Biology

New

• PNE Bioinformatics Bookmarks･ (local)
• Molecular Toolbox･ Useful Molecular Biology Bookmarks by Dr. Sidney Morris.
• the BIODIDAC image collection･freely available for teaching, non-profit purposes.
• Sculpt･molecular modeling software. (ref. H. Mangalam (1996) TIBS 21 (10) 398-9)
• Statistics for biologists @nature.com

Tools in Protocols

• Plot Amino Acid Physico-chemical Properties･ eg. hydropathy profiles.
• PredictProtein ·
• GenomeNet · Bioinformatics Tools ·
• PDBe · Structural biology services · PDBeFold, PDBePISA, PDBeMotif, wwPDB validation server
• PDBe Bioinformatics services
• CATH･
• 2次構造予測 > DSSP · PHD · PSIpred · PREDATOR · Jpred2

• 学術情報センター研究者公募情報サービス･
• NACSIS CIS(Career Information Service)-J
• Art's Biotech Resource･journal links & free software.
• BioMedNet of Current Biology Ltd. [ Free Evaluated MEDLINE | BioMedLink]
• BIOSCI [ Home Page][ bionet archive]
• bionet.* keyword search @Trieste
• ChemPage･link to the chemical industry
• CytoBytes･Cell & Molecular Biology Online.

• The ExPASy Molecular Bilogy Server･
• GenomeNet WWW server
• SHIGEN Home Page･ SHared Information of GENetic resources. @NIG
• ACS:Articles on Command
• biosciences of the WWW Virtual Library･
• MEDLINE
  • Internet Medline Comparison Table･ at Medical Matrix. A comprehensive analysis of the medline sites.
  • Advanced PubMed Search @NCBI
  • Free Evaluated MEDLINE･ by BioMedNet
  • Medline Workbench ･(USA)( Japan)
  • SilverPlatter-Medline
• Entrez by NCBI.
• Bibliography on Features, Patterns, Correlations in DNA and Protein Sequences･
• Protein databases
  • MMDB･ Molecular Modelling DataBase, Entre's Structure Database.
  • VAST･ Vector Alignment Search Tool, for structure comparison. @NCBI.
  • VAST Search･NCBI's structure-structure similarity search service
  • PDB( Osaka mirror)
  • PDB links to Software･@Osaka.
  • PDB 3DBrowser･
  • PDBsum･ a web-based DB of summaries and analyses of all PDB structures
  • PDBtool･ a tool to browse and analyze features (predominantly geometry) of a macromolecular structure contained in a PDB file (for SGI and SUN)
  • proWeb･ links to sites for a specific protein families
  • PIR-- the Protein Information Resource･ comprehensive, annotated, and non-redundant protein sequence database
  • Relibase･ for searching protein-ligand databases. @ EBI.
  • Swiss-MODEL･ at expasy, an Automated Protein Modelling Server.
  • Swiss-3DImage Collection･ タンパク質・他の生体高分子の３次元構造のデータベース
  • The IMB--The Jena Image Library of Biological Macromolecules.
  • CATH･ タンパク質の構造分類
  • SCOP･ タンパク質の構造分類
  • FSSP･ 構造類似タンパク質ファミリーのデータベース
  • DSSP ( database files) is a database of secondary structure assignments (and much more) for all of the entries in PDB.
  • NRL_3D･ a sequence--structure database.
• Main Metabolic Pathways･
• DNA Information and Stock Center in National Institute of Agrobiological Resources, Tsukuba, Japan.･
• The Human Genome Project at Columbia University
• The PCR Primers database･@EBI. fully tested and optimized primers for PCR reactions
• 2D gel database･ @ExPASy
• The Antibody Resource Page･

