Using GooRedFix to fix FireFox browser redirection problems.
http://forums.majorgeeks.com/showthread.php?t=182559
Monday, May 24, 2010
Thursday, May 20, 2010
biopython and jython
$ jython setup.py build
$ jar cvf BioPython.jar -C build/lib ./
Include the produced jar file in your CLASSPATH or server build.
Have you run "jython setup.py install" yet? That will compile the *.py
files into Java class files, and should put them where jython looks.
See also:
http://www.jython.org/docs/using/cmdline.html#environment-variables
... from the biopython-dev mailist
$ jar cvf BioPython.jar -C build/lib ./
Include the produced jar file in your CLASSPATH or server build.
Have you run "jython setup.py install" yet? That will compile the *.py
files into Java class files, and should put them where jython looks.
See also:
http://www.jython.org/docs/using/cmdline.html#environment-variables
... from the biopython-dev mailist
grad
advice:
- do what you like / interests you
- beware of fame
- open as many doors as you can
- network
- understand that they're only models
- teach while public speaking
- understand
- "Most researchers spend the majority of their time reading papers, discussing ideas with colleagues, writing and revising papers, staring blankly into space -- and, of course, having brilliant ideas and implementing them."
- "becoming part of a larger research community"
- http://heibeck.freeshell.org/Grad_Advice/how2b/how.2b.research.html
- Keeping a journal of your research activities
- are the assumptions valid
- doing research is much easier if you have someone to bounce ideas off of and to give you feedback.
- divide and conquer
- learn to cope with criticism, and even that you actively seek it out
- Don't just say "I'm doing my thesis on foobar applications of whatsis algorithms" -- tell them as much as they're willing to listen to. You should have 30-second, 2-minute, 5-minute and 10-minute summaries of your thesis ready at a moment's notice
- be critical
- RA position from a faculty member may be a good way to become involved in a research project
- you may need to tailor your proposal to the interests and needs of the particular funding agency or program you're applying to, but stick to something you know about and are sincerely interested in.
http://www.sfu.ca/sfunews/sfu_news/regular_features/comment03220601.htm
- do what you like / interests you
- beware of fame
- open as many doors as you can
- network
- understand that they're only models
- teach while public speaking
- understand
- "Most researchers spend the majority of their time reading papers, discussing ideas with colleagues, writing and revising papers, staring blankly into space -- and, of course, having brilliant ideas and implementing them."
- "becoming part of a larger research community"
- http://heibeck.freeshell.org/Grad_Advice/how2b/how.2b.research.html
- Keeping a journal of your research activities
- are the assumptions valid
- doing research is much easier if you have someone to bounce ideas off of and to give you feedback.
- divide and conquer
- learn to cope with criticism, and even that you actively seek it out
- Don't just say "I'm doing my thesis on foobar applications of whatsis algorithms" -- tell them as much as they're willing to listen to. You should have 30-second, 2-minute, 5-minute and 10-minute summaries of your thesis ready at a moment's notice
- be critical
- RA position from a faculty member may be a good way to become involved in a research project
- you may need to tailor your proposal to the interests and needs of the particular funding agency or program you're applying to, but stick to something you know about and are sincerely interested in.
http://www.sfu.ca/sfunews/sfu_news/regular_features/comment03220601.htm
Wednesday, May 19, 2010
BCID
Bioinformatics for Infectious Disease
Overview
Infectious diseases are a leading cause of productivity loss and are responsible for roughly a third of annual deaths worldwide; sepsis and mortality caused by infectious diseases are also on the rise in the U.S. Antimicrobial resistance is increasing rapidly and newly emerging diseases are causing considerable concern: a new global pandemic could have a significant economic impact.
http://www.bcid.ca/resources.htm
Overview
Infectious diseases are a leading cause of productivity loss and are responsible for roughly a third of annual deaths worldwide; sepsis and mortality caused by infectious diseases are also on the rise in the U.S. Antimicrobial resistance is increasing rapidly and newly emerging diseases are causing considerable concern: a new global pandemic could have a significant economic impact.
