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) gmx.de
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