Group Meeting Schedule
All group meetings are open to anyone who is interested in attending.
Fall 2009
Tuesdays, 10:30-noon
Location TBA
|
8/4 |
--- |
No group meeting |
|
8/11 |
Siegfried |
Introduction/prior work with Jorgensen |
|
8/18 |
Lan |
|
|
8/25 |
Arjun |
|
|
9/1 |
--- |
No group meeting |
|
9/8 |
Monica |
practice oral exam |
|
9/15 |
Daisuke |
introduction/prior work on antibodies |
|
9/22 |
Jona |
introduction/prior work on PK modeling |
|
9/29 |
--- |
No group meeting |
|
10/6 |
OPEN |
|
|
10/13 |
Salma |
|
|
10/20 |
CK |
|
|
10/27 |
Chris |
|
|
11/3 |
Colin |
|
|
11/10 |
OPEN |
|
|
11/17 |
--- |
No group meeting |
|
11/24 |
Brad Webb |
PI3K regulation |
|
12/1 |
Matt |
progress on coarse-grained modeling |
|
12/8 |
Michael |
|
|
12/15 |
Lena |
|
Spring 2009
Wednesday, 10:30-noon
Location TBA
|
1/7 |
--- |
No group meeting |
|
1/14 |
Alrun Koller |
introduction |
|
1/21 |
Matt |
practice for faculty lunch talk |
|
1/28 |
Henry |
rotation report |
|
2/4 |
Monica |
microtubule simulations/crowding |
|
2/11 |
Li Tian |
work in Friesner group |
|
2/18 |
Chris |
|
|
3/11 |
CK |
|
|
3/18 |
Arjun |
|
|
3/25 |
Andrew |
|
|
4/1 (different time, TBA) |
Colin |
|
|
4/8 |
--- |
No group meeting |
|
4/15 |
Salma |
|
|
4/22 |
Lan |
|
|
4/29 |
Nora |
|
Fall 2008
Thursdays, 10:30-noon
N436A
|
When |
Who |
What |
|
10/2 |
Pradipta |
Gly rich loop dynamics |
|
10/9 |
Lan |
introduction |
|
10/16 |
--- |
No group meeting |
|
10/23 |
Francesca and Salma |
progress on HARC center research |
|
10/30 |
CK |
glycolysis pathway |
|
11/6 |
Kris |
simulations of androgen receptor |
|
11/13 |
Colin |
progress in wet lab |
|
11/20 |
Tack |
evolution |
|
11/27 |
--- |
No group meeting |
|
12/4 |
--- |
Probably no group meeting |
|
12/11 |
Henry |
rotation report |
|
12/18 |
Matt/Chris |
|
Summer 2008
Thursdays, 10:30-noon
N436A
|
When |
Who |
What |
|
7/3 |
Salma |
PhD work |
|
7/9* |
Vageli |
loop sampling etc. |
|
7/17 |
--- |
No group meeting |
|
7/24 |
Amy |
summer research |
|
7/31 |
--- |
No group meeting |
|
8/7 |
Ben |
side projects |
|
8/14 |
Pradipta |
|
|
8/21 |
--- |
No group meeting |
|
8/28 |
Francesca |
|
|
9/4 |
Lan |
PhD work |
|
9/11 |
Jerome |
|
Spring 2008
Thursdays, 10:30-noon
N436A
|
When |
Who |
What |
|
4/10 |
Matt |
|
|
4/17 |
--- |
No group meeting |
|
4/24 |
Arjun |
follow ups on Arp2/3, antibodies |
|
5/1 |
Francesca/Chris |
Update on Nef |
|
5/8 |
Zach Newby |
water/glycerol channel selectivity |
|
5/15 |
--- |
No group meeting |
|
5/22 |
Jerome |
|
|
5/29 |
Brian Tuch |
|
|
6/5 |
Eli |
GPCR side-project |
|
6/12 |
Monica |
rotation report |
Thursdays, 10:30-noon
