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Hidden Markov models

Hydrophobicity analyses

Topology and helix packing

Protein localization

Secondary structure

Super-secondary structure

3D structure


    Software in Molecular Biology (2004):

    An overview about molecular biological software is given each year in a special issue of Nucleic Acids Research. The published articles are very useful to get fast and qualified answers to related questions. Please enjoy the list of articles published in July 2004:

  • Nicola Harte, Ville Silventoinen, Emmanuel Quevillon, Stephen Robinson, Kimmo Kallio, Xavier Fustero, Pravin Patel, Petteri Jokinen, and Rodrigo Lopez
    Public web-based services from the European Bioinformatics Institute
    Nucl. Acids Res. 32: W3-W9.

  • Tien Huynh and Isidore Rigoutsos
    The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update
    Nucl. Acids Res. 32: W10-W15.

  • Karsten Hokamp and Kenneth H. Wolfe
    PubCrawler: keeping up comfortably with PubMed and GenBank
    Nucl. Acids Res. 32: W16-W19.

  • Scott McGinnis and Thomas L. Madden
    BLAST: at the core of a powerful and diverse set of sequence analysis tools
    Nucl. Acids Res. 32: W20-W25.

  • John B. Spalding and Peter J. Lammers
    BLAST Filter and GraphAlign: rule-based formation and analysis of sets of related DNA and protein sequences
    Nucl. Acids Res. 32: W26-W32.

  • Burkhard Morgenstern
    DIALIGN: multiple DNA and protein sequence alignment at BiBiServ
    Nucl. Acids Res. 32: W33-W36.

  • Olivier Poirot, Karsten Suhre, Chantal Abergel, Eamonn O'Toole, and Cedric Notredame
    3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment
    Nucl. Acids Res. 32: W37-W40.

  • Michael Brudno, Rasmus Steinkamp, and Burkhard Morgenstern
    The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences
    Nucl. Acids Res. 32: W41-W44.

  • Ji Qi, Hong Luo, and Bailin Hao
    CVTree: a phylogenetic tree reconstruction tool based on whole genomes
    Nucl. Acids Res. 32: W45-W47.

  • Radek Zika, Jan Paces, Adam Pavlícek, and Václav Paces
    WAViS server for handling, visualization and presentation of multiple alignments of nucleotide or amino acids sequences
    Nucl. Acids Res. 32: W48-W49.

  • Jahnavi C. Prasad, Sandor Vajda, and Carlos J. Camacho
    Consensus alignment server for reliable comparative modeling with distant templates
    Nucl. Acids Res. 32: W50-W54.

  • Masato Ohtsuka, Shohei Horiuchi, Jerzy K. Kulski, Minoru Kimura, and Hidetoshi Inoko
    CHOP: visualization of ‘wobbling’ and isolation of highly conserved regions from aligned DNA sequences
    Nucl. Acids Res. 32: W55-W58.

  • William C. Ray
    MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence alignments
    Nucl. Acids Res. 32: W59-W63.

  • Dmitry A. Afonnikov and Nikolay A. Kolchanov
    CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences
    Nucl. Acids Res. 32: W64-W68.

  • Soon-Heng Tan, Zhuo Zhang, and See-Kiong Ng
    ADVICE: Automated Detection and Validation of Interaction by Co-Evolution
    Nucl. Acids Res. 32: W69-W72.

  • Zhuo Zhang and See-Kiong Ng
    InterWeaver: interaction reports for discovering potential protein interaction partners with online evidence
    Nucl. Acids Res. 32: W73-W75.

  • Darby Tien-Hau Chang, Chien-Yu Chen, Wen-Chin Chung, Yen-Jen Oyang, Hsueh-Fen Juan, and Hsuan-Cheng Huang
    ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures
    Nucl. Acids Res. 32: W76-W82.

  • Brian P. Kelley, Bingbing Yuan, Fran Lewitter, Roded Sharan, Brent R. Stockwell, and Trey Ideker
    PathBLAST: a tool for alignment of protein interaction networks
    Nucl. Acids Res. 32: W83-W88.

  • Kyungsook Han, Byong-Hyon Ju, and Haemoon Jung
    WebInterViewer: visualizing and analyzing molecular interaction networks
    Nucl. Acids Res. 32: W89-W95.

  • Stephen R. Comeau, David W. Gatchell, Sandor Vajda, and Carlos J. Camacho
    ClusPro: a fully automated algorithm for protein–protein docking
    Nucl. Acids Res. 32: W96-W99.

