Molecular Bioscience Sites


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Sequence Databases & Tools

Keyword Search for Gene/Protein Sequences

Entrez & PubMed Search Window (NCBI/NLM/NIH USA)
GenomeNet_JP Search Window (BC/ICR Kyoto Univ.)
Search for
Clickable Biological Database Map (GenomeNet_JP)

Homology Search & Alignment for Gene/Protein Sequences

BLAST -- Homology Search (NCBI/NLM/NIH USA)
__ Explanation of BLAST Output (BIMAS/DCRT NIH USA)
BLAST server -- Sequence Homology Search (GenomeNet_JP)
FASTA server -- Sequence Homology Search (GenomeNet_JP)
Clustal-W Multiple Alignment (EMBL-EBI UK)
Clustal-W Multiple Alignment (GenomeNet_JP)
T Coffee -- A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, Protein Sequences and Structures (ICS lab. CNRS FR & SIB CH)
MAFFT -- Multiple alignment program for amino acid or nucleotide sequences & NJ/UPGMA phylogeny (M.I.BioReg. Kyushu Univ.)
Virtual Sequence Editor w/ Several Analyses (GIRC Osaka Univ. & SIII)

Multifunction Tools for Sequence Analyses

EMBOSS -- European Molecular Biology Open Software Suite (suported by CCP11 UK) & EMBOSS-GUI perl scripts for Web(BioInfo/PBI/NRC CA), JEMBOSS Java interface(HGMP/MRC UK)
All-in-One Seq Analyzer -- A Javascript for Sequence Analyses (N.Inohara Dep.Patho. UMICH)
bioFOX & Biobar -- Add-ons of FireFox Web Brawser for Bioinfomatics Database Search

Tools for Gene Analyses & Genomic Data

in-silico.com -- Theoretical Exprements with Complete Bacterial Genomes; ; PCR, multiplex-PCR, PCR-RFLP,AFLP-PCR, SRF & PFG
Primer3 -- Pick PCR Primers from Nucleotide Sequence (WIBR/MIT-CGR)
Primer3plus -- Pick PCR Primers from Nucleotide Sequence (Wageningen Bioinformatics Webportal)
Primer Now -- A Real-Time PCR Primer Design Tool (SWMCD Univ.Texas)
PrimerStation -- multiplex PCR primer design site. (BioInfo/GSFS Univ.Tokyo)
FastPCR -- an integrated tool for automatic and manual PCR primers or probe design, alignment and any repeat searching (Viikki Research Group Organization in Molecular Biosciences)
REBASE Home Page -- Restriction Enzyme Database
BioConductor -- Computational and Statistical Tools for Genomic Data (w/ Microarray Data Objects), Based on R Language & CRAN
TRRD -- Transcription Regulatory Regions Database of Eukaryotic Genes (a part of GeneNetWorks/NSC[ICG] RU)

Data Mining for Gene Research

Genomatrix BiblioSphere -- 3D gene mapper in biomedical and life sciences journal literature (GmbH DE)

from Gene to Protein...

Translate Tool for DNA/RNA sequence (ExPASy CH)
Translate a DNA sequence (Colorado State Univ.)
Codon Table (KDRI JP)
GENESCAN -- Prediction of the locations and exon-intron structures of gene(MIT-Dep.Biol)

Characterization & Classification of Protein Sequences

MOTIF server -- Protein & DNA Motif Search (GenomeNet-JP)
PROSITE -- Database of protein families and domains(SIB CH)
BLOCKS Searcher on BLOCKS WWW Server (FHCRC USA)
PRINTS -- Protein Fingerprints Database (UMBER)
ClusTr Sever -- Automatic classification database of proteins (EMBL-EBI UK)
Pfam -- Protein Families Database of Multiple Sequence Alignments & Hidden Markov Models (Sanger Institute UK)
ENZYME -- Enzyme nomenclature database (SIB CH)
Search Similar Sequences in the Pathway Maps related with Metabolic & Regulatory Pathways (KEGG/GenomeNet-JP)
Protein Hydrophobicity Plots in predicting membrane-spanning domains, epitopic sites and exposing regions (Colorado State Univ.)