• Archives
  • 遺伝研 ftp-site
  • bioinformatik.de
  • Art's Biotech Resource･journal links & free software.
  • Biocatalog: database of software for molecular biology. By EBI - European Bioinformatics Institute
  • Links to molbio software･ MGC-Department Cell Biology and Genetics, Center for Biomedical Genetics Erasmus University
  • IUBio Archive･an archive of biology data and software.
  • Jeff's Bio-links･ Index to Biological Dababases, Software Archives, Journals.
  • The Bio-Soft Web Ring･
  • 礒合＠旭硝子さんの Sites for the Molecular Biology･ 分子生物学研究用ツール集･
  • 東京理科大のSunSITE･
  • Pedro's BioMolecular Research Tools ( mirror in Japan)
    : A Collection of WWW Links to Information and Services Useful to Molecular Biologists
  • BioPerl･web links for developers of Perl-based software for life science research.
  • BioToolKit･an annotated directory of over 600 online molecular biology resources.
  • Research Tools･ @nih.go.jp
  • Brookhaven National Laboratory:Genome Sequencing Facility
    : Polypeptide Analysis Software
  • molbio programs by Rolf Kocherhans･Digest Preview, Dilution Calculator, Adaptor Design.
  • NCBI tool ftp site･
  • CMS-SDSC *** The CMS-SDSC Molecular Biology Resources
  • ExPASy - Proteomics Tools
  • Molecular Linux･ Molecular Biology related programs for Linux
• タンパク質構造予測
  • HSSP･ アミノ酸配列の相同性に基づく２次構造予測
  • DSSP･ タンパク質の２次構造予測
  • DSC Protein Secondary Structure Prediction ･
    (1) Given a single sequence. A multiple sequence alignmentt will be formed and DSC used to predict secondary structure.
    (2) Given a multiple sequence alignmnet. DSC will use this alignment to predict secondary structure.
  • PredictProtein (EMBL, Heidelberg, Germany)
  • Institute of Biology and Chemistry of Proteins･(France)
    ･アミノ酸配列から二次構造を推測 via e-mail
  • Protein Sequence Analysis (PSA) server analyzes your protein sequence and determines which of 209 sequence-structure models, spanning 15 different protein folding classes, are the most probable.
  • SSPAL･Prediction of protein secondary sturcture･
  • PSORT･ タンパク質のsorting signalの予測
  • TFSEARCH･ 転写因子の結合配列の検索
  • Bipartite Nuclear Localisation Sequence Locator runs a search through an amino acid sequence, looking for bipartite nuclear localisation sequences (pair of basics + spacer of any 10 amino acids + cluster of 3/5 basics). Please note that with both pages you have to enter the sequence without any spaces or carriage returns. (Ref) Robbins, J., et al. (1991) Cell 64, 615-623.
• Searching similar structure in Protein Data Bank
  • TOP via WWW | download the unix version
  • DALI via WWW | Email to dali@embl-heidelberg.de.
  • superimpose (ftp) by K. Diederichs (1995) Structural Superposition of Proteins with Unknown Alignment and Detection of Topological Simi- larity using a Six-dimensional Search Algorithm
  • SCOP･
• タンパク質の同定
  • MOTIF (Searching Protein Sequence Motifs)･ アミノ酸配列中のモチーフ構造の検索
  • ProFound･ ペプチドマップの比較によるタンパク質の同定
  • PepFrag･ 断片化パターンの比較によるタンパク質の同定
• 蛋白質の解析
  • k2d ( Home Page)( server) predict protein 2ndary structure % from UV CD spectra. MORE
• GCG･Wisconsin Sequence Analysis Package. a Unix based sequence analysis software.
• Oligonucleotide Vital Stats･ Accepts an oligo sequence and sends back useful information on it such as length, composition, percentage GC content, melting point (calculated by 2 methods), and various molar and concentration equivalents. The salt concentration can be determined by the user (with a default of 150mM, of course!)
• Gene-Finder programs ･
• genetic linkage analysis at Rockefeller University ･ LINKAGE, FASTLINK, CRIMAP, MAPMAKER, LIPED, VITESSE, MULTIMAP,GAS, HOMOG
• Procrustes･gene recognition software. (ref) Gelfand, M.S., Mironov, A.A.,Pevzner, P.A. "Gene recognition via spliced sequence alignment", Proc. Natl. Acad. Sci. USA (1996), 93, 9061-9066
• WebIn･New EBI WWW Sequence Submission Tool
• WWWtacg･ Restriction Enzyme Analysis via the Web. The WWW interface to ' tacg'.
• Sequence Alignment
  • Multiple Alignment software list･
  • BoxShade Server･
  • ClustalW 1.6 on-line help･a french site
  • Hyperlattice Path･ a Java-based Multiple Alignment Visualizer.
  • SeaView･ graphical multiple sequence alignment editor.
  • T-Coffee･ multiple sequence alignment package.
• 系統樹を描くプログラム
  • SINCA (Re: Phylogeny Research)
  • Colorful DNA sequence Alignment Software
  • MegAlign (part of the DNA* suite)
  • Cameleon from Oxford Molecular (www)
  • ALSCRIPT
• LSD: Life Science Dictionary Project Home Page ( japanese)( english)
• 科研費マクロ

• ImageJ ·
• Icy @ Bio Image Analysis.org · an open community platform for bioimage informatics

