For calculating Hydrogen Bond

HBPLUS, which is distributed with LIGPLOT: http://www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html

There's also HBOND, which comes with the JOY package:
http://www-cryst.bioc.cam.ac.uk/~joy/

they are free, but they all need Academic License which I can't apply individually, has to apply by UMDNJ.

for example, I want to know the H-Bonds in protein 1a2p, I go to

http://bioportal.weizmann.ac.il/oca-bin/csu?PDB_ID=1a2p

I found there's four sheet strands for each chain.
I click on "Strand 1" on "A sheet" (residue 96-99)
I'll go to this page
from this page, if there's a "+" sign under HB colume, I know there's a H-Bond.

Virtual Stock Simulation/Game/Practice

free
http://game.marketwatch.com/Home/default.asp

fee need
http://www.stocktrak.com/

track flight
web based
http://www.flightexplorer.com/
http://www.flightview.com/TravelTools/default.asp
http://www.flytecomm.com/cgi-bin/trackflight
http://dps1.travelocity.com/dparrqst.ctl?Service=TRAVELOCITY

Software
AirNav
Jacars
Wacars

for Taipei, Taiwan's Aerial image, I use
this one as whole taiwan
http://921farmers.cultureworld.org/image/TaiwanNo1.jpg
+
this one for more detail image
http://iws.csrsr.ncu.edu.tw:8080/JSP/CSRSR/homepage.jsp?UserId=guest
+
this one for very very detail image
http://addr.tcg.gov.tw/

http://www.globalsecurity.org/military/world/taiwan/taipei.htm
this one as black and white detail

weather
http://www.aprs.net/
http://www.googleguide.com/search_by_number.html

air control
http://www.airnavsystems.com/
=
http://www.geocities.com/CapeCanaveral/Cockpit/9870/acars.html
+
http://leclair.homedns.org/jacars/

local google demo (marshall's around 07024)

meta search engine
http://www.kartoo.com/
http://vivisimo.com/search?query=markchiang&v%3Asources=Web
http://zapmeta.com/search/meta/zapfor04.pl?query=markchiang&search=web&match=all

use xslt to translate xml data, and use treeview to display it.
http://aspnet.4guysfromrolla.com/articles/051403-1.2.aspx

TreeView (@msdn)

Fixed the input problem (sometimes it's in Chinese input mode, but don't let me input Chinese)
it's because I hit the Shift key, it changes to temporary English mode, but shows it's in Chinese mode. (If you show the input bar in system bar, you'll find the difference.)

web folder can be easily setup if you use IIS server, just create a folder and done.
But, because my tablet use FAT32 format, I can't set permission for files.

XML sorting, paging, multilevel, etc.
http://www.screenbooks.net/jorr/js/
Creating a Pageable, Sortable DataGrid using ASP.NET
http://msdn.microsoft.com/library/default.asp?url=/library/en-us/dnaspp/html/aspnet-pageablesortable.asp

there are some web sites related to http://geneticassociationdb.nih.gov/
http://www-alis.tokyo.jst.go.jp/HOWDY/
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=snp
http://hgvbase.cgb.ki.se/ (can't get final result 04/08/05)

You must install the .NET Framework Redistributable Package version 1.1 prior to installing the .NET Framework SDK.

use
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl
to check pubmed data

ex:
Feasibility of simplifying balloon mitral valvuloplasty by obviating left-sided cardiac catheterization using on-line guidance with transesophageal echocardiography.
PMID: 12796174

1. use run_eSearch
db=pubmed
term=Feasibility+of+simplifying+balloon+mitral+valvuloplasty
field=titl
you'll get PMID: 12796174
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=Feasibility+of+simplifying+balloon+mitral+valvuloplasty&field=titl

2.use run_eSummary
db=pubmedid=12796174
you'll get:
Feasibility of simplifying balloon mitral valvuloplasty by obviating left-sided cardiac catheterization using on-line guidance with transesophageal echocardiography.
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=12796174&retmode=xml

online microarray analysis tools
http://gepas.bioinfo.cnio.es/tools.html

microarray softwares
http://ihome.cuhk.edu.hk/~b400559/arraysoft.html

inorder to implement a Dr. Lee's version of
http://geneticassociationdb.nih.gov

use this to transfer access data to mysql
http://www.kitebird.com/articles/access-migrate.html

use this to search pubmed through soap interface (XML,wsdl)
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html

Use this to calculate ANOVA
http://lgsun.grc.nia.nih.gov/ANOVA/bin/login.cgi
http://bioinformatics.uams.edu/page/

Use this to translate gene identifier
http://discover.nci.nih.gov/matchminer/html/MatchMinerInteractiveLookup.jsp

Use EXCEL to add color to updowngene.txt and use this to get it in pathway (colored)
http://www.genome.ad.jp/kegg-bin/mk_point_multi_html

I'm thinking about use pathway data and microarray data to form an automatic functional genetic discoverer. (use the same algorithm I do for Dr. Gu)

for researcher M.S.Chang
these tools might help.

ex:
String http://string.embl.de/
input sequence, get "predict functional associations proteins/genes"
supported by microarray, textmining, Co-occurrence, etc.

IntAct http://www.ebi.ac.uk/intact/index.html
input gene, it will give you proteins interact with the given gene.
supported by Experiments.

InterDom
input sequence, it will give you putative domain interactions
for example, it will give you some domains which has complexes with domain in given sequence (derived from PDB), or has protein interactions with domain in given sequence (derived from DIP).

after visit Mackay memorial hospital (in Taiwan)
I done some research on Database of Interacting Proteins (DIP)
ex: I want to know what proteins interact with P53
enter P53 in NodeID or Name field in this page
you will get DIP nodes for p53 in human and mouse
(DIP:368N, DIP:369N, DIP:5978N, DIP:24202N, etc)
in each DIP node, you can click on the "graph" link at top right corner
you'll see what other proteins interact with P53.

it also provides links to related information in
PDB, NCBI, Prosite, Smart, InterPro databases.

another one similar to this