  • Chittibabu Guda, Sifang Lu, Eric D. Scheeff, Philip E. Bourne, and Ilya N. Shindyalov
    CE-MC: a multiple protein structure alignment server
    Nucl. Acids Res. 32: W100-W103.

  • Shandar Ahmad and Akinori Sarai
    Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins
    Nucl. Acids Res. 32: W104-W107.

  • Kirill Rotmistrovsky, Wonhee Jang, and Gregory D. Schuler
    A web server for performing electronic PCR
    Nucl. Acids Res. 32: W108-W112.

  • Andreas Henschel, Frank Buchholz, and Bianca Habermann
    DEQOR: a web-based tool for the design and quality control of siRNAs
    Nucl. Acids Res. 32: W113-W120.

  • Peter Dudek and Didier Picard
    TROD: T7 RNAi Oligo Designer
    Nucl. Acids Res. 32: W121-W123.

  • Yuki Naito, Tomoyuki Yamada, Kumiko Ui-Tei, Shinichi Morishita, and Kaoru Saigo
    siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference
    Nucl. Acids Res. 32: W124-W129.

  • Bingbing Yuan, Robert Latek, Markus Hossbach, Thomas Tuschl, and Fran Lewitter
    siRNA Selection Server: an automated siRNA oligonucleotide prediction server
    Nucl. Acids Res. 32: W130-W134.

  • Ye Ding, Chi Yu Chan, and Charles E. Lawrence
    Sfold web server for statistical folding and rational design of nucleic acids
    Nucl. Acids Res. 32: W135-W141.

  • Hélène Touzet and Olivier Perriquet
    CARNAC: folding families of related RNAs
    Nucl. Acids Res. 32: W142-W145.

  • Jianhua Ruan, Gary D. Stormo, and Weixiong Zhang

  • ILM: a web server for predicting RNA secondary structures with pseudoknots
    Nucl. Acids Res. 32: W146-W149.

  • Xiaomin Ying, Hong Luo, Jingchu Luo, and Wuju Li
    RDfolder: a web server for prediction of RNA secondary structure
    Nucl. Acids Res. 32: W150-W153.

  • Peter Bengert and Thomas Dandekar
    Riboswitch finder—a tool for identification of riboswitch RNAs
    Nucl. Acids Res. 32: W154-W159.

  • André Lambert, Jean-Fred Fontaine, Matthieu Legendre, Fabrice Leclerc, Emmanuelle Permal, François Major, Harald Putzer, Olivier Delfour, Bernard Michot, and Daniel Gautheret
    The ERPIN server: an interface to profile-based RNA motif identification
    Nucl. Acids Res. 32: W160-W165.

  • Sònia Casillas and Antonio Barbadilla
    PDA: a pipeline to explore and estimate polymorphism in large DNA databases
    Nucl. Acids Res. 32: W166-W169.

  • Stefan Weckx, Peter De Rijk, Christine Van Broeckhoven, and Jurgen Del-Favero
    SNPbox: web-based high-throughput primer design from gene to genome
    Nucl. Acids Res. 32: W170-W172.

  • Wolfgang Helmberg, Raymond Dunivin, and Michael Feolo
    The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences
    Nucl. Acids Res. 32: W173-W175.

  • Jean-Marie Rouillard, Woonghee Lee, Gilles Truan, Xiaolian Gao, Xiaochuan Zhou, and Erdogan Gulari
    Gene2Oligo: oligonucleotide design for in vitro gene synthesis
    Nucl. Acids Res. 32: W176-W180.

  • Namshin Kim, Seokmin Shin, and Sanghyuk Lee
    ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences
    Nucl. Acids Res. 32: W181-W186.

  • William G. Fairbrother, Gene W. Yeo, Rufang Yeh, Paul Goldstein, Matthew Mawson, Phillip A. Sharp, and Christopher B. Burge
    RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
    Nucl. Acids Res. 32: W187-W190.

  • Anason S. Halees and Zhiping Weng
    PromoSer: improvements to the algorithm, visualization and accessibility
    Nucl. Acids Res. 32: W191-W194.

  • Wynand B.L. Alkema, Öjvind Johansson, Jens Lagergren, and Wyeth W. Wasserman
    MSCAN: identification of functional clusters of transcription factor binding sites
    Nucl. Acids Res. 32: W195-W198.