http://www.bcid.ca/resources.htm
Tuesday, May 18, 2010
100 Best Novels
http://www.randomhouse.com/modernlibrary/100bestnovels.html
http://www.truly-free.org/
www.gutenberg.org
1. ULYSSES by James Joyce
2. THE GREAT GATSBY by F. Scott Fitzgerald
3. A PORTRAIT OF THE ARTIST AS A YOUNG MAN by James Joyce
4. LOLITA by Vladimir Nabokov
5. BRAVE NEW WORLD by Aldous Huxley
6. THE SOUND AND THE FURY by William Faulkner
7. CATCH-22
8. DARKNESS AT NOON by Arthur Koestler
9. SONS AND LOVERS by D.H. Lawrence
10. THE GRAPES OF WRATH by John Steinbeck
11. UNDER THE VOLCANO by Malcolm Lowry
12. THE WAY OF ALL FLESH by Samuel Butler
13. 1984 by George Orwell
14. I, CLAUDIUS by Robert Graves
15. TO THE LIGHTHOUSE by Virginia Woolf
16. AN AMERICAN TRAGEDY by Theodore Dreiser
17. THE HEART IS A LONELY HUNTER by Carson McCullers
18. SLAUGHTERHOUSE-FIVE by Kurt Vonnegut
19. INVISIBLE MAN by Ralph Ellison
20. NATIVE SON by Richard Wright
21. HENDERSON THE RAIN KING by Saul Bellow
22. APPOINTMENT IN SAMARRA by John O'Hara
23. U.S.A. (trilogy) by John Dos Passos
24. WINESBURG, OHIO by Sherwood Anderson
25. A PASSAGE TO INDIA by E.M. Forster
26. THE WINGS OF THE DOVE by Henry James
27. THE AMBASSADORS by Henry James
28. TENDER IS THE NIGHT by F. Scott Fitzgerald
29. THE STUDS LONIGAN TRILOGY by James T. Farrell
30. THE GOOD SOLDIER by Ford Madox Ford
31. ANIMAL FARM by George Orwell
32. THE GOLDEN BOWL by Henry James
33. SISTER CARRIE by Theodore Dreiser
34. A HANDFUL OF DUST by Evelyn Waugh
35. AS I LAY DYING by William Faulkner
36. ALL THE KING'S MEN by Robert Penn Warren
37. THE BRIDGE OF SAN LUIS REY by Thornton Wilder
38. HOWARDS END by E.M. Forster
39. GO TELL IT ON THE MOUNTAIN by James Baldwin
40. THE HEART OF THE MATTER by Graham Greene
41. LORD OF THE FLIES by William Golding
42. DELIVERANCE by James Dickey
43. A DANCE TO THE MUSIC OF TIME (series) by Anthony Powell
44. POINT COUNTER POINT by Aldous Huxley
45. THE SUN ALSO RISES by Ernest Hemingway
46. THE SECRET AGENT by Joseph Conrad
47. NOSTROMO by Joseph Conrad
48. THE RAINBOW by D.H. Lawrence
49. WOMEN IN LOVE by D.H. Lawrence
50. TROPIC OF CANCER by Henry Miller
51. THE NAKED AND THE DEAD by Norman Mailer
52. PORTNOY'S COMPLAINT by Philip Roth
53. PALE FIRE by Vladimir Nabokov
54. LIGHT IN AUGUST by William Faulkner
55. ON THE ROAD by Jack Kerouac
56. THE MALTESE FALCON by Dashiell Hammett
57. PARADE'S END by Ford Madox Ford
58. THE AGE OF INNOCENCE by Edith Wharton
59. ZULEIKA DOBSON by Max Beerbohm
60. THE MOVIEGOER by Walker Percy
61. DEATH COMES FOR THE ARCHBISHOP by Willa Cather
62. FROM HERE TO ETERNITY by James Jones
63. THE WAPSHOT CHRONICLES by John Cheever
64. THE CATCHER IN THE RYE by J.D. Salinger
65. A CLOCKWORK ORANGE by Anthony Burgess
66. OF HUMAN BONDAGE by W. Somerset Maugham
67. HEART OF DARKNESS by Joseph Conrad
68. MAIN STREET by Sinclair Lewis
69. THE HOUSE OF MIRTH by Edith Wharton
70. THE ALEXANDRIA QUARTET by Lawrence Durell
71. A HIGH WIND IN JAMAICA by Richard Hughes
72. A HOUSE FOR MR BISWAS by V.S. Naipaul
73. THE DAY OF THE LOCUST by Nathanael West
74. A FAREWELL TO ARMS by Ernest Hemingway
75. SCOOP by Evelyn Waugh
76. THE PRIME OF MISS JEAN BRODIE by Muriel Spark
77. FINNEGANS WAKE by James Joyce
78. KIM by Rudyard Kipling
79. A ROOM WITH A VIEW by E.M. Forster
80. BRIDESHEAD REVISITED by Evelyn Waugh
81. THE ADVENTURES OF AUGIE MARCH by Saul Bellow
82. ANGLE OF REPOSE by Wallace Stegner
83. A BEND IN THE RIVER by V.S. Naipaul
84. THE DEATH OF THE HEART by Elizabeth Bowen