• Structural Biology Software Database･ @Bechman Institute of U Illinois.
• Electron Microscopy
  • Electron Microscopy Yellow Pages･ (software )
  • MicroWorld･ Internet guide to microscopy and electron microscopy. Image Processing, Stimulation, and Display and 3-D Electron Microscopy Public Domain Software for Electron Microscopy
  • Calidris - Home Page
  • HREM and Surface Structure Facility･** E/M image processing software/links and more.
• New ideas for bulk solvent correction･
• 7th International Conference on the Crystallisation of Biological Macromolecules･to be held in Granada (Spain) on May 3-8, 1998.
• PRC -- Protein Research Communication ･ news letter.
• bionet.xtallography archive @BIOSCI
• bionet.software.x-plore archive @BIOSCI
• sci.techniques.xtallography HomePage ･
• MAC Science/Nonius DIP Users Group Web page･
• Cryocrystallography
  • Cryo-Notes from SSRL Workshop October 1995, by Hakon Hope, Bernard Rupp, Sean Parkin and co, desribes some tools and useful info. about cryocrystallography.
  • Bernhard Rupp's Cryocrystal Page･
  • Cryocrystallography Product Guide･
• School of Crystallography @ Birkbeck College.
• Structures and Modelling group at University College･
• Purdue University's Markey Center for Structural Biology･
• Crystallography at SDSC
• UCL Protein Crystallography Group Home Page
• Protein Structure Group HP at Univ. York
• Photon Factory, KEK, Japan
• NIH: Center for Molecular Modeling
• Linux Application Homepage for Crystallography･
• CCP4 Home Page ( mirror at SDSC)
  • CCP4 ftp site ( mirror at SDSC)( mirror at KEK)
  • CCP4 problem page･
• CCP14･
• CCP11･the UK Collaborative Computational Project for biosequence and structure analysis.
• Cn3D･3D molecular structure viewer. by NCBI
• GRASP Home Page･ is a molecular visualization and analysis program. Honig Lab. at Columnbia Univ.
• GROMOS･is a general-purpose molecular dynamics computer simulation package.
• HKL package by HKL-Research, Inc.･ Denzo, XDisplayF and Scalepack.
• MolScript･by Per J. Kraulis ( Avatar Software AB)
• NAOMI･is a computer program system for studying 3-D structures of proteins.
• NCS･the use of non-crystallographic symmetry in protein structure refinement (preprint by Gerard Kleywegt, BMC, Uppsala)
• The O Home Page･
• ORTEP-III home page
  The Oak Ridge Thermal Ellipsoid Plot Program for Crystal Structure Illustrations
• The WWW PovChem Manual
• Raster3D･ photorealistic molecular graphics.
• SHELX･
• SQUID･ display/analysis/validate molecular structures, carry out MD analysis, draw 2D/3D/4D grapical representation of data. by Tom Oldfield.
• X-PLOR ･ Axel Brunger's Research Group Homepage
  X-PLOR Topology and Parameter Library for Hetero Compounds
• HIC-Up -- Hetero-compound Information Centre - Uppsala ･ containing all sorts of information regarding hetero-compounds
• XtalView･a package for macromolecular crystallography which includes electron density fitting
• Index of /hypermail/PROTEIN-CRYSTALLOGRAPHY/
• Darcy Clark's page on VRML and introductory crystallography
• IUCr--Crystallography World Wide ･ (japan mirror)
• Crystallographic Topology 101 describes an application of geometric topology to structural crystallography. The point, plane, and space groups are represented by orbifolds, and simple crystal structures by Morse function critical nets. A critical net on orbifold diagram provides a concise closed space representation of a crystal's asymmetric unit (fundamental domain) with all equivalent points on the boundary superimposed. Lattice complexes are also integrated into the representation.

• Beyond Bio 101: The Transformation of Undergraduate Biology Education by The Howard Hughes Medical Institute.
• The VSNS BioComputing Hypertext Coursebook･
• Microbiology Web Page For Undergraduate Research
• 「ザ・インターネットwith Macintosh & Windows」･ メーリングリスト･

