Naoki Sato's bookmarks

Last update: July 26, 2001

MOLECULAR BIOLOGY

BIOSCI/bionet Electronic Newsgroup Network for Biology

Institutes

Programs

General Molecular Biology Software

Molecular Linux -- Now available at new site

Biology software for linux
Biology Software for alpha NT
JaMBW: Java Molecular Biology Directory
Research Tools(NIH)
Computational Biology Software
DNA Graphical User Interface (DNA/GUI)

CITI2 DEAMBULUM : Molecular biology
MAGPIE - Multipurpose Automated Genome Project Investigation Environment
BAC Manual Table of Contents
IUBio Archive for Biology data and software
TACG web interface Link to tacg2 program may be available here
the Bioperl Project -- new web site

xbbtools Tcl/Tk-based tools -- obsolete - see Molecular Linux page
Plasmid Processor Homepage
Prophet Overview -- Life science tools for Win95

Sequence annotation tools

Artemis from Sanger Centre
Glimmer from TIGR

Alignment and Phylogeny Software

OLIVIER GASCUEL's lab
BioNJ, a revised NJ.
ClustalX
NJplot
Shadybox
BoxShade experimental 'C' version
BoxShade HP
AG BIODV: Software Development for Molecular Biology
Pratt Project Main Page
DIALIGN, a novel alignment algorithm

The TREE-PUZZLE Software -- Revised PUZZLE software
Cladistic Software -- The Willi Hennig Society
TopWise
PHYLIP
Genedoc
TreeView
PGAPack Parallel Genetic Algorithm Library
BIONJ
an improved version of the NJ algorithm
SEView: a Java applet for browsing molecular sequence data
Pyramids homepage
LAMARC - estimating population parameters
Phylogeny Programs
INCA Download Page-- Iterative Neighborhood Cluster Analysis


Structue Analysis

Molecular surface
Connolly Surfaces
PROCHECK - protein structure checks
Crystallography software available via the Web

GROMOS home page
D.T. Jones Home Page - THREADER
MSCI XMol User Guide
RasMol Home Page(old?)
OpenRasMol Home Page
Molecular Simulations Inc
ProMod: Users Guide
MOLMOL
WHAT IF, a molecular graphics software
Directory ftp.imag.fr:/pub/
RNAdraw
The NAOMI WWW site
RNA Secondary Structures
WPDB - The Protein Data Bank through Microsoft Windows
VMD Home Page Molecular model viewer
TINKER Molecular Modeling Package
The DRAGON's Lair -- Molecular modelling
MolScript Web Site -- Molecular graphics
ESSA RNA SOFTWARE HOME PAGE

Homology Search

WU-BLAST Archives

Basic Local Alignment Search Tool
PROCRUSTES: Similarity-Based Gene Recognition via Spliced Alignment

WU-BLAST Archives
WPDB - The Protein Data Bank through Microsoft Windows

Unclassified
Welcome to GROMACS
NAMD Home Page
Jay Ponder Lab
Informax, Inc.
Doug Eernisse's Home Page
BMERC main page
CCMS Home Page

Information services

Catalogs of general information

Alex's Cyber-Science links -- Catalog of Bio-science links
Biology Links
Bio-wURLd
Pedro's BioMolecular Research Tools Top Page
Nucleic Acid Information on Internet
Maize Genome WWW server list of Links to Biological Science WWW Servers


Major institutes home page

National Institute of Genetics (NIG) Idengaku Kenkyu Jo in Mishima
JICST WWW Home Page
European Molecular Biology Laboratory (EMBL)
European Bioinformatics Institute (EBI)
Cambridge School of Biological Sciences
SANGER CENTRE
European Molecular Biology Network (EMBnet)
ExPASy -- Protein database in Switzerland
THE INSTITUTE FOR GENOMIC RESEARCH (TIGR)
Hopkins Bio-Informatics Home Page
ATG Homepage
Max Plank Institut Molecular Genetics
The National Center for Biotechnology Information (NCBI)
CBIL -- Computational Biology and Informatics Laboratory