85. LORD JIM by Joseph Conrad
86. RAGTIME by E.L. Doctorow
87. THE OLD WIVES' TALE by Arnold Bennett
88. THE CALL OF THE WILD by Jack London
89. LOVING by Henry Green
90. MIDNIGHT'S CHILDREN by Salman Rushdie
91. TOBACCO ROAD by Erskine Caldwell
92. IRONWEED by William Kennedy
93. THE MAGUS by John Fowles
94. WIDE SARGASSO SEA by Jean Rhys
95. UNDER THE NET by Iris Murdoch
96. SOPHIE'S CHOICE by William Styron
97. THE SHELTERING SKY by Paul Bowles
98. THE POSTMAN ALWAYS RINGS TWICE by James M. Cain
99. THE GINGER MAN by J.P. Donleavy
100. THE MAGNIFICENT AMBERSONS by Booth Tarkington
http://www.truly-free.org/
www.gutenberg.org
1. ULYSSES by James Joyce
2. THE GREAT GATSBY by F. Scott Fitzgerald
3. A PORTRAIT OF THE ARTIST AS A YOUNG MAN by James Joyce
4. LOLITA by Vladimir Nabokov
5. BRAVE NEW WORLD by Aldous Huxley
6. THE SOUND AND THE FURY by William Faulkner
7. CATCH-22
8. DARKNESS AT NOON by Arthur Koestler
9. SONS AND LOVERS by D.H. Lawrence
10. THE GRAPES OF WRATH by John Steinbeck
11. UNDER THE VOLCANO by Malcolm Lowry
12. THE WAY OF ALL FLESH by Samuel Butler
13. 1984 by George Orwell
14. I, CLAUDIUS by Robert Graves
15. TO THE LIGHTHOUSE by Virginia Woolf
16. AN AMERICAN TRAGEDY by Theodore Dreiser
17. THE HEART IS A LONELY HUNTER by Carson McCullers
18. SLAUGHTERHOUSE-FIVE by Kurt Vonnegut
19. INVISIBLE MAN by Ralph Ellison
20. NATIVE SON by Richard Wright
21. HENDERSON THE RAIN KING by Saul Bellow
22. APPOINTMENT IN SAMARRA by John O'Hara
23. U.S.A. (trilogy) by John Dos Passos
24. WINESBURG, OHIO by Sherwood Anderson
25. A PASSAGE TO INDIA by E.M. Forster
26. THE WINGS OF THE DOVE by Henry James
27. THE AMBASSADORS by Henry James
28. TENDER IS THE NIGHT by F. Scott Fitzgerald
29. THE STUDS LONIGAN TRILOGY by James T. Farrell
30. THE GOOD SOLDIER by Ford Madox Ford
31. ANIMAL FARM by George Orwell
32. THE GOLDEN BOWL by Henry James
33. SISTER CARRIE by Theodore Dreiser
34. A HANDFUL OF DUST by Evelyn Waugh
35. AS I LAY DYING by William Faulkner
36. ALL THE KING'S MEN by Robert Penn Warren
37. THE BRIDGE OF SAN LUIS REY by Thornton Wilder
38. HOWARDS END by E.M. Forster
39. GO TELL IT ON THE MOUNTAIN by James Baldwin
40. THE HEART OF THE MATTER by Graham Greene
41. LORD OF THE FLIES by William Golding
42. DELIVERANCE by James Dickey
43. A DANCE TO THE MUSIC OF TIME (series) by Anthony Powell
44. POINT COUNTER POINT by Aldous Huxley
45. THE SUN ALSO RISES by Ernest Hemingway
46. THE SECRET AGENT by Joseph Conrad
47. NOSTROMO by Joseph Conrad
48. THE RAINBOW by D.H. Lawrence
49. WOMEN IN LOVE by D.H. Lawrence
50. TROPIC OF CANCER by Henry Miller
51. THE NAKED AND THE DEAD by Norman Mailer
52. PORTNOY'S COMPLAINT by Philip Roth
53. PALE FIRE by Vladimir Nabokov
54. LIGHT IN AUGUST by William Faulkner
55. ON THE ROAD by Jack Kerouac
56. THE MALTESE FALCON by Dashiell Hammett
57. PARADE'S END by Ford Madox Ford
58. THE AGE OF INNOCENCE by Edith Wharton
59. ZULEIKA DOBSON by Max Beerbohm
60. THE MOVIEGOER by Walker Percy
61. DEATH COMES FOR THE ARCHBISHOP by Willa Cather
62. FROM HERE TO ETERNITY by James Jones
63. THE WAPSHOT CHRONICLES by John Cheever
64. THE CATCHER IN THE RYE by J.D. Salinger
65. A CLOCKWORK ORANGE by Anthony Burgess
66. OF HUMAN BONDAGE by W. Somerset Maugham
67. HEART OF DARKNESS by Joseph Conrad
68. MAIN STREET by Sinclair Lewis
69. THE HOUSE OF MIRTH by Edith Wharton
70. THE ALEXANDRIA QUARTET by Lawrence Durell
71. A HIGH WIND IN JAMAICA by Richard Hughes
72. A HOUSE FOR MR BISWAS by V.S. Naipaul
