Subject: Nucleic Acids Research Table of Contents for 2 July 2018 ------=_Part_1812598695.1530636918427 Content-Type: text/plain;charset=UTF-8 This email is intended for bionet@evol.biology.mcmaster.ca. ------=_Part_1812598695.1530636918427 Content-Type: text/html;charset=UTF-8 Oxford Academic
 
 
 
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Nucleic Acids Research  
Volume 46 Issue W1
 
2 July 2018
 
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Editorial
 
 
 
Editorial: The 16th annual Nucleic Acids Research web server issue 2018 border= 
 
 
 
Web Server Issue
 
 
 
cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA border= 
 
Lennart De Bruin; John H Maddocks
 
 
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization border= 
 
Joachim Wolff; Vivek Bhardwaj; Stephan Nothjunge; Gautier Richard; Gina Renschler ...
 
 
KnotGenome: a server to analyze entanglements of chromosomes border= 
 
Joanna I Sulkowska ; Szymon Niewieczerzal; Aleksandra I Jarmolinska; Jonathan T Siebert; Peter Virnau ...
 
 
Freiburg RNA tools: a central online resource for RNA-focused research and teaching border= 
 
Martin Raden; Syed M Ali ; Omer S Alkhnbashi; Anke Busch; Fabrizio Costa ...
 
 
RNApdbee 2.0: multifunctional tool for RNA structure annotation border= 
 
Tomasz Zok; Maciej Antczak; Michal Zurkowski ; Mariusz Popenda; Jacek Blazewicz ...
 
 
SPAR: small RNA-seq portal for analysis of sequencing experiments border= 
 
Pavel P Kuksa; Alexandre Amlie-Wolf; ┼Żivadin Katani─ç; Otto Valladares ; Li-San Wang ...
 
 
pirScan: a webserver to predict piRNA targeting sites and to avoid transgene silencing in C. elegans border= 
 
Wei-Sheng Wu; Wei-Che Huang; Jordan S Brown; Donglei Zhang; Xiaoyan Song ...
 
 
psRNATarget: a plant small RNA target analysis server (2017 release) border= 
 
Xinbin Dai ; Zhaohong Zhuang; Patrick Xuechun Zhao
 
 
CSAR-web: a web server of contig scaffolding using algebraic rearrangements border= 
 
Kun-Tze Chen; Chin Lung Lu
 
 
GeneMANIA update 2018 border= 
 
Max Franz; Harold Rodriguez; Christian Lopes; Khalid Zuberi ; Jason Montojo ...
 
 
GIANT 2.0: genome-scale integrated analysis of gene networks in tissues border= 
 
Aaron K Wong; Arjun Krishnan; Olga G Troyanskaya
 
 
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update border= 
 
Jia Ye; Yong Zhang; Huihai Cui; Jiawei Liu ; Yuqing Wu ...
 
 
PhytoNet: comparative co-expression network analyses across phytoplankton and land plants border= 
 
Camilla Ferrari; Sebastian Proost; Colin Ruprecht; Marek Mutwil
 
 
PANNZER2: a rapid functional annotation web server border= 
 
Petri Törönen; Alan Medlar ; Liisa Holm
 
 
INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species border= 
 
Daehong Kwon; Daehwan Lee; Juyeon Kim; Jongin Lee; Mikang Sim ...
 
 
dbCAN2: a meta server for automated carbohydrate-active enzyme annotation border= 
 
Han Zhang ; Tanner Yohe; Le Huang; Sarah Entwistle; Peizhi Wu ...
 
 
Mutalisk: a web-based somatic MUTation AnaLyIS toolKit for genomic, transcriptional and epigenomic signatures border= 
 
Jongkeun Lee; Andy Jinseok Lee; June-Koo Lee; Jongkeun Park; Youngoh Kwon ...
 
 
SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine border=  
 
Abu Z Dayem Ullah; Jorge Oscanoa; Jun Wang ; Ai Nagano; Nicholas R Lemoine ...
 