  • Giulio Pavesi, Paolo Mereghetti, Giancarlo Mauri, and Graziano Pesole STRONG>Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes
    Nucl. Acids Res. 32: W199-W203.

  • Yueyi Liu, Liping Wei, Serafim Batzoglou, Douglas L. Brutlag, Jun S. Liu, and X. Shirley Liu
    A suite of web-based programs to search for transcriptional regulatory motifs
    Nucl. Acids Res. 32: W204-W207.

  • D. Y. Oshchepkov, E. E. Vityaev, D. A. Grigorovich, E. V. Ignatieva, and T. M. Khlebodarova
    SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition
    Nucl. Acids Res. 32: W208-W212.

  • Peter M. Haverty, Martin C. Frith, and Zhiping Weng
    CARRIE web service: automated transcriptional regulatory network inference and interactive analysis
    Nucl. Acids Res. 32: W213-W216.

  • Gabriela G. Loots and Ivan Ovcharenko
    rVISTA 2.0: evolutionary analysis of transcription factor binding sites
    Nucl. Acids Res. 32: W217-W221.

  • Matti Kankainen and Liisa Holm
    POBO, transcription factor binding site verification with bootstrapping
    Nucl. Acids Res. 32: W222-W229.

  • Hong Pan, Li Zuo, Vidhu Choudhary, Zhuo Zhang, Shoi Houi Leow, Fui Teen Chong, Yingliang Huang, Victor Wui Siong Ong, Bijayalaxmi Mohanty, Sin Lam Tan, S. P. T. Krishnan, and Vladimir B. Bajic
    Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining
    Nucl. Acids Res. 32: W230-W234.

  • Zhenjun Hu, Yutao Fu, Anason S. Halees, Szymon M. Kielbasa, and Zhiping Weng
    SeqVISTA: a new module of integrated computational tools for studying transcriptional regulation
    Nucl. Acids Res. 32: W235-W241.

  • Lucía Conde, Juan M. Vaquerizas, Javier Santoyo, Fátima Al-Shahrour, Sergio Ruiz-Llorente, Mercedes Robledo, and Joaquín Dopazo
    PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level
    Nucl. Acids Res. 32: W242-W248.

  • Albin Sandelin, Wyeth W. Wasserman, and Boris Lenhard
    ConSite: web-based prediction of regulatory elements using cross-species comparison
    Nucl. Acids Res. 32: W249-W252.

  • Roded Sharan, Asa Ben-Hur, Gabriela G. Loots, and Ivan Ovcharenko
    CREME: Cis-Regulatory Module Explorer for the human genome
    Nucl. Acids Res. 32: W253-W256.

  • Vinsensius B. Vega, Dhinoth Kumar Bangarusamy, Lance D. Miller, Edison T. Liu, and Chin-Yo Lin
    BEARR: Batch Extraction and Analysis of cis-Regulatory Regions
    Nucl. Acids Res. 32: W257-W260.

  • Klaus Karl Lohmann and Claus-W. von der Lieth
    GlycoFragment and GlycoSearchMS: web tools to support the interpretation of mass spectra of complex carbohydrates
    Nucl. Acids Res. 32: W261-W266.

  • Kiyoko F. Aoki, Atsuko Yamaguchi, Nobuhisa Ueda, Tatsuya Akutsu, Hiroshi Mamitsuka, Susumu Goto, and Minoru Kanehisa
    KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains
    Nucl. Acids Res. 32: W267-W272.

  • Kelly A. Frazer, Lior Pachter, Alexander Poliakov, Edward M. Rubin, and Inna Dubchak
    VISTA: computational tools for comparative genomics
    Nucl. Acids Res. 32: W273-W279.

  • Ivan Ovcharenko, Marcelo A. Nobrega, Gabriela G. Loots, and Lisa Stubbs
    ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes
    Nucl. Acids Res. 32: W280-W286.

  • José L. Oliver, Pedro Carpena, Michael Hackenberg, and Pedro Bernaola-Galván
    IsoFinder: computational prediction of isochores in genome sequences
    Nucl. Acids Res. 32: W287-W292.

  • Marco Masseroli, Dario Martucci, and Francesco Pinciroli
    GFINDer: Genome Function INtegrated Discoverer through dynamic annotation, statistical analysis, and mining
    Nucl. Acids Res. 32: W293-W300.