Genome information

Cyanosite
Cyanonews
Human Genome Center Home Page
YPD HOME PAGE
Weeds World -- Arabidopsis newsletter
Arabidopsis thaliana Database (TAIR)
Saccharomyces Genome Database
Pasteur Culture Collection
Genome Sequence DataBase: Home Page
The Genome Database
Kazusa DNA Research Institute Home Page
Microbial Genome WWW Home Page
Molecular Evolution & Organelle Genomics
Organellar Genomes -- gopher site --
Micado Main Menu -- Bacillus subtilis databases
SubtiList Web Server -- Bacillus subtilis information

Other databases

Micado database
DNA Data Bank of JAPAN WWW Title Page
Ribosomal Database Project II
The Protein Structure Database (PSdb)
AGIS: Database: PhytochemDB
ProDom -- protein domain database
Directory ftp.infobiogen.fr:/pub/doc/bio/

Nicelist
PENCE
Protein Engineering Network Centre of Excellence
Laboratory of Plant Pigment Biochemistry and Photobiology

Phylogenetic analysis

Laboratory of experimental modelling of evolutionary processes
Molecular Analysis of Symbiosis

Structure analysis

MIPS
Munich information center for protein science, PEDANT etc
GBF MSF HOMEPAGE

NCBI Structure Group Home Page
BIOMOLECULAR ENGINEERING & STRUCTURAL BIOLOGY
Institute of Biology and Chemistry of Proteins
Reconstruction Home Page

PERI
Protein engineering research institute
RNA Secondary Structures

Bioinformatics

Molecular Information Theory and the Theory of Molecular Machines

Unclassified
Mendel (Europe)
NASC Home Page
ISMB-96 Home Page
NCGR: Home Page
The Antibody Resource Page
The O.C.M.S. Home Page

Searching servers

PDB WWW Server

BCM Search Launcher
CINEMA
Color interactive editor for multiple alignments
Match-Box Web Server
Amino acid seq alignment server
CCP11 - Biosequences and Structure Analysis
TargetP, ChloroP etc. server -- prediction of targeting and transit peptide
GenomeNet WWW server
Java PDB Viewer
UCLA-DOE STRUCTURE PREDICTION SERVER
PredictProtein
PredictProtein: email service for prediction of protein structure (secondary structure, solvent accessibility, transmembrane helices, transmembrane helix topology, multiple alignments, threading, fold recognition, remote homology detection, evaluation of secondary structure prediction accuracy)
WebLogo Sequence Logo Generation Main Form
Bork Group's BLAST2 Search Service at EMBL
PSI BLAST Search
STRIDE Documentation
Mail ServerIBCP
Medline Subset Query Form
Agricultural Genome Information Server (AGIS)
Genbank Database Query Form
ABIM Online analysis tools
EMBL WWW Services
SAM: Sequence Alignment and Modeling System
Query form(acnuc_u-lyon)
SCOP: Structural Classification of Proteins

INTERNET (GENERAL)

Software archives
RingServer Home
FTP.FUNET.FI alias: ftp.funet.fi
FUNET Network Services, CSC Finland
Directory micros.hensa.ac.uk:/micros/ibmpc/dos/
Directory ftp.rarf.riken.go.jp:/pub/Linux/
SunSITE Japan - Science University of Tokyo
Linux
Linux-JDK
Java-Linux
Linux PCMCIA Information
We Love Linux!
NetatalkAn Apple Ethertalk Protocol for unix
JLUGJapanese Linux Users Group

Various WWW links

Archives for Graphics Software and Databases Around the World

InfoSphere Lite
WWW Servers in Japan
Matthias Kahlert's WWW Hotlinks
NYNEX Interactive Yellow Pages - Home Page
NHK Home Page
Asahi NewsPaper main
- Computers and Internet

UNIVERSITIES AND INSTITUTES

Academic societies

JSPP -- Janese Society for Plant Physiologists
BSJ -- Botanical Society of Japan
ASPP Home Page
ISPMB