 
GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits border= 
 
Dandan Huang; Xianfu Yi; Shijie Zhang; Zhanye Zheng ; Panwen Wang ...
 
 
GlobAl Distribution of GEnetic Traits (GADGET) web server: polygenic trait scores worldwide border= 
 
Aroon T Chande; Lu Wang; Lavanya Rishishwar; Andrew B Conley; Emily T Norris ...
 
 
Kinact: a computational approach for predicting activating missense mutations in protein kinases border= 
 
Carlos HM Rodrigues ; David B Ascher; Douglas EV Pires
 
 
CoNekT: an open-source framework for comparative genomic and transcriptomic network analyses border= 
 
Sebastian Proost; Marek Mutwil
 
 
CellAtlasSearch: a scalable search engine for single cells border= 
 
Divyanshu Srivastava; Arvind Iyer; Vibhor Kumar; Debarka Sengupta
 
 
GDA, a web-based tool for Genomics and Drugs integrated analysis border= 
 
Jimmy Caroli ; Giovanni Sorrentino; Mattia Forcato; Giannino Del Sal; Silvio Bicciato
 
 
CircadiOmics: circadian omic web portal border= 
 
Nicholas Ceglia; Yu Liu ; Siwei Chen; Forest Agostinelli; Kristin Eckel-Mahan ...
 
 
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets border= 
 
Ashwini Jeggari; Zhanna Alekseenko; Iurii Petrov ; José M Dias; Johan Ericson ...
 
 
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks border= 
 
Daniel J B Clarke; Maxim V Kuleshov; Brian M Schilder; Denis Torre ; Mary E Duffy ...
 
 
TAM 2.0: tool for MicroRNA set analysis border= 
 
Jianwei Li; Xiaofen Han; Yanping Wan; Shan Zhang; Yingshu Zhao ...
 
 
Coloc-stats: a unified web interface to perform colocalization analysis of genomic features border= 
 
Boris Simovski ; Chakravarthi Kanduri; Sveinung Gundersen; Dmytro Titov; Diana Domanska ...
 
 
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis border= 
 
V P Nagraj; Neal E Magee ; Nathan C Sheffield
 
 
HMMER web server: 2018 update border= 
 
Simon C Potter; Aurélien Luciani; Sean R Eddy; Youngmi Park; Rodrigo Lopez ...
 
 
Patscanui: an intuitive web interface for searching patterns in DNA and protein data border= 
 
Kai Blin ; Wolfgang Wohlleben; Tilmann Weber
 
 
RSAT 2018: regulatory sequence analysis tools 20th anniversary border= 
 
Nga Thi Thuy Nguyen; Bruno Contreras-Moreira; Jaime A Castro-Mondragon; Walter Santana-Garcia ; Raul Ossio ...
 
 
The BaMM web server for de-novo motif discovery and regulatory sequence analysis border= 
 
Anja Kiesel; Christian Roth; Wanwan Ge; Maximilian Wess; Markus Meier ...
 
 
SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data border= 
 
Maya Polishchuk ; Inbal Paz; Zohar Yakhini; Yael Mandel-Gutfreund
 
 
oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements border=  
 
Xiaobin Li; Yingzhou Xie; Meng Liu ; Cui Tai; Jingyong Sun ...
 
 
PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants border= 
 
Izabella Krystkowiak; Jean Manguy; Norman E Davey
 
 
CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens border= 
 
Jean-Paul Concordet; Maximilian Haeussler
 
 
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins border= 
 
David Couvin; Aude Bernheim; Claire Toffano-Nioche; Marie Touchon; Juraj Michalik ...
 
 
Oli2go: an automated multiplex oligonucleotide design tool border= 
 
Michaela Hendling; Stephan Pabinger ; Konrad Peters; Noa Wolff; Rick Conzemius ...
 