  • Jan Krüger, Alexander Sczyrba, Stefan Kurtz, and Robert Giegerich
    e2g: an interactive web-based server for efficiently mapping large EST and cDNA sets to genomic sequences
    Nucl. Acids Res. 32: W301-W304.

  • Leila Taher, Oliver Rinner, Saurabh Garg, Alexander Sczyrba, and Burkhard Morgenstern
    AGenDA: gene prediction by cross-species sequence comparison
    Nucl. Acids Res. 32: W305-W308.

  • Mario Stanke, Rasmus Steinkamp, Stephan Waack, and Burkhard Morgenstern
    AUGUSTUS: a web server for gene finding in eukaryotes
    Nucl. Acids Res. 32: W309-W312.

  • Detlef Groth, Hans Lehrach, and Steffen Hennig
    GOblet: a platform for Gene Ontology annotation of anonymous sequence data
    Nucl. Acids Res. 32: W313-W317.

  • Sailu Yellaboina, Jayashree Seshadri, M. Senthil Kumar, and Akash Ranjan
    PredictRegulon: a web server for the prediction of the regulatory protein binding sites and operons in prokaryote genomes
    Nucl. Acids Res. 32: W318-W320.

  • Burkhard Rost, Guy Yachdav, and Jinfeng Liu
    The PredictProtein server
    Nucl. Acids Res. 32: W321-W326.

  • Aron Marchler-Bauer and Stephen H. Bryant
    CD-Search: protein domain annotations on the fly
    Nucl. Acids Res. 32: W327-W331.

  • Marco Pagni, Vassilios Ioannidis, Lorenzo Cerutti, Monique Zahn-Zabal, C. Victor Jongeneel, and Laurent Falquet
    MyHits: a new interactive resource for protein annotation and domain identification
    Nucl. Acids Res. 32: W332-W335.

  • François Enault, Karsten Suhre, Olivier Poirot, Chantal Abergel, and Jean-Michel Claverie
    Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis
    Nucl. Acids Res. 32: W336-W339.

  • Richard D. LeDuc, Gregory K. Taylor, Yong-Bin Kim, Thomas E. Januszyk, Lee H. Bynum, Joseph V. Sola, John S. Garavelli, and Neil L. Kelleher
    ProSight PTM: an integrated environment for protein identification and characterization by top-down mass spectrometry
    Nucl. Acids Res. 32: W340-W345.

  • Victor G. Levitsky
    RECON: a program for prediction of nucleosome formation potential
    Nucl. Acids Res. 32: W346-W349.

  • Johann Lenffer, Paulo Lai, Wafaa El Mejaber, Asif M. Khan, Judice L. Y. Koh, Paul T. J. Tan, Seng H. Seah, and Vladimir Brusic
    CysView: protein classification based on cysteine pairing patterns
    Nucl. Acids Res. 32: W350-W355.

  • Lesheng Kong, Bernett Teck Kwong Lee, Joo Chuan Tong, Tin Wee Tan, and Shoba Ranganathan
    SDPMOD: an automated comparative modeling server for small disulfide-bonded proteins
    Nucl. Acids Res. 32: W356-W359.

  • Brian D. O'Connor and Todd O. Yeates
    GDAP: a web tool for genome-wide protein disulfide bond prediction
    Nucl. Acids Res. 32: W360-W364.

  • Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Brett Poulin, Roman Eisner, Zhiyong Lu, John Anvik, Cam Macdonell, Alona Fyshe, and David Meeuwis
    Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations
    Nucl. Acids Res. 32: W365-W371.

  • Chittibabu Guda, Purnima Guda, Eoin Fahy, and Shankar Subramaniam
    MITOPRED: a web server for the prediction of mitochondrial proteins
    Nucl. Acids Res. 32: W372-W374.

  • Karsten Hiller, Andreas Grote, Maurice Scheer, Richard Münch, and Dieter Jahn
    PrediSi: prediction of signal peptides and their cleavage positions
    Nucl. Acids Res. 32: W375-W379.

  • P. K. Papasaikas, P. G. Bagos, Z. I. Litou, V. J. Promponas, and S. J. Hamodrakas
    PRED-GPCR: GPCR recognition and family classification server
    Nucl. Acids Res. 32: W380-W382.

  • Manoj Bhasin and G. P. S. Raghava
    GPCRpred: an SVM-based method for prediction of families and subfamilies of G-protein coupled receptors
    Nucl. Acids Res. 32: W383-W389.

