, J., Hwang, S., Kim, C., Shim, H., Kim, H., Kim, H., Lee, I.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.50 MB

english, 2014

20

Nucleic Acids Research: WEB SERVER ISSUE JULY 1, 2014

Journal:

Nucleic Acids Research

Year:

2014

File:

PDF, 213 KB

2014

21

POSA: a user-driven, interactive multiple protein structure alignment server

Li, Z., Natarajan, P., Ye, Y., Hrabe, T., Godzik, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.28 MB

english, 2014

22

InterMine: extensive web services for modern biology

Kalderimis, A., Lyne, R., Butano, D., Contrino, S., Lyne, M., Heimbach, J., Hu, F., Smith, R., t pan, R., Sullivan, J., Micklem, G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 553 KB

english, 2014

23

COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures

Firdaus-Raih, M., Hamdani, H. Y., Nadzirin, N., Ramlan, E. I., Willett, P., Artymiuk, P. J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.47 MB

english, 2014

24

RASS: a web server for RNA alignment in the joint sequence-structure space

He, G., Steppi, A., Laborde, J., Srivastava, A., Zhao, P., Zhang, J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.07 MB

english, 2014

25

Nucleic Acids Research: Editorial Board

Journal:

Nucleic Acids Research

Year:

2014

File:

PDF, 421 KB

2014

26

A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies

Aleman, A., Garcia-Garcia, F., Salavert, F., Medina, I., Dopazo, J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 688 KB

english, 2014

27

PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes

Baspinar, A., Cukuroglu, E., Nussinov, R., Keskin, O., Gursoy, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.78 MB

english, 2014

28

SEPPA 2.0--more refined server to predict spatial epitope considering species of immune host and subcellular localization of protein antigen

Qi, T., Qiu, T., Zhang, Q., Tang, K., Fan, Y., Qiu, J., Wu, D., Zhang, W., Chen, Y., Gao, J., Zhu, R., Cao, Z.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 788 KB

english, 2014

29

CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains

Wright, P. R., Georg, J., Mann, M., Sorescu, D. A., Richter, A. S., Lott, S., Kleinkauf, R., Hess, W. R., Backofen, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 970 KB

english, 2014

30

e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation

Lai, D., Meyer, I. M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 571 KB

english, 2014

31

PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling

Pauthenier, C., Faulon, J.-L.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 455 KB

english, 2014

32

RBPmap: a web server for mapping binding sites of RNA-binding proteins

Paz, I., Kosti, I., Ares, M., Cline, M., Mandel-Gutfreund, Y.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.05 MB

english, 2014

33

The DynaMine webserver: predicting protein dynamics from sequence

Cilia, E., Pancsa, R., Tompa, P., Lenaerts, T., Vranken, W. F.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 949 KB

english, 2014

34

Deciphering key features in protein structures with the new ENDscript server

Robert, X., Gouet, P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.81 MB

english, 2014

35

deepTools: a flexible platform for exploring deep-sequencing data

Ramirez, F., Dundar, F., Diehl, S., Gruning, B. A., Manke, T.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.17 MB

english, 2014

36

ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites

Konc, J., Jane i , D.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.90 MB

english, 2014

37

EvoCor: a platform for predicting functionally related genes using phylogenetic and expression profiles

Dittmar, W. J., McIver, L., Michalak, P., Garner, H. R., Valdez, G.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 610 KB

english, 2014

38

MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering

Bonde, M. T., Klausen, M. S., Anderson, M. V., Wallin, A. I. N., Wang, H. H., Sommer, M. O. A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1002 KB

english, 2014

39

The CAD-score web server: contact area-based comparison of structures and interfaces of proteins, nucleic acids and their complexes

Olechnovi , K., Venclovas, eslovas

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.98 MB

english, 2014

40

A multi-fingerprint browser for the ZINC database

Awale, M., Reymond, J.-L.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.40 MB

english, 2014

41

DMINDA: an integrated web server for DNA motif identification and analyses

Ma, Q., Zhang, H., Mao, X., Zhou, C., Liu, B., Chen, X., Xu, Y.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.81 MB

english, 2014

42

iMODS: internal coordinates normal mode analysis server

Lopez-Blanco, J. R., Aliaga, J. I., Quintana-Orti, E. S., Chacon, P.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.63 MB

english, 2014

43

Alignment-Annotator web server: rendering and annotating sequence alignments

Gille, C., Fahling, M., Weyand, B., Wieland, T., Gille, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 921 KB

english, 2014

44

VAP: a versatile aggregate profiler for efficient genome-wide data representation and discovery

Coulombe, C., Poitras, C., Nordell-Markovits, A., Brunelle, M., Lavoie, M.-A., Robert, F., Jacques, P.-E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.69 MB

english, 2014

45

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches

Horwege, S., Lindner, S., Boden, M., Hatje, K., Kollmar, M., Leimeister, C.-A., Morgenstern, B.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.16 MB

english, 2014

46

TargetRNA2: identifying targets of small regulatory RNAs in bacteria

Kery, M. B., Feldman, M., Livny, J., Tjaden, B.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 730 KB

english, 2014

47

DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections

Liu, C.-C., Tseng, Y.-T., Li, W., Wu, C.-Y., Mayzus, I., Rzhetsky, A., Sun, F., Waterman, M., Chen, J. J. W., Chaudhary, P. M., Loscalzo, J., Crandall, E., Zhou, X. J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.90 MB

english, 2014

48

NeuroPID: a classifier of neuropeptide precursors

Karsenty, S., Rappoport, N., Ofer, D., Zair, A., Linial, M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 681 KB

english, 2014

49

PIQMIe: a web server for semi-quantitative proteomics data management and analysis