 
ProTox-II: a webserver for the prediction of toxicity of chemicals border= 
 
Priyanka Banerjee; Andreas O Eckert; Anna K Schrey; Robert Preissner
 
 
BRepertoire: a user-friendly web server for analysing antibody repertoire data border= 
 
Christian Margreitter ; Hui-Chun Lu; Catherine Townsend; Alexander Stewart; Deborah K Dunn-Walters ...
 
 
geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data border= 
 
Matthias Döring ; Joachim Büch; Georg Friedrich; Alejandro Pironti; Prabhav Kalaghatgi ...
 
 
BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins border= 
 
Auke J van Heel; Anne de Jong ; Chunxu Song; Jakob H Viel; Jan Kok ...
 
 
The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level border=  
 
Luis M Rodriguez-R; Santosh Gunturu; William T Harvey ; Ramon Rosselló-Mora; James M Tiedje ...
 
 
The Ocean Gene Atlas: exploring the biogeography of plankton genes online border= 
 
Emilie Villar; Thomas Vannier; Caroline Vernette; Magali Lescot ; Miguelangel Cuenca ...
 
 
SWISS-MODEL: homology modelling of protein structures and complexes border= 
 
Andrew Waterhouse; Martino Bertoni; Stefan Bienert; Gabriel Studer; Gerardo Tauriello ...
 
 
UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics border= 
 
Cezary Czaplewski; Agnieszka Karczy┼"ska; Adam K Sieradzan; Adam Liwo
 
 
FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps border=  
 
Johanna KS Tiemann; Alexander S Rose; Jochen Ismer ; Mitra D Darvish; Tarek Hilal ...
 
 
BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra border= 
 
András Micsonai; Frank Wien; Éva Bulyáki; Judit Kun ; Éva Moussong ...
 
 
MISTIC2: comprehensive server to study coevolution in protein families border= 
 
Eloy A Colell; Javier A Iserte; Franco L Simonetti; Cristina Marino-Buslje
 
 
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding border= 
 
Bálint Mészáros ; Gábor Erd┼'s; Zsuzsanna Dosztányi
 
 
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures border= 
 
Aleksander Kuriata; Aleksandra Maria Gierut; Tymoteusz Oleniecki; Maciej Pawe┼é Ciemny ; Andrzej Kolinski ...
 
 
CalFitter: a web server for analysis of protein thermal denaturation data border= 
 
Stanislav Mazurenko; Jan Stourac; Antonin Kunka; Sava Nedeljkovi─ç; David Bednar ...
 
 
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability border= 
 
Carlos HM Rodrigues ; Douglas EV Pires; David B Ascher
 
 
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information border= 
 
Lenka Sumbalova; Jan Stourac; Tomas Martinek; David Bednar ; Jiri Damborsky
 
 
CASTp 3.0: computed atlas of surface topography of proteins border= 
 
Wei Tian; Chang Chen; Xue Lei; Jieling Zhao; Jie Liang
 
 
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update) border= 
 
Luká┼í Pravda ; David Sehnal; Dominik Tou┼íek; Veronika Navrátilová; Václav Bazgier ...
 
 
CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction border= 
 
Youjun Xu ; Shiwei Wang; Qiwan Hu; Shuaishi Gao; Xiaomin Ma ...
 
 
mTM-align: a server for fast protein structure database search and multiple protein structure alignment border= 
 
Runze Dong; Shuo Pan ; Zhenling Peng; Yang Zhang; Jianyi Yang
 
 
GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models border= 
 
Przemysław Miszta; Paweł Pasznik; Jakub Jakowiecki ; Agnieszka Sztyler; Dorota Latek ...
 
 
TCRmodel: high resolution modeling of T cell receptors from sequence border= 
 
Ragul Gowthaman; Brian G Pierce
 
 
RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins border= 
 
Layla Hirsh; Lisanna Paladin; Damiano Piovesan; Silvio C E Tosatto
 
 
InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs border= 
 
Chloé Quignot; Julien Rey; Jinchao Yu; Pierre Tufféry; Raphaël Guerois ...
 
