Subject: Nucleic Acids Research Table of Contents for 3 July 2017 Oxford Academic
                                 

 
 
 
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New issue alert
 
Nucleic Acids Research  
Volume 45 Issue W1
 
3 July 2017
 
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Web Server issue
 
 
 
 
CAFE: aCcelerated Alignment-FrEe sequence analysis border= 
 
Yang Young Lu; Kujin Tang; Jie Ren; Jed A. Fuhrman ; Michael S. Waterman ...
 
 
 
 
 
VCF.Filter: interactive prioritization of disease-linked genetic variants from sequencing data border= 
 
Heiko MĂĽller ; Raul Jimenez-Heredia; Ana Krolo; Tatjana Hirschmugl; Jasmin Dmytrus ...
 
 
 
 
 
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy border= 
 
Björn A. Grüning; Jörg Fallmann; Dilmurat Yusuf; Sebastian Will; Anika Erxleben ...
 
 
Editorial
 
 
 
Editorial: the 15th annual Nucleic Acids Research Web Server issue 2017 border= 
 
 
 
Web Server issue
 
 
 
GeSeq ' versatile and accurate annotation of organelle genomes border= 
 
Michael Tillich; Pascal Lehwark ; Tommaso Pellizzer; Elena S. Ulbricht-Jones; Axel Fischer ...
 
 
 
 
CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features border= 
 
Yu-Jian Kang; De-Chang Yang; Lei Kong; Mei Hou ; Yu-Qi Meng ...
 
 
PIGSPro: prediction of immunoGlobulin structures v2 border= 
 
Rosalba Lepore; Pier P. Olimpieri; Mario A. Messih; Anna Tramontano
 
 
BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes border= 
 
Martin Closter Jespersen; Bjoern Peters ; Morten Nielsen; Paolo Marcatili
 
 
IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets border= 
 
Claire Bertelli; Matthew R Laird; Kelly P Williams; Simon Fraser University Research Computing Group ; Britney Y Lau ...
 
 
antiSMASH 4.0'improvements in chemistry prediction and gene cluster boundary identification border= 
 
Kai Blin; Thomas Wolf; Marc G. Chevrette; Xiaowen Lu; Christopher J. Schwalen ...
 
 
 
 
The Antibiotic Resistant Target Seeker (ARTS), an exploration engine for antibiotic cluster prioritization and novel drug target discovery border= 
 
Mohammad Alanjary ; Brent Kronmiller; Martina Adamek; Kai Blin; Tilmann Weber ...
 
 
PRISM 3: expanded prediction of natural product chemical structures from microbial genomes border= 
 
Michael A. Skinnider; Nishanth J. Merwin ; Chad W. Johnston; Nathan A. Magarvey
 
 
plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters border= 
 
Satria A. Kautsar; Hernando G. Suarez Duran; Kai Blin; Anne Osbourn ; Marnix H. Medema
 
 
SeMPI: a genome-based secondary metabolite prediction and identification web server border= 
 
Paul F. Zierep; NatĂ lia Padilla; Dimitar G. Yonchev; Kiran K. Telukunta; Dennis Klementz ...
 
 
SBSPKSv2: structure-based sequence analysis of polyketide synthases and non-ribosomal peptide synthetases border= 
 
Shradha Khater ; Money Gupta; Priyesh Agrawal; Neetu Sain; Jyoti Prava ...
 
 
RiPPMiner: a bioinformatics resource for deciphering chemical structures of RiPPs based on prediction of cleavage and cross-links border= 
 
Priyesh Agrawal ; Shradha Khater; Money Gupta; Neetu Sain; Debasisa Mohanty
 
 
DNAproDB: an interactive tool for structural analysis of DNA'protein complexes border= 
 
Jared M. Sagendorf; Helen M. Berman ; Remo Rohs
 
 
GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses border= 
 
Zefang Tang; Chenwei Li; Boxi Kang; Ge Gao; Cheng Li ...
 
 
CSTEA: a webserver for the Cell State Transition Expression Atlas border= 
 
Guanghui Zhu ; Hui Yang; Xiao Chen; Jun Wu; Yong Zhang ...
 
 
WoPPER: Web server for Position Related data analysis of gene Expression in Prokaryotes border= 
 
Simone Puccio; Giorgio Grillo ; Flavio Licciulli; Marco Severgnini; Sabino Liuni ...
 
 
minepath.org: a free interactive pathway analysis web server border= 
 
Lefteris Koumakis; Panos Roussos; George Potamias
 
 
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update border= 
 
Tian Tian; Yue Liu ; Hengyu Yan; Qi You; Xin Yi ...
 