• EndNote･ ユサコ･
  • EndNote mailing list archive･ by Adept Scientific.
  • 3360 Medline Terms･(www) @the Company of Biologists.
  • the Notre Dame EndNote Companion･
  • Zoology/Entomology Journals Term List･ containing about 900 journalsy. The Abbreviation 1 column contains BIOSIS abbreviations for these titles.
  • EndNote - University of Queensland Library･ Medical Journal Titles and EndNote.
  • Endnote filter information･ @ University of Technology Sydney
  • Endnote at Lehigh･
  • Endnote to Access data transfer instructions･
• All That JAS: Journal Abbreviation Sources･ a registry of Web resources that list or provide access to the full title of journal abbreviations
• Scholar's Quest･ Reference Project, Publications, & Services
  • Scholar's Quest Archive･ Public FTP site for the Bibliographic Software Community
  • Bibliographic Software･ Resources & Guides･
  • ERIC Resource Page･:
  • CDS/ISIS Resource Page･:
  • Library Software Page ･(Preliminary):
  • Steve's Academic Home Page･bibliography resources.
• NLM's Sources of journal abbreviations in the biological sciences
  • Journal abbriviation search
  • Index Medicus: List of all journals
  • List of Serials Indexed for Online Users @ NLM･is designed to provide complete bibliographic information on serials cited in three MEDLARS (Medical Literature Analysis and Retrieval System) files: MEDLINE (including the backfiles), AIDSLINE, and HealthSTAR.
• MLA Style Electronic Formats･models for references that might appear in the bibliography sectionof a business writer's research paper.
• Bibliographic Software Board ･ logs of the mailing lists.
• Evaluation of Reference Management Software on NT･
• Bibliography Formatting Software: An Evaluation Template･
• Note-taking software
  • Keynote･ open-source database for notes, outlining, etc.
  • Scribe･
  • Scolars Aid･

• Van Osta's page on Medicine, Molecular Biology, Computers and Biocomputing (Univ. Gent, Belgium)
• Analytical Ultracentrifugation WWW Page
  dedicated to analytical ultracentrifugation with the Beckman XL-A analytical ultracentrifuge.
• APOPTOSIS Online･
• CyanoBase･
• Chaperonin Web page･
• Electrophoresis Pages
• Histotechnology home page･
• ECO2DBASE: E.coli 2D gel database, linked from Swiss-Plot. Also indexed from the SRS server
• FlyBase･a Drosophila Genome Database.
• GOBASE･the Organelle Genome Database.
• HPLC - WIZARD･
• Ion Channel Web Page･
• IMGT･An integrated immumogenetics database (IMGT/LIGM) specialising in Ig and TcR
• Integrin Page･
• Kimball's Biology Pages･antigen presentation, protein kinesis, histocompatibility molecules.
• Mass Spectrometry Internet Resources FAQ･
• Microscopy UK･
• Micscape on-line･
• WWW site for PCR Service and Consultant･
• PhosphoBase･
• Reptile-Associated Salmonellosis WebPage･
• The rRNA WWW Server･
• SegNet DB･networks of genes controlling segmentation in Drosophila
• SRS TIPS･
• Thoretical Biophysics Page
• 植物生産のためのインターネット道しるべ
  農業・園芸・植物学などの植物に関連したリンク集
• 家畜ゲノムデータベース
  -- Java言語を用いた連鎖地図の表示、検索システム : ブタ(USDA,PIGM):ウシ(USDA):マウス(MGD)
• 水中生物ネットワーク･
• Amphibian Information Center･by Patuxent Wildlife Research Center (USGS/BRD).

• 日本生物物理学会･
• 日本蛋白質科学会･
• Harvard University
  • Dept. of Molecular and Cellular Biology [ Home Page][ Walter Gilbert Laboratory]
• 国立遺伝学研究所･
  • GIB - Genome Information Broker. 環状ゲノム閲覧システム
  • PMD - Protein Mutant Data Base [ ftp]
• NLM HyperDOC-- National Library of Medicine.
• NCBI-- National Center for Biotechnology Information. of NLM, NIH.
• TIFR: The Tata Institute of Fundamental Research in Bombay, India
  • Molecular Biology Group at TIFR
• Institute of Biology and Chemistry of Proteins･(France)
• Wadsworth Center
• Whitehead Institute

• Amersham -- News Letter
• BioCrystal Home Page
• Calbiochem
• Charles Supper Company･
• コスモ・バイオ
• 同仁化学研究所
• フナコシ
• Hampton Research : crystallization devices
• HiTech Web･
• (株)井内盛栄堂
• Siyaku.com･ [CPJLDO3W/passwd] by 和光純薬.
• KAIROS Scientific Inc.･ GFP, spectroscopy, rhodopsin
• Millipore
• Molecular Structure Corporation( Synchrotron beamline components)
• Merck･
• ナカライテスク
• Nanoprobes Inc.･ colloidal gold, undecagold
• Omega Engineering Inc.･
• OceanOptics･fiber optic spectrometers.
• Oxford Cryosystems･ Email: info@OxfordCryosystems.co.uk
• Pharmacia
• ファルマシアバイオテク（株）･
• Recombinant BioCatalysis : enzymes
• Siemens x-ray analytical instruments･
• Sigma
• Scientific Equipment Exchange--New Source for Used Scientific Instruments.