73. THE DAY OF THE LOCUST by Nathanael West
74. A FAREWELL TO ARMS by Ernest Hemingway
75. SCOOP by Evelyn Waugh
76. THE PRIME OF MISS JEAN BRODIE by Muriel Spark
77. FINNEGANS WAKE by James Joyce
78. KIM by Rudyard Kipling
79. A ROOM WITH A VIEW by E.M. Forster
80. BRIDESHEAD REVISITED by Evelyn Waugh
81. THE ADVENTURES OF AUGIE MARCH by Saul Bellow
82. ANGLE OF REPOSE by Wallace Stegner
83. A BEND IN THE RIVER by V.S. Naipaul
84. THE DEATH OF THE HEART by Elizabeth Bowen
85. LORD JIM by Joseph Conrad
86. RAGTIME by E.L. Doctorow
87. THE OLD WIVES' TALE by Arnold Bennett
88. THE CALL OF THE WILD by Jack London
89. LOVING by Henry Green
90. MIDNIGHT'S CHILDREN by Salman Rushdie
91. TOBACCO ROAD by Erskine Caldwell
92. IRONWEED by William Kennedy
93. THE MAGUS by John Fowles
94. WIDE SARGASSO SEA by Jean Rhys
95. UNDER THE NET by Iris Murdoch
96. SOPHIE'S CHOICE by William Styron
97. THE SHELTERING SKY by Paul Bowles
98. THE POSTMAN ALWAYS RINGS TWICE by James M. Cain
99. THE GINGER MAN by J.P. Donleavy
100. THE MAGNIFICENT AMBERSONS by Booth Tarkington
Eclipse Launch Last Run Configuration
Pressing Ctrl+F11 by default runs the current Run configuration, but what if you want to always run the same thing?
http://dev.eclipse.org/newslists/news.eclipse.newcomer/msg29808.html
This "feature" can be changed in Window->Preferences->Run/Debug->Launching->Launch Operations. You can choose to always run the previous application.
http://dev.eclipse.org/newslists/news.eclipse.newcomer/msg29808.html
This "feature" can be changed in Window->Preferences->Run/Debug->Launching->Launch Operations. You can choose to always run the previous application.
Kaggle
For three weeks Kaggle, a platform for data prediction competitions, has
been running a bioinformatics competition
(http://kaggle.com/hivprogression). The competition requires competitors
to pick markers in HIV's genetic sequence that predict a change in viral
load.
been running a bioinformatics competition
(http://kaggle.com/hivprogression). The competition requires competitors
to pick markers in HIV's genetic sequence that predict a change in viral
load.
Monday, May 17, 2010
Ruby on Rails
http://railstutorial.org/book
http://guides.rubyonrails.org/getting_started.html
http://edgeguides.rubyonrails.org/3_0_release_notes.html#creating-a-rails-3-0-application (v 3.0)
http://railstutorial.org/book?version=2.3.8 (v 2.3.8)
RVM to manage different versions
http://rvm.beginrescueend.com/rvm/install/
$ rvm update --head
$ rvm reload
$ rvm install 1.8.7
$ rvm install 1.9.2
app/ Core application (app) code, including models, views, controllers, and helpers
config/ Application configuration
db/ Files to manipulate the database
doc/ Documentation for the application
lib/ Library modules
log/ Application log files
public/ Data accessible to the public (e.g., web browsers), such as images and cascading style sheets (CSS)
script/rails A script provided by Rails for generating code, opening console sessions, or starting a local web server
test/ Application tests (made obsolete by the spec/ directory in Section 3.1.2)
tmp/ Temporary files
vendor/ Third-party code such as plugins and gems
README A brief description of the application
Rakefile Utility tasks available via the rake command
Gemfile Gem requirements for this app
config.ru A configuration file for Rack middleware
.gitignore Patterns for files that should be ignored by Git
http://www.wellho.net/solutions/ruby-conditionals-loops-and-iterators-in-ruby.html