 
WebGestalt 2017: a more comprehensive, powerful, flexible and interactive gene set enrichment analysis toolkit border= 
 
Jing Wang; Suhas Vasaikar; Zhiao Shi; Michael Greer ; Bing Zhang
 
 
Gene ORGANizer: linking genes to the organs they affect border= 
 
David Gokhman; Guy Kelman; Adir Amartely; Guy Gershon; Shira Tsur ...
 
 
RegulatorTrail: a web service for the identification of key transcriptional regulators border= 
 
Tim Kehl ; Lara Schneider; Florian Schmidt; Daniel Stöckel; Nico Gerstner ...
 
 
GWAB: a web server for the network-based boosting of human genome-wide association data border= 
 
Jung Eun Shim; Changbae Bang ; Sunmo Yang; Tak Lee; Sohyun Hwang ...
 
 
NOREVA: normalization and evaluation of MS-based metabolomics data border= 
 
Bo Li; Jing Tang; Qingxia Yang; Shuang Li ; Xuejiao Cui ...
 
 
BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation border= 
 
Cedric C. Laczny; Christina Kiefer; Valentina Galata; Tobias Fehlmann; Christina Backes ...
 
 
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data border= 
 
Achal Dhariwal ; Jasmine Chong; Salam Habib; Irah L. King; Luis B. Agellon ...
 
 
HGVA: the Human Genome Variation Archive border= 
 
Javier Lopez; Jacobo Coll ; Matthias Haimel; Swaathi Kandasamy; Joaquin Tarraga ...
 
 
A PanorOmic view of personal cancer genomes border= 
 
Lidia Mateo; Oriol Guitart-Pla; Carles Pons; Miquel Duran-Frigola ; Roberto Mosca ...
 
 
DEOGEN2: prediction and interactive visualization of single amino acid variant deleteriousness in human proteins border= 
 
Daniele Raimondi; Ibrahim Tanyalcin; Julien Ferté; Andrea Gazzo; Gabriele Orlando ...
 
 
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud border= 
 
Siwei Chen ; Juan F. Beltrán; Clara Esteban-Jurado; Sebastià Franch-Expósito; Sergi Castellví-Bel ...
 
 
mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers border= 
 
Mulin Jun Li; Hongcheng Yao; Dandan Huang; Huanhuan Liu; Zipeng Liu ...
 
 
PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update border= 
 
VĂ­ctor LĂłpez-Ferrando; Andrea Gazzo; Xavier de la Cruz; Modesto Orozco; Josep Ll GelpĂ­
 
 
SDM: a server for predicting effects of mutations on protein stability border= 
 
Arun Prasad Pandurangan; Bernardo Ochoa-Montaño; David B. Ascher; Tom L. Blundell
 
 
SODA: prediction of protein solubility from disorder and aggregation propensity border= 
 
Lisanna Paladin; Damiano Piovesan ; Silvio C. E. Tosatto
 
 
mCSM'NA: predicting the effects of mutations on protein'nucleic acids interactions border= 
 
Douglas E.V. Pires; David B. Ascher
 
 
PhD-SNPg: a webserver and lightweight tool for scoring single nucleotide variants border= 
 
Emidio Capriotti; Piero Fariselli
 
 
GenProBiS: web server for mapping of sequence variants to protein binding sites border= 
 
Janez Konc; Blaz Skrlj; Nika Erzen; Tanja Kunej ; Dusanka Janezic
 
 
TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites border= 
 
Eli Levy Karin; Haim Ashkenazy; Susann Wicke; Tal Pupko; Itay Mayrose
 
 
P4P: a peptidome-based strain-level genome comparison web tool border= 
 
Aitor Blanco-Míguez ; Florentino Fdez-Riverola; Anália Lourenço; Borja Sánchez
 
 
SCENERY: a web application for (causal) network reconstruction from cytometry data border= 
 
Georgios Papoutsoglou; Giorgos Athineou; Vincenzo Lagani; Iordanis Xanthopoulos; Angelika Schmidt ...
 
 
compleXView: a server for the interpretation of protein abundance and connectivity information to identify protein complexes border= 
 
Victor Solis-Mezarino; Franz Herzog
 
 
The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation border= 
 
Giuseppe Profiti; Pier Luigi Martelli; Rita Casadio
 
 
COFACTOR: improved protein function prediction by combining structure, sequence and protein'protein interaction information border= 
 
Chengxin Zhang; Peter L. Freddolino; Yang Zhang
 
 
ProteoSign: an end-user online differential proteomics statistical analysis platform border= 
 
Georgios Efstathiou; Andreas N. Antonakis; Georgios A. Pavlopoulos; Theodosios Theodosiou; Peter Divanach ...
 