  • Masafumi Arai, Hironori Mitsuke, Masami Ikeda, Jun-Xiong Xia, Takashi Kikuchi, Masanobu Satake, and Toshio Shimizu
    ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability
    Nucl. Acids Res. 32: W390-W393.

  • Frode S. Berven, Kristian Flikka, Harald B. Jensen, and Ingvar Eidhammer
    BOMP: a program to predict integral ß-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria
    Nucl. Acids Res. 32: W394-W399.

  • Pantelis G. Bagos, Theodore D. Liakopoulos, Ioannis C. Spyropoulos, and Stavros J. Hamodrakas
    PRED-TMBB: a web server for predicting the topology of ß-barrel outer membrane proteins
    Nucl. Acids Res. 32: W400-W404.

  • Mohd. Zeeshan Ansari, Gitanjali Yadav, Rajesh S. Gokhale, and Debasisa Mohanty
    NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases
    Nucl. Acids Res. 32: W405-W413.

  • Manoj Bhasin and G. P. S. Raghava
    ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST
    Nucl. Acids Res. 32: W414-W419.

  • Yutao Fu, Martin C. Frith, Peter M. Haverty, and Zhiping Weng
    MotifViz: an analysis and visualization tool for motif discovery
    Nucl. Acids Res. 32: W420-W423.

  • Olga V. Kalinina, Pavel S. Novichkov, Andrey A. Mironov, Mikhail S. Gelfand, and Aleksandra B. Rakhmaninova
    SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins
    Nucl. Acids Res. 32: W424-W428.

  • Cédric Muller, Mathieu Denis, Laurent Gentzbittel, and Thomas Faraut
    The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species
    Nucl. Acids Res. 32: W429-W434.

  • Véronique Giudicelli, Denys Chaume, and Marie-Paule Lefranc
    IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V–J and V–D–J rearrangement analysis
    Nucl. Acids Res. 32: W435-W440.

  • Kei-Hoi Cheung, Janet Hager, Deyun Pan, Ranjana Srivastava, Shrikant Mane, Yuli Li, Perry Miller, and Kenneth R. Williams
    KARMA: a web server application for comparing and annotating heterogeneous microarray platforms
    Nucl. Acids Res. 32: W441-W444.

  • Lars Juhl Jensen, Julien Lagarde, Christian von Mering, and Peer Bork
    ArrayProspector: a web resource of functional associations inferred from microarray expression data
    Nucl. Acids Res. 32: W445-W448.

  • Purvesh Khatri, Pratik Bhavsar, Gagandeep Bawa, and Sorin Draghici
    Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments
    Nucl. Acids Res. 32: W449-W456.

  • Karsten Hokamp, Fiona M. Roche, Michael Acab, Marc-Etienne Rousseau, Byron Kuo, David Goode, Dana Aeschliman, Jenny Bryan, Lorne A. Babiuk, Robert E. W. Hancock, and Fiona S. L. Brinkman
    ArrayPipe: a flexible processing pipeline for microarray data
    Nucl. Acids Res. 32: W457-W459.

  • Hee-Joon Chung, Mingoo Kim, Chan Hee Park, Jihoon Kim, and Ju Han Kim
    ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics
    Nucl. Acids Res. 32: W460-W464.

  • Misha Kapushesky, Patrick Kemmeren, Aedín C. Culhane, Steffen Durinck, Jan Ihmels, Christine Körner, Meelis Kull, Aurora Torrente, Ugis Sarkans, Jaak Vilo, and Alvis Brazma
    Expression Profiler: next generation—an online platform for analysis of microarray data
    Nucl. Acids Res. 32: W465-W470.

  • Fiona M. Roche, Karsten Hokamp, Michael Acab, Lorne A. Babiuk, Robert E. W. Hancock, and Fiona S. L. Brinkman
    ProbeLynx: a tool for updating the association of microarray probes to genes
    Nucl. Acids Res. 32: W471-W474.

  • Suresh Karanam and Carlos S. Moreno
    CONFAC: automated application of comparative genomic promoter analysis to DNA microarray datasets
    Nucl. Acids Res. 32: W475-W484.

  • Javier Herrero, Juan M. Vaquerizas, Fátima Al-Shahrour, Lucía Conde, Álvaro Mateos, Javier Santoyo Ramón Díaz-Uriarte, and Joaquín Dopazo
    New challenges in gene expression data analysis and the extended GEPAS
    Nucl. Acids Res. 32: W485-W491.