$ ruby
# An iterator object revealed!
(5..15).each do |k|
print k," "
end
print "\n"
5 6 7 8 9 10 11 12 13 14 15
REpresentational State Transfer (REST)
As a Rails application developer, the RESTful style of development helps you make choices about which controllers and actions to write: you simply structure the application using resources that get created, read, updated, and deleted.
http://guides.rubyonrails.org/getting_started.html
http://edgeguides.rubyonrails.org/3_0_release_notes.html#creating-a-rails-3-0-application (v 3.0)
http://railstutorial.org/book?version=2.3.8 (v 2.3.8)
RVM to manage different versions
http://rvm.beginrescueend.com/rvm/install/
$ rvm update --head
$ rvm reload
$ rvm install 1.8.7
$ rvm install 1.9.2
app/ Core application (app) code, including models, views, controllers, and helpers
config/ Application configuration
db/ Files to manipulate the database
doc/ Documentation for the application
lib/ Library modules
log/ Application log files
public/ Data accessible to the public (e.g., web browsers), such as images and cascading style sheets (CSS)
script/rails A script provided by Rails for generating code, opening console sessions, or starting a local web server
test/ Application tests (made obsolete by the spec/ directory in Section 3.1.2)
tmp/ Temporary files
vendor/ Third-party code such as plugins and gems
README A brief description of the application
Rakefile Utility tasks available via the rake command
Gemfile Gem requirements for this app
config.ru A configuration file for Rack middleware
.gitignore Patterns for files that should be ignored by Git
http://www.wellho.net/solutions/ruby-conditionals-loops-and-iterators-in-ruby.html
$ ruby
# An iterator object revealed!
(5..15).each do |k|
print k," "
end
print "\n"
5 6 7 8 9 10 11 12 13 14 15
REpresentational State Transfer (REST)
As a Rails application developer, the RESTful style of development helps you make choices about which controllers and actions to write: you simply structure the application using resources that get created, read, updated, and deleted.
Sunday, May 16, 2010
FreeHostia and Drupal
http://wtanaka.com/drupal/freehostia.com
Some changes are needed to get Drupal to work on freehostia.com's free hosting.
1. Comment out the following line in .htaccess:
Options +FollowSymLinks
2. Change the line
Options -Indexes
to
IndexIgnore *
Web Hosting
http://www.webhostingtopten.com/
http://www.justhost.com/
Some changes are needed to get Drupal to work on freehostia.com's free hosting.
1. Comment out the following line in .htaccess:
Options +FollowSymLinks
2. Change the line
Options -Indexes
to
IndexIgnore *
Web Hosting
http://www.webhostingtopten.com/
http://www.justhost.com/
Saturday, May 15, 2010
to PhD or nort?