 
BIS2Analyzer: a server for co-evolution analysis of conserved protein families border= 
 
Francesco Oteri ; Francesca Nadalin; Raphaël Champeimont; Alessandra Carbone
 
 
GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms border= 
 
Joao P. A. Moraes; Gisele L. Pappa; Douglas E. V. Pires; Sandro C. Izidoro
 
 
GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure border= 
 
Minkyung Baek ; Taeyong Park; Lim Heo; Chiwook Park; Chaok Seok
 
 
TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets border= 
 
Antonia Stank; Daria B. Kokh ; Max Horn; Elena Sizikova; Rebecca Neil ...
 
 
LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands border= 
 
Leela S. Dodda; Israel Cabeza de Vaca; Julian Tirado-Rives; William L. Jorgensen
 
 
ProteinsPlus: a web portal for structure analysis of macromolecules border= 
 
Rainer Fährrolfes ; Stefan Bietz; Florian Flachsenberg; Agnes Meyder; Eva Nittinger ...
 
 
NNAlign: a platform to construct and evaluate artificial neural network models of receptor'ligand interactions border= 
 
Morten Nielsen; Massimo Andreatta
 
 
AMMOS2: a web server for protein'ligand'water complexes refinement via molecular mechanics border= 
 
Céline M. Labbé ; Tania Pencheva; Dessislava Jereva; Dimitri Desvillechabrol; Jérôme Becot ...
 
 
PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database border= 
 
Xia Wang; Yihang Shen; Shiwei Wang; Shiliang Li; Weilin Zhang ...
 
 
The pepATTRACT web server for blind, large-scale peptide'protein docking border= 
 
Sjoerd J. de Vries; Julien Rey; Christina E. M. Schindler; Martin Zacharias; Pierre Tuffery
 
 
HDOCK: a web server for protein'protein and protein'DNA/RNA docking based on a hybrid strategy border= 
 
Yumeng Yan; Di Zhang; Pei Zhou; Botong Li; Sheng-You Huang
 
 
DynOmics: dynamics of structural proteome and beyond border= 
 
Hongchun Li ; Yuan-Yu Chang; Ji Young Lee; Ivet Bahar; Lee-Wei Yang
 
 
XSuLT: a web server for structural annotation and representation of sequence-structure alignments border= 
 
Bernardo Ochoa-Montaño; Tom L. Blundell
 
 
Amino Acid Interaction (INTAA) web server border= 
 
Jakub Galgonek ; Jiří Vymětal; David Jakubec; Jiří Vondrášek
 
 
FireProt: web server for automated design of thermostable proteins border= 
 
Milos Musil; Jan Stourac; Jaroslav Bendl; Jan Brezovsky ; Zbynek Prokop ...
 
 
ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly border= 
 
Yan Wang; Jian Wang; Ruiming Li; Qiang Shi; Zhidong Xue ...
 
 
GPCR-SSFE 2.0'a fragment-based molecular modeling web tool for Class A G-protein coupled receptors border= 
 
Catherine L. Worth ; Franziska Kreuchwig; Johanna K.S. Tiemann; Annika Kreuchwig; Michele Ritschel ...
 
 
ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models border= 
 
Ali H. A. Maghrabi; Liam J. McGuffin
 
 
ReFOLD: a server for the refinement of 3D protein models guided by accurate quality estimates border= 
 
Ahmad N. Shuid ; Robert Kempster; Liam J. McGuffin
 
 
I-TASSER-MR: automated molecular replacement for distant-homology proteins using iterative fragment assembly and progressive sequence truncation border= 
 
Yan Wang; Jouko Virtanen; Zhidong Xue; Yang Zhang
 
 
IntaRNA 2.0: enhanced and customizable prediction of RNA'RNA interactions border= 
 
Martin Mann; Patrick R. Wright ; Rolf Backofen
 
 
RNA-MoIP
: prediction of RNA secondary structure and local 3D motifs from sequence data border=
 
 
Jason Yao; Vladimir Reinharz; François Major; Jérôme Waldispühl
 
 
Omicseq: a web-based search engine for exploring omics datasets border= 
 
Xiaobo Sun; William S. Pittard ; Tianlei Xu; Li Chen; Michael E. Zwick ...
 