Overseas

Eddy Lab, Dept. of Genetics, Wash.U., St. Louis
Caltech

Directory csvax.cs.caltech.edu:/
Laboratory of Plant Pigment Biochemistry and Photobiology
NIH Scientific Resources
Indiana University Department of Biology
Institutt for Informatikk
Institut Pasteur
The University of Manitoba
Welcome Page, Physical Chemistry, THD
ILL home
Meinke Lab Home Page
John Innes Centre
Birkbeck College, London, Software Engineering Group

Japan

Saitama University
Home page
Tokyo Gakugei University Home Page

National Institute of Genetics
The University of Tokyo
Motoyuki Tanaka's Home Page
SCUJ HOME PAGE
SuperCard group etc.
Yamanashi Univ. home page in Japanese
Ministry of Agriculture, Forestry and Fisheries Research Network
National Instiute for Basic Biology HOME PAGE
Directory ftp.kuis.kyoto-u.ac.jp:/

COMPANIES

Chemicals

TopoGEN, Inc.
Cosmo Bio
TOYOBO_HOMEPAGE
TaKaRa Biomedicals Home Page
Boehringer Mannheim Home page
Millipore Home Page
The Antibody Resource Page

Computer

Melco Inc.
FLORA CITY
Microsoft
Institute for Scientific Information (ISI)
Home Page: Database publisher of the Science Citation Index and Current Contents
SGI
Symantec Corporation
Research Information Systems
Claris Corporation Home Page
ORIX Rentec
Solaris Products Information
Foster Findlay Associates WWW Home Page
software for image analysis and processing.
Apple Japan

Macintosh WWW Tools Compendium
Apple Internet Sites
Directory gatekeeper.dec.com:/
TurboLinux-J Web Site
Adobe Systems Incorporated Home Page
Adobe ftp site
White Pine Software

GENERAL SOFTWARE

ARDI (Executor) -- Executor is a software Macintosh emulator for PC
HTML Access Counter 4.0

Home page counter for Unix WWW server
Windows 95 Service Pack
Mac Software Catalog Search
Software Components For HyperCard
Software Components For SuperCard
Java(tm) - Programming for the Internet
Netscape Tech Support
Software Net Products
VersionCheck Home Page
Internet Grateful Med
UCSF MidasPlus
ApacheAn httpd server
WebalizerAn analysis program for web server log
ChemInnovation Software
TOOLS.ofthe.NET
Clipart GIFs
Index(softshell)
The Ultimate Collection of Winsock Software
Index of /HyperArchive/
Welcome to mirror.apple.com
Ghostscript, Ghostview and GSview
Samba
NLREG -- Nonlinear Regression Program
OCTAVE -- a calculation package
slatec -- a mathematical library

Computer languages

Tcl/Tk language developper's site
Active State -- New Tcl site etc.
Japanese Tcl/Tk
Cygwin, a UNIX-like environment for Windows
DJGPP, another UNIX-like environment for Windows
MacPerl Homepage
Perl subroutine database
JAVA main web site

JOURNALS

The World-Wide Web Virtual Library:
Elsevier Science Services
SD21
IDEAL -- Library search
Academic Press - APNet Home Page
BioMedNet -- Trends journals, Current Contents etc.
LINK database (Springer)
Electronic Protein Science
The Proceedings of the National Academy of Sciences Online ProcNAS
Nature UK
Nature Japan
Science
The Journal of Biological Chemistry Online JBC
JMB Online
European Journal of Biochemistry
The EMBO Journal Online
Cell Online
Oxford Journals
Nucleic Acids Research
Bioinformatics
RNA RNA is now a CSH journal
Genome Research
Structure
THE PLANT CELL
PLANT PHYSIOLOGY
PLANT SCIENCE
Kluwer Online: Plant Molecular Biology etc.
ASM Online (J. Bacteriology etc.)
Annual Reviews

To access PCP, go to the Home of JSPP above.