Kuzniar, A., Kanaar, R.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.75 MB

english, 2014

50

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network

Hwang, S., Kim, E., Yang, S., Marcotte, E. M., Lee, I.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.76 MB

english, 2014

51

The personal genome browser: visualizing functions of genetic variants

Juan, L., Teng, M., Zang, T., Hao, Y., Wang, Z., Yan, C., Liu, Y., Li, J., Zhang, T., Wang, Y.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.10 MB

english, 2014

52

STarMir: a web server for prediction of microRNA binding sites

Rennie, W., Liu, C., Carmack, C. S., Wolenc, A., Kanoria, S., Lu, J., Long, D., Ding, Y.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.36 MB

english, 2014

53

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model

Kawano, S., Watanabe, T., Mizuguchi, S., Araki, N., Katayama, T., Yamaguchi, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.81 MB

english, 2014

54

Motif Enrichment Tool

Blatti, C., Sinha, S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.50 MB

english, 2014

55

GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs

Zhao, Q., Xie, Y., Zheng, Y., Jiang, S., Liu, W., Mu, W., Liu, Z., Zhao, Y., Xue, Y., Ren, J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.32 MB

english, 2014

56

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

Pires, D. E. V., Ascher, D. B., Blundell, T. L.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.08 MB

english, 2014

57

PTHGRN: unraveling post-translational hierarchical gene regulatory networks using PPI, ChIP-seq and gene expression data

Guan, D., Shao, J., Zhao, Z., Wang, P., Qin, J., Deng, Y., Boheler, K. R., Wang, J., Yan, B.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.01 MB

english, 2014

58

CFM-ID: a web server for annotation, spectrum prediction and metabolite identification from tandem mass spectra

Allen, F., Pon, A., Wilson, M., Greiner, R., Wishart, D.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 978 KB

english, 2014

59

NEP: web server for epitope prediction based on antibody neutralization of viral strains with diverse sequences

Chuang, G.-Y., Liou, D., Kwong, P. D., Georgiev, I. S.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.69 MB

english, 2014

60

BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data

Garcia-Albornoz, M., Thankaswamy-Kosalai, S., Nilsson, A., Varemo, L., Nookaew, I., Nielsen, J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.66 MB

english, 2014

61

NetworkAnalyst - integrative approaches for protein-protein interaction network analysis and visual exploration

Xia, J., Benner, M. J., Hancock, R. E. W.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 2.13 MB

english, 2014

62

StemCellNet: an interactive platform for network-oriented investigations in stem cell biology

Pinto, J. P., Reddy Kalathur, R. K., Machado, R. S. R., Xavier, J. M., Braganca, J., Futschik, M. E.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.82 MB

english, 2014

63

Lynx web services for annotations and systems analysis of multi-gene disorders

Sulakhe, D., Taylor, A., Balasubramanian, S., Feng, B., Xie, B., Bornigen, D., Dave, U. J., Foster, I. T., Gilliam, T. C., Maltsev, N.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 387 KB

english, 2014

64

LocTree3 prediction of localization

Goldberg, T., Hecht, M., Hamp, T., Karl, T., Yachdav, G., Ahmed, N., Altermann, U., Angerer, P., Ansorge, S., Balasz, K., Bernhofer, M., Betz, A., Cizmadija, L., Do, K. T., Gerke, J., Greil, R., Joerd

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 686 KB

english, 2014

65

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support

Stockinger, H., Altenhoff, A. M., Arnold, K., Bairoch, A., Bastian, F., Bergmann, S., Bougueleret, L., Bucher, P., Delorenzi, M., Lane, L., Mercier, P. L., Lisacek, F., Michielin, O., Palagi, P. M., R

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 511 KB

english, 2014

66

OncoSearch: cancer gene search engine with literature evidence

Lee, H.-J., Dang, T. C., Lee, H., Park, J. C.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 105 KB

english, 2014

67

AIDA: ab initio domain assembly server

Xu, D., Jaroszewski, L., Li, Z., Godzik, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 761 KB

english, 2014

68

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications

Hach, F., Sarrafi, I., Hormozdiari, F., Alkan, C., Eichler, E. E., Sahinalp, S. C.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 258 KB

english, 2014

69

R. S. WebTool, a web server for random sampling-based significance evaluation of pairwise distances

Villiers, F., Bastien, O., Kwak, J. M.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 1.23 MB

english, 2014

70

BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives

Becker, D., Lutsik, P., Ebert, P., Bock, C., Lengauer, T., Walter, J.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 642 KB

english, 2014

71

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

Duan, Q., Flynn, C., Niepel, M., Hafner, M., Muhlich, J. L., Fernandez, N. F., Rouillard, A. D., Tan, C. M., Chen, E. Y., Golub, T. R., Sorger, P. K., Subramanian, A., Ma'ayan, A.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 3.93 MB

english, 2014

72

SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

Di Tommaso, P., Bussotti, G., Kemena, C., Capriotti, E., Chatzou, M., Prieto, P., Notredame, C.

Journal:

Nucleic Acids Research

Year:

2014

Language:

english

File:

PDF, 79 KB

english, 2014

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