[ Information for Individuals. ]

NetPhos Server -- Prediction of Ser, Thr and Tyr Phosphorylation Sites using Neural Networks (CBSA/DTU)
Phospho.ELM Search -- a collection of experimentally verified Serine, Threonine and Tyrosine sites in eukaryotic proteins (EMBL)
ImMunoGeneTics Database Links to IMGT/HLA-DB(MHC-HLA) and IMGT/LIGM-DB(Ig.s & T cell Reteptors) (CINES FR)
GPCRDB -- Information system for G protein-coupled receptors (CMBI/EMBL, etc)
__ & MCSIS Molecular Class-Specific Information System project including NucleaRDB, KChannelDB, PrionDB (CMBI/EMBL, etc)
Receptor DB -- Index Database of Sequences & Structures for Membrane Receptors & Nuclear Receptors (Div. Chem-Bio Info. NIHS JP)
NuReBase -- Nuclear Receptor Database (LBMC/ENS-Lyon FR)
VKCDB -- Voltage-Gated Potassium Channel Database (Dept.Biol.Sci., Univ.Alberta)
Ligand-Gated Ion Channel Database (Institut Pasteur FR)

Databases & Tools Related with Proteomic Analyses

Compute pI/Mw Tool, MultiIdent, PeptideCutter, FindMod & GlycoMod in ExPASy(SIB CH)
SWISS-2DImage -- 2D Polyacrylamide Gel Electrophoresis Database of Protein(SIB CH)
ProteinProspector for mining sequence databases in conjunction with Mass Spectrometry (UCSF)
Protein Calculator (TSRI)
BIND -- Biomolecular Interaction Network Database (The Blueprint Initiative CA)
DIP -- Database of Interacting Protein (DOE/MBI UCLA)
HUP-ML -- Human Proteome Markup Language (JapanHUPO)
PEDRoDB -- Proteome Experimental Data Repository DataBase(UMBER)
HUPO Proteomics Standards Initiative

Access to Human Gene

GDB hosted by JHUSM & GDB JP Node -- Human Genome Project
OMIM -- Online Mendelian Inheritance in Man(NCBI/NIH USA)
HUGE DB of Human Unidentified Gene-Encoded large proteins generated by cDNA analyses (KDRI JP)
H-Inv DB Human gene database, with Integrative Annotation Validated by Full-Length cDNA Clones (JBIRC JP)
Human Genome Variation Society stemmed from HUGO-Mutation Database Initiative
Human Gene Mutation Database(IMGC UK)
Cancer Genetic Web on the CancerIndex(Simon Cotterill)
AD&FTD-MDB -- Alzheimer Disease & Frontotemporal Dementia Mutation Database (Dept.Mol.Gen. Univ.Antwerp)
JSNP -- Japanese Single Nucleotide Polymorphisns Database (IMS & JST JP)
DNA Mutation Checker 2(EBI/EMBL UK)
Genetic Association Database (NIA/NIH + DCB/CIT/NIH USA)
Genome and Disease Map (NCBI/NLM/NIH USA)
Genetic Linckage Analysis Software (CIT/CBEL/BIMAS/NIH USA)
GeneClinics A medical knowledge base relating genetic testing & genetic counseling (Univ.Washington)

Miscellaneous Database & Tools

SRS WWW -- Browser for Databanks in Molecular Biology (EMBL DE)
Geneton English version (CRGH FR)
Plant Genome Database (ARS/USDA USA)

Vender Sites of Biotechnology and Computational Analyses

PREMIER Biosoft

3D Analyses for Biomolecules

Keyword Search for Analyzed Coordinates of Macromolecules

Protein Data Bank(RCSB USA)
__ PDB ID or keyword Author | Advanced Search
Protein Data Bank Japan, xml-based Protein Structure Search Service (IPR Osaka Univ.)
__ PDB ID Search:
.. __ Keyward Search:
.. __ Advanced Search
MSD Search Index: Macromolecular Structure Databases w/ Ligand Search, Secondary Structure Matching, etc.(EMBL-EBI UK)
PDBsum A database of the known 3D structures of proteins & nucleic acids (BSM/BioChem., Univ.Coll.London)
BioMagResBank Search Biological NMR Database w/ NMR Browse (Dept.Biochem., Univ. Wisconsin-Madison)
ModBase Search Page -- Database of Comparative Protein Models (Andrej Sali Lab. UCSF)
PubChem -- Chemical Structures of Small Molecules Related to Medical Science (NCBI/NIH)

Characterization & Classification of Protein Structures

SCOP Structural Classification of Proteins(MRC-LMB Cambrigde UK)
PAPIA Parallel Protein Information Analysis system(TRC/RWCP JP)
GETAREA Solvent Accessible Surface Areas & Atomic Solvation Energies (SCSB/UTMB)
PROCHECK Stereochemical Quality of Protein Structure (UCL, UK)
MSDfold(SSM) Secondary structure matching for protein structure comparison (EMBL-EBI, UK)
DaliLite Pairwise comparison of protein structures (EMBL-EBI, UK)
The ProSup WebServer for Protein Structure Superimposition (CAME/ICB, Univ. Salzburg)