http://sciencecareers.sciencemag.org/career_development/previous_issues/articles/2007_09_14/caredit_a0700130
Friday, May 14, 2010
sciencedaily
http://www.sciencedaily.com/releases/2010/05/100513162755.htm?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+sciencedaily+%28ScienceDaily%3A+Latest+Science+News%29
Tuesday, May 11, 2010
Friday, May 7, 2010
Google Summer of Code
http://www.open-bio.org/wiki/Google_Summer_of_Code
* (BioPerl) Major BioPerl reorganization
* (BioPerl) Lightweight Sequence objects and Lazy Parsing
* (BioPerl) Alignment Subsystem Refactoring
* (BioPerl) Perl Run Wrappers for External Programs in a Flash
* (BioPerl) BioPerl 2.0: Modern::Perl, Perl6, and BioPerl
* (Biopython) Biopython and PyCogent interoperability
* (Biopython) Galaxy phylogenetics pipeline development
* (Biopython) Accessing R phylogenetic tools from Python
* (Biopython) PDB-Tidy: Command-line tools for manipulating PDB files
* (BioJava) All-Java Multiple Sequence Alignment
* (BioRuby) Ruby 1.9.2 support of BioRuby
* (BioRuby) Implementation of algorithm to infer gene duplications in BioRuby
* (Biolib) Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI
* (BioDAS) Redesign of the DAS Registry
* (BioDAS) DAS Server for large files on local filesystems
BioDAS
http://www.biodas.org/wiki/Main_Page
http://www.biodas.org/wiki/DASWorkshop2010
* (BioPerl) Major BioPerl reorganization
* (BioPerl) Lightweight Sequence objects and Lazy Parsing
* (BioPerl) Alignment Subsystem Refactoring
* (BioPerl) Perl Run Wrappers for External Programs in a Flash
* (BioPerl) BioPerl 2.0: Modern::Perl, Perl6, and BioPerl
* (Biopython) Biopython and PyCogent interoperability
* (Biopython) Galaxy phylogenetics pipeline development
* (Biopython) Accessing R phylogenetic tools from Python
* (Biopython) PDB-Tidy: Command-line tools for manipulating PDB files
* (BioJava) All-Java Multiple Sequence Alignment
* (BioRuby) Ruby 1.9.2 support of BioRuby
* (BioRuby) Implementation of algorithm to infer gene duplications in BioRuby
* (Biolib) Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI
* (BioDAS) Redesign of the DAS Registry
* (BioDAS) DAS Server for large files on local filesystems
BioDAS
http://www.biodas.org/wiki/Main_Page
http://www.biodas.org/wiki/DASWorkshop2010
BIOINFORMATICS ISCB NEWS
ISCB NEWS. Vol. 25 no. 1 2009, pages 144–146 doi:10.1093/bioinformatics/btn619. ISMB 2008 conference report. Clare Sansom ...
bioinformatics.oxfordjournals.org/cgi/reprint/25/1/144.pdf
http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000101
bioinformatics.oxfordjournals.org/cgi/reprint/25/1/144.pdf
http://www.ploscompbiol.org/article/info:doi%2F10.1371%2Fjournal.pcbi.1000101
A WHAT IF check report: what does it mean?
http://swift.cmbi.kun.nl/gv/pdbreport/checkhelp/explain.html
Some of the 20 amino acid types in proteins have atoms that "look" the same. So, for instance, the C-delta-1 and C-delta-2 atoms in phenylalanine look the same, and thus all PHE residues would have two ways of naming the atoms:
Naming in Phenylalanine
This would result in infinite confusion. So, a committee designed a standard: the torsion angle Chi-2 (defined by C-alpha, C-beta, C-gamma, C-delta-1) should always be between -90 and 90 degrees.
Similar considerations hold for ASP, GLU, PHE and TYR.
Some of the 20 amino acid types in proteins have atoms that "look" the same. So, for instance, the C-delta-1 and C-delta-2 atoms in phenylalanine look the same, and thus all PHE residues would have two ways of naming the atoms:
Naming in Phenylalanine
This would result in infinite confusion. So, a committee designed a standard: the torsion angle Chi-2 (defined by C-alpha, C-beta, C-gamma, C-delta-1) should always be between -90 and 90 degrees.
Similar considerations hold for ASP, GLU, PHE and TYR.
Thursday, May 6, 2010
Physiological ionization and pKa prediction
http://www.daylight.com/meetings/emug00/Sayle/pkapredict.html
Physiological ionization and pKa prediction
Roger Sayle
Bioinformatics Group,
Metaphorics LLC,
Santa Fe, New Mexico.
HA <=> H+ + A- or HB+ <=> H+ + B
This provides a measure of the ease of proton disassociation of a site in a compound, the disassociation (or ionization) constant pKa, defined by the equation:
pKa = pH + log(protonated/unprotonated)
Alternatively, the pKa of a site can be thought of the pH at which the protonated and deprotonated fractions are equal. If the pH is higher than the pKa, the site is mostly deprotonated, and if the pH is lower than the pKa, the site is mostly protonated.
Physiological ionization and pKa prediction
Roger Sayle
Bioinformatics Group,
Metaphorics LLC,
Santa Fe, New Mexico.
HA <=> H+ + A- or HB+ <=> H+ + B
This provides a measure of the ease of proton disassociation of a site in a compound, the disassociation (or ionization) constant pKa, defined by the equation:
pKa = pH + log(protonated/unprotonated)
Alternatively, the pKa of a site can be thought of the pH at which the protonated and deprotonated fractions are equal. If the pH is higher than the pKa, the site is mostly deprotonated, and if the pH is lower than the pKa, the site is mostly protonated.
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