  • Stefano Volinia, Rita Evangelisti, Francesca Francioso, Diego Arcelli, Massimo Carella, and Paolo Gasparini
    GOAL: automated Gene Ontology analysis of expression profiles
    Nucl. Acids Res. 32: W492-W499.

  • Matthias Heinig and Dmitrij Frishman
    STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins
    Nucl. Acids Res. 32: W500-W502.

  • Maxim Shatsky, Oranit Dror, Dina Schneidman-Duhovny, Ruth Nussinov, and Haim J. Wolfson
    BioInfo3D: a suite of tools for structural bioinformatics
    Nucl. Acids Res. 32: W503-W507.

  • R. Gautier, A.-C. Camproux, and P. Tufféry
    SCit: web tools for protein side chain conformation analysis
    Nucl. Acids Res. 32: W508-W511.

  • Alexander V. Diemand and Holger Scheib
    iMolTalk: an interactive, internet-based protein structure analysis server
    Nucl. Acids Res. 32: W512-W516.

  • Rajesh Nair and Burkhard Rost
    LOCnet and LOCtarget: sub-cellular localization for structural genomics targets
    Nucl. Acids Res. 32: W517-W521.

  • Jun-tao Guo, Kyle Ellrott, Won Jae Chung, Dong Xu, Serguei Passovets, and Ying Xu
    PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction
    Nucl. Acids Res. 32: W522-W525.

  • David E. Kim, Dylan Chivian, and David Baker
    Protein structure prediction and analysis using the Robetta server
    Nucl. Acids Res. 32: W526-W531.

  • Andrew E. Torda, James B. Procter, and Thomas Huber
    Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices
    Nucl. Acids Res. 32: W532-W535.

  • Jessica Shapiro and Douglas Brutlag
    FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web
    Nucl. Acids Res. 32: W536-W541.

  • Giridhar Chukkapalli, Chittibabu Guda, and Shankar Subramaniam
    SledgeHMMER: a web server for batch searching the Pfam database
    Nucl. Acids Res. 32: W542-W544.

  • Frédéric Guyon, Anne-Claude Camproux, Joëlle Hochez, and Pierre Tufféry
    SA-Search: a web tool for protein structure mining based on a Structural Alphabet
    Nucl. Acids Res. 32: W545-W548.

  • Vladimir A. Ivanisenko, Sergey S. Pintus, Dmitry A. Grigorovich, and Nickolay A. Kolchanov
    PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
    Nucl. Acids Res. 32: W549-W554.

  • T. Andrew Binkowski, Patrick Freeman, and Jie Liang
    pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins
    Nucl. Acids Res. 32: W555-W558.

  • Balvinder Singh
    PepBuild: a web server for building structure data of peptides/proteins
    Nucl. Acids Res. 32: W559-W561.

  • Fan Xue, Zhong Gu, and Jin-an Feng
    LINKER: a web server to generate peptide sequences with extended conformation
    Nucl. Acids Res. 32: W562-W565.

  • William J. Salerno, Samuel M. Seaver, Brian R. Armstrong, and Ishwar Radhakrishnan
    MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data
    Nucl. Acids Res. 32: W566-W568.

  • Jinfeng Liu and Burkhard Rost
    CHOP: parsing proteins into structural domains
    Nucl. Acids Res. 32: W569-W571.

  • Chi-Ren Shyu, Pin-Hao Chi, Grant Scott, and Dong Xu
    ProteinDBS: a real-time retrieval system for protein structure comparison
    Nucl. Acids Res. 32: W572-W575.

  • Krzysztof Ginalski, Marcin von Grotthuss, Nick V. Grishin, and Leszek Rychlewski
    Detecting distant homology with Meta-BASIC
    Nucl. Acids Res. 32: W576-W581.

  • Yuzhen Ye and Adam Godzik
    FATCAT: a web server for flexible structure comparison and structure similarity searching
    Nucl. Acids Res. 32: W582-W585.

  • Joanna M. Sasin and Janusz M. Bujnicki
    COLORADO3D, a web server for the visual analysis of protein structures
    Nucl. Acids Res. 32: W586-W589.

  • Rajarshi Maiti, Gary H. Van Domselaar, Haiyan Zhang, and David S. Wishart
    SuperPose: a simple server for sophisticated structural superposition
    Nucl. Acids Res. 32: W590-W594.