Comparative Modeling & Optimization of Folding Potentials

MODELLER -- Homology Protein Structure Modelling (Andrej Sali Lab. UCSF)
ModWeb -- Server for Comparative Protein Structure Modeling (Andrej Sali Lab. UCSF)
ModLoop -- Modeling of Loops in Protein Structures (Andrej Sali Lab. UCSF)
RAPPER -- an ab initio conformational search algorithm for restraint-based protein modelling. (Dept.Biochem. SBS Univ.Cambridge)
7TM Recepter Modeling (GPCR mode) in SWISS-MODEL (SIB CH)
3D-JIGSAW Comparative Modelling Server (BMM/ImperialCancerResearchFund UK)
CPHModels Comparative Modelling Server (CBS BioCentrum-DTU, Technical Univ. DK)
LOOPP Learning, Observating Outputting Protein Patterns & Related Documents (CBSU-CTC Cornell Univ.)
TraceSuite II Evolutionary Trace Server for Structure-Function Analysis in Protein Family (CBG/Dept. Biochem, Univ. Cambridge)
SILA Structural Initial data Library of Amino acid residues & related tools(ALIS/JST JP)
Atlas of Protein Side-Chain Interactions based on 533 proteins solved by X-ray crystallography to 2.0Å, or better (BSM/BioChem., Univ.Coll.London)
The Dundee PRODRUG Server for easy 3D-modelling of small molecules with enegy minimization (Div.BioChMolMicro Univ.Dundee)

Databases & Tools for Specific Protein Structures

IMGT/3D 3D Structure Database of Immunogloburins. T-cell Receptors & MHC (CNRS&CINES FR)
WAM Web Antibody Modelling (Univ. Bath UK)
Antibodies - Structure and Sequence Kabat related Resources etc. (R.U.Bi.C UK)
PK Structure - 3D Tools -- Index of Resources for Protein Kinase Structure (SDSC)
HIV Structural Database & Chem-BLAST (NIST USA)
DSMM --- Database of Simulated Molecular Motions (MCM/EML projects)
Database of Macromolecular Movements (MB&B Yale Univ.)

Visualization Tools for Macromolecular Structures

FirstGlance in Jmol : A simple tool for macromolecular visualization (SDSC)
__ Visualize a structure; PDB code:  
RasMol/OpenRasmol & Chime -- Molecular Visualization Tools & "select" commands (UMASS)
DeepView--SwissPdbViewer -- Molecular Visualization Tool for Analyses of Protein Structure (GlaxoSmithKline R&D)
WebMol -- Java PDB Viewer (CMP/UCSF)
MolSurfer -- a Macromolecular Interface Navigator (MCM/EML projects)
UCSF Chimera -- an Extensive Molecular Modeling System (CGL/UCSF)
YASARA View -- Yet Another Scientific Artificial Reality Application (Dr. Elmar Krieger)
PyMol -- Python embedded MOLecular graphics system (PyMOL Project)
MolScript -- Displaying Protein 3D Structures in Schimatic & Detailed Representations (Avatur Software SE)
Raster3D -- Generating High Quality Raster Images of Proteins (BMSC Univ. Washington)
SPOCK -- The Structural Properties Observation and Calculation Kit (C.M.D. Texas A&M Univ.)
MOLDA -- Protein Modeling Tool (Dept.Chem. Hiroshima Univ.)
PIRX iMol for MacOSX & Biodesigner for Windows (Piotr Rotkiewicz)
Open Babel -- Format Converter for Molecular Modeling [GPL]
Friends -- An Integrated Analytical Front-End Application for Bioinfomatics (Ilyin Lab / Northeasten Univ.)
LIGPLOT -- Program for automatically plotting protein-ligand interactions (Andrew Wallace & Roman Laskowski)

Structural Optimization & Molecular Dynamics

Amber -- A Package of Molecular Simulation Programs (Kollman Group/UCSF)
MD Display -- A 3D Stereo Molecular Dynamics Trajectory Visualization Package for Amber(CSB/Vanderbilt Univ.)
CHARMm Chemistry at HARvard Molecular Mechanics (Karplus Group/Harvard Univ.)
--- & CHARMm Development and Implementation (ScrippsRI et al)
GROMACS -- A versatile package to perform molecular dynamics [GPL]
NAMD & VMD -- Scalable & Visual Molecular Dynamics (TBG UIUC)
TINKER and Force Field Explorer -- Software Tools for Molecular Design & GUI (Jay Ponder Lab, WUSTL)
MDynaMix -- a Molecular Dynamics Program for simulations of mixtures of either rigid or flexible molecules w/ MPICH (Alexander Lyubartsev Div. of Phys. Chem., Stockholm Uni.)
Dock and AutoDock for Docking Studies (UCSF and ScrippsRI)
Biskit is a modular, object-oriented Python library for structural bioinformatics research.(CRG.es/Institut Pasteur/NMR.se)
Information on MM2/MM3 -- Molecular Mechanics program(Dpt.Chem Univ.Georgia)
Molecular Mechanics and Force Field References (EMBL-EBI UK)