 
SpartaABC: a web server to simulate sequences with indel parameters inferred using an approximate Bayesian computation algorithm border= 
 
Haim Ashkenazy; Eli Levy Karin; Zach Mertens ; Reed A Cartwright; Tal Pupko
 
 
GibbsCluster: unsupervised clustering and alignment of peptide sequences border= 
 
Massimo Andreatta; Bruno Alvarez; Morten Nielsen
 
 
SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions border= 
 
Izabella Krystkowiak; Norman E. Davey
 
 
HH-MOTiF: de novo detection of short linear motifs in proteins by Hidden Markov Model comparisons border= 
 
Roman Prytuliak; Michael Volkmer ; Markus Meier; Bianca H. Habermann
 
 
Olelo: a web application for intuitive exploration of biomedical literature border= 
 
Milena Kraus; Julian Niedermeier; Marcel Jankrift; Sören Tietböhl ; Toni Stachewicz ...
 
 
LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes border= 
 
Andres Cañada; Salvador Capella-Gutierrez; Obdulia Rabal; Julen Oyarzabal; Alfonso Valencia ...
 
 
ConTra v3: a tool to identify transcription factor binding sites across species, update 2017 border= 
 
Ĺ ukasz Kreft ; Arne Soete; Paco Hulpiau; Alexander Botzki; Yvan Saeys ...
 
 
C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms border= 
 
Balaguru Ravikumar ; Zaid Alam; Gopal Peddinti; Tero Aittokallio
 
 
Pathview Web: user friendly pathway visualization and data integration border= 
 
Weijun Luo; Gaurav Pant; Yeshvant K. Bhavnasi; Steven G. Blanchard, Jr ; Cory Brouwer
 
 
Interactive microbial distribution analysis using BioAtlas border= 
 
Jesper Beltoft Lund; Markus List; Jan Baumbach
 
 
Exploring background mutational processes to decipher cancer genetic heterogeneity 
 
Alexander Goncearenco; Stephanie L. Rager; Minghui Li; Qing-Xiang Sang ; Igor B. Rogozin ...
 
 
Web3DMol: interactive protein structure visualization based on WebGL border= 
 
Maoxiang Shi; Juntao Gao; Michael Q. Zhang
 
 
DSSR-enhanced visualization of nucleic acid structures in Jmol border= 
 
Robert M. Hanson; Xiang-Jun Lu
 
 
kpLogo: positional k-mer analysis reveals hidden specificity in biological sequences border=  
 
Xuebing Wu; David P. Bartel
 
 
Web Services
 
 
 
The Proteins API: accessing key integrated protein and genome information border= 
 
Andrew Nightingale; Ricardo Antunes ; Emanuele Alpi; Borisas Bursteinas; Leonardo Gonzales ...
 
 
The EBI search engine: EBI search as a service'making biological data accessible for all border= 
 
Young M. Park; Silvano Squizzato; Nicola Buso; Tamer Gur ; Rodrigo Lopez
 
 
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017 border= 
 
Szymon Chojnacki; Andrew Cowley; Joon Lee; Anna Foix; Rodrigo Lopez
 
 
Stand alone programs
 
 
 
The Proteins API: accessing key integrated protein and genome information border= 
 
Andrew Nightingale ; Ricardo Antunes; Emanuele Alpi; Borisas Bursteinas; Leonardo Gonzales ...
 
 
The EBI search engine: EBI search as a service'making biological data accessible for all border= 
 
Young M. Park; Silvano Squizzato ; Nicola Buso; Tamer Gur; Rodrigo Lopez
 
 
Programmatic access to bioinformatics tools from EMBL-EBI update: 2017 border= 
 
Szymon Chojnacki; Andrew Cowley; Joon Lee; Anna Foix ; Rodrigo Lopez
 
 
Corrigendum
 
 
 
RNA-MoIP: prediction of RNA secondary structure and local 3D motifs from sequence data border= 
 
Jason Yao; Vladimir Reinharz; François Major; Jérôme Waldispühl
 
 
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