  • Goran Neshich, Walter Rocchia, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato Fileto, Christian Baudet, Ivan P. Pinto, Arnaldo J. Montagner, Juliana F. Palandrani, Joao N. Krauchenco, Renato C. Torres, Savio Souza, Roberto C. Togawa, and Roberto H. Higa
    JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure
    Nucl. Acids Res. 32: W595-W601.

  • A. Bhaduri, G. Pugalenthi, N. Gupta, and R. Sowdhamini
    iMOT: an interactive package for the selection of spatially interacting motifs
    Nucl. Acids Res. 32: W602-W605.

  • Jean-Baptiste Claude, Karsten Suhre, Cédric Notredame, Jean-Michel Claverie, and Chantal Abergel
    CaspR: a web server for automated molecular replacement using homology modelling
    Nucl. Acids Res. 32: W606-W609.

  • Karsten Suhre and Yves-Henri Sanejouand
    ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
    Nucl. Acids Res. 32: W610-W614.

  • Ian W. Davis, Laura Weston Murray, Jane S. Richardson, and David C. Richardson
    MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes
    Nucl. Acids Res. 32: W615-W619.

  • Neil Maudling and Teresa K. Attwood
    FAN: fingerprint analysis of nucleotide sequences
    Nucl. Acids Res. 32: W620-W623.

  • Tiziana Castrignanò, Alessandro Canali, Giorgio Grillo, Sabino Liuni, Flavio Mignone, and Graziano Pesole
    CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison
    Nucl. Acids Res. 32: W624-W627.

  • Y. L. Orlov and V. N. Potapov
    Complexity: an internet resource for analysis of DNA sequence complexity
    Nucl. Acids Res. 32: W628-W633.

  • Sven Mika and Burkhard Rost
    NLProt: extracting protein names and sequences from papers
    Nucl. Acids Res. 32: W634-W637.

  • Brian D. Halligan, Victor Ruotti, Weihong Jin, Scott Laffoon, Simon N. Twigger, and Edward A. Dratz
    ProMoST (Protein Modification Screening Tool): a web-based tool for mapping protein modifications on two-dimensional gels
    Nucl. Acids Res. 32: W638-W644.

  • P. Selvarani, V. Shanthi, C. K. Rajesh, S. Saravanan, and K. Sekar
    BSDD: Biomolecules Segment Display Device—a web-based interactive display tool
    Nucl. Acids Res. 32: W645-W648.

  • Jeff Reneker, Chi-Ren Shyu, Peiyu Zeng, Joseph C. Polacco, and Walter Gassmann
    ACMES: fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval
    Nucl. Acids Res. 32: W649-W653.

  • Mikhail Rozanov, Uwe Plikat, Colombe Chappey, Andrey Kochergin, and Tatiana Tatusova
    A web-based genotyping resource for viral sequences
    Nucl. Acids Res. 32: W654-W659.

  • Xiaoli Dong, Paul Stothard, Ian J. Forsythe, and David S. Wishart
    PlasMapper: a web server for drawing and auto-annotating plasmid maps
    Nucl. Acids Res. 32: W660-W664.

  • Todd J. Dolinsky, Jens E. Nielsen, J. Andrew McCammon, and Nathan A. Baker
    PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations
    Nucl. Acids Res. 32: W665-W667.

  • Lee Whitmore and B. A. Wallace
    DICHROWEB, an online server for protein secondary structure analyses from circular dichroism spectroscopic data
    Nucl. Acids Res. 32: W668-W673.

  • Jorge Fernandez-de-Cossio, Luis Javier Gonzalez, Yoshinori Satomi, Lazaro Betancourt, Yassel Ramos, Vivian Huerta, Abel Amaro, Vladimir Besada, Gabriel Padron, Naoto Minamino, and Toshifumi Takao
    Isotopica: a tool for the calculation and viewing of complex isotopic envelopes
    Nucl. Acids Res. 32: W674-W678.

  • Z. W. Cao, Y. Xue, L. Y. Han, B. Xie, H. Zhou, C. J. Zheng, H. H. Lin, and Y. Z. Chen
    MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids
    Nucl. Acids Res. 32: W679-W685.


Latest update: October 1, 2004

Ralf Koebnik
Institut für Genetik
Abt. Pflanzengenetik
Weinbergweg 10
06120 Halle/Saale
Telefon: 0345 / 55 26 293 (Büro) bzw. 296 (Labor)
Fax: 0345 / 55 27 151
Email: koebnik (at)
Please replace (at) by @.

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