Tools for Crystallography & NMR

CCP4 Programs for Protein Crystallography (Daresbury Laboratory/BBSRC UK)
XTAL Programs for Crystallographic Computing Techniques w/ Macromolecules (Purdue Univ.)
SHELX -- A set of programs for crystal structure determination from single-crystal diffraction data (Str.Chem.Dept., Univ.Gottingen)
MOSFLM help and guidance -- A program for integrating single crystal diffraction data from area detectors (MRC-LMB Cambridge, UK)
Solve/Resolve -- Automated Structure Solution for MIR & MAD (Los Alamos Nat.Lab. USA)
X-PLOR & CNX -- A System for X-ray Crystallography and NMR (Yale Univ. & Accelrys)
CNSsolve Crystallography & NMR System w/ HTML-interface (Yale Univ.)
XtalView for Solving Macromolecular Crystal Structure (CCMS/SDSC)
O distribution & The O Files -- An interactive system for building and manipulating models in electron density maps (SBL/BMC/Uppsala Univ.)
ORTEP-III -- Oak Ridge Thermal Ellipsoid Plot Program (ORNL USA)

Electron Densities & Molecular Orbitals

GAUSSIAN -- Programs for semi-empirical and ab initio molecular orbital calculations (Gaussian Inc.)
GAMESS -- The General Atomic and Molecular Electronic Structure System (Ames Laboratory/Iowa State University)
MOPAC2007 -- semi-empirical Molecular Orbital PACkage
gOpenMol -- A graphic interface for chemical properties, electron densities and molecular orbitals of small molecules (CSC FI)
SMxGauss -- ab initio Molecular Orbital Calculation in Liquid Phase (Dep.Chem.&SCI Univ.Minesota)

Tools for Analyses of Chemical Reactions

POLYRATE -- a Computer Program for the Calculation of Chemical Reaction Rates for Polyatomics (Dep.Chem.&SCI Univ.Minesota / SDSC et.al. )
GAUSSRATE -- a Interface between POLYRATE and Gaussian (Dep.Chem.&SCI Univ.Minesota)
CHARMMRATE -- a Module of CHARMM for Carrying out Variational Transition State Theory (VTST) Calculations (Dep.Chem.&SCI Univ.Minesota)

All-in-one package for molecular modeling

VigyaanCD.org -- A bio/chemical software workbench based on KNOPPIX (CD-booting Linux)

Vender Sites of Structural Bioscience

accelrys Life Science QUANTA/CHARMm and DS_ViewerPro
Chemical Computing Group Inc. MOE (Molecular Operating Environment) & Japanese Support Pages(RSI)
Tripos Online SYBYL/Biopolymer, Alchemy
CONFLEX High Performance Conformation Analysis
MDL Information Systems Inc. ISIS and Chemscape
MolSoft ICM-Browser (& Pro)
CambridgeSoft Co. ChemOffice/ChemDraw/Chem3D
SSE:NetScience Database of Commercial Softwares for Science(Japanese Site)

Organization & Information Pages Related to Molecular Biology

NCBI in NLM and NHGRI (NIH USA)
EMBL European Molecular Biology Laboratory (DE)
DDBJ DNA Data Bank in Japan(NIG-JP)
National Center for Genome Resources (USA)
Los Alamos National Laboratory (USA)
HUPO The Human Proteome Organization
BIOSCI -- bionet NetNews & ML
Instructions to Authors in the Health Sciences (Lib.Med.Coll.Ohio USA)
Molecular Biology Protocol (NOAA/USA)
Molecular Biology Protocols (Highveld.Com)
Proteomics tools on ExPASy[Expert Protein Analysis System] server (SIB. CH)
Bioinformatic Tools and Databases (SciClips.com)
BioWeb / Society and Meeting informations etc...
BIONEWS from Biotechnology Japan
BIOINFORMATICS (Online Journal)
Microbes.info The Microbiology Information Portal
Molecular Biology Resources Online in WheelChair.Com
InTechOpen Free Academic Open Accesss Books

Information Pages Related to Drug Design

Open Access Therapuetic and Potential Drug Targets Database (SciClips.com)

Sites Related to Physical and Computational Chemistry

IUPAC INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY
Cambridge Crystallographic Data Centre (CCDC UK)
SPARC on-line calculator pKa, Properties, Kinetics & Hydrolysis of small molecules (Dpt.Chem Univ.Georgia)
Atomic Radii Tables (MSC Indiana Univ.)
Linux4Chemistry Linux Software for Chemistry, a part of The WWW Virtual Library
Measurement Converter (ConvertIt.com)
UCSD-TV Video Archives for Science Education (UCSD)


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