 
Identification and visualization of protein binding regions with the ArDock server border= 
 
Sébastien Reille ; Mélanie Garnier; Xavier Robert; Patrice Gouet; Juliette Martin ...
 
 
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry border= 
 
Yumeng Yan; Huanyu Tao; Sheng-You Huang
 
 
ComplexContact: a web server for inter-protein contact prediction using deep learning border= 
 
Hong Zeng; Sheng Wang; Tianming Zhou; Feifeng Zhao; Xiufeng Li ...
 
 
COACH-D: improved protein'ligand binding sites prediction with refined ligand-binding poses through molecular docking border= 
 
Qi Wu ; Zhenling Peng; Yang Zhang; Jianyi Yang
 
 
HPEPDOCK: a web server for blind peptide'protein docking based on a hierarchical algorithm border= 
 
Pei Zhou; Bowen Jin; Hao Li; Sheng-You Huang
 
 
AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses border= 
 
Min Huang ; Kun Song; Xinyi Liu; Shaoyong Lu; Qiancheng Shen ...
 
 
BUSCA: an integrative web server to predict subcellular localization of proteins border= 
 
Castrense Savojardo; Pier Luigi Martelli ; Piero Fariselli; Giuseppe Profiti; Rita Casadio
 
 
EasyFRAP-web: a web-based tool for the analysis of fluorescence recovery after photobleaching data border= 
 
Grigorios Koulouras; Andreas Panagopoulos; Maria A Rapsomaniki ; Nickolaos N Giakoumakis; Stavros Taraviras ...
 
 
xiSPEC: web-based visualization, analysis and sharing of proteomics data border= 
 
Lars Kolbowski; Colin Combe; Juri Rappsilber
 
 
AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination border= 
 
Alan J Medlar ; Petri Törönen; Liisa Holm
 
 
MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis border= 
 
Jasmine Chong; Othman Soufan; Carin Li; Iurie Caraus ; Shuzhao Li ...
 
 
MetExplore: collaborative edition and exploration of metabolic networks border= 
 
Ludovic Cottret; Clément Frainay; Maxime Chazalviel; Floréal Cabanettes; Yoann Gloaguen ...
 
 
PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data border= 
 
Rafael Hernández-de-Diego ; Sonia Tarazona; Carlos Martínez-Mira; Leandro Balzano-Nogueira; Pedro Furió-Tarí ...
 
 
iPath3.0: interactive pathways explorer v3 border= 
 
Youssef Darzi; Ivica Letunic ; Peer Bork; Takuji Yamada
 
 
OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space border= 
 
Guangyan Zhou; Jianguo Xia
 
 
ezTag: tagging biomedical concepts via interactive learning 
 
Dongseop Kwon; Sun Kim; Chih-Hsuan Wei; Robert Leaman ; Zhiyong Lu
 
 
LitVar: a semantic search engine for linking genomic variant data in PubMed and PMC 
 
Alexis Allot ; Yifan Peng; Chih-Hsuan Wei; Kyubum Lee; Lon Phan ...
 
 
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update border= 
 
Enis Afgan; Dannon Baker ; Bérénice Batut; Marius van den Beek; Dave Bouvier ...
 
 
Stand-alone Programs
 
 
 
VarAFT: a variant annotation and filtration system for human next generation sequencing data border= 
 
Jean-Pierre Desvignes; Marc Bartoli; Valérie Delague; Martin Krahn ; Morgane Miltgen ...
 
 
gRINN: a tool for calculation of residue interaction energies and protein energy network analysis of molecular dynamics simulations border= 
 
Onur Serçino─člu; Pemra Ozbek
 
 
Web Services
 
 
 
An update on PUG-REST: RESTful interface for programmatic access to PubChem 
 
Sunghwan Kim ; Paul A Thiessen; Tiejun Cheng; Bo Yu; Evan E Bolton
 
 
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