N436A
|
When |
Who |
What |
|
1/3 |
--- |
No group meeting |
|
1/10 |
--- |
No group meeting |
|
1/17 |
Matt |
State of the Group |
|
1/24 |
Francesca |
pKa prediction |
|
1/31 |
Andrew Krutchinsky |
phosphorylation/mass spec |
|
2/7 |
CK |
new results on enolase project |
|
2/14 |
Jerome |
progress towards graduating |
|
2/21 |
Arjun |
Arp2/3 phosphorylation |
|
2/28 |
Kris Kuchenbecker |
targeting the AR coactivator site |
|
3/6 |
--- |
No group meeting |
|
3/13 |
Colin |
|
|
3/20 |
Eli |
Practice talk |
|
3/27 |
Ben |
progress towards graduating |
Summer/Fall 2007
Thursdays, 10:30-noon
N436A
|
When |
Who |
What |
|
8/9 |
Matt |
report from my sabbatical etc. |
|
8/16 |
CK |
prep for PPG meeting |
|
8/23 |
Gabriela |
talin wrap-up |
|
8/30 |
Chris |
IL-2 |
|
9/6 |
--- |
No group meeting |
|
9/13 (10 am) |
Chris |
practice orals |
|
9/20 |
Ben/Eli |
practice talks for Biophysics retreat |
|
9/27 |
Jerome |
progress towards graduating |
|
10/4 |
Arjun |
antibody domain orientations |
|
10/11 (4 pm) |
Dan Mandell |
joint meeting with Kortemme lab |
|
10/18 |
Colin |
|
|
10/25 |
Jed Lampe |
P450’s |
|
11/1 |
Kati Medzihradszky |
post-translational modifications by MS |
|
11/8 |
Chris Fennell |
|
|
11/15 |
Ilya Chorny |
|
|
11/22 |
--- |
No group meeting |
|
11/29 |
Eli |
progress towards graduating |
|
12/6 |
Ben |
progress towards graduating |
|
12/13 |
|
|
|
12/20 |
--- |
No group meeting |
|
12/27 |
--- |
No group meeting |
Winter/Spring 2007
Thursdays, 10:30-noon
N436A
* Joint group meetings with Kortemme group in BH 215 *
|
When |
Who |
What |
|
1/4 |
Jeremy Philips |
rotation report |
|
1/11 |
Matt |
Practice for lunch talk |
|
1/18 |
Nima/CK |
progress on enolase project |
|
1/25 |
Laura |
final talk |
|
2/1 (4 PM)* |
Colin |
First joint meeting with Tanja’s group |
|
2/8 |
--- |
No group meeting |
|
2/15 |
Matt |
State of the Group |
|
2/22 |
--- |
No group meeting |
|
3/1 |
Eli |
progress towards graduating |
|
3/8 (4 PM)* |
Greg Friedland |
|
|
3/15 |
Kris |
rotation report |
|
3/22 |
Gabriela |
PIP2 |
|
3/29 |
Chris |
IL-2 and PTP1B |
|
4/5 (4 PM)* |
Ben |
antibody modeling |
|
4/12 |
--- |
No group meeting |
|
4/19 (4 pm) |
Stephen Floor |
dynamics by NMR (S436A) |
|
4/26 |
Niu |
last talk |
|
Matt on sabbatical May 1 until end of July |
||
Fall 2006
Thursdays, 10:30-noon
N436A
|
When |
Who |
What |
|
9/21 |
everyone |
ACS reports |
|
9/28 |
--- |
No group meeting |
|
10/5 |
Colin |
work in Tanja’s group |
|
10/12 |
CK |
covalent ligand docking |
|
10/19 |
Jerome |
new MC methods |
|
10/26 |
Nima |
progress on alpha-beta barrels |
|
11/2 |
--- |
No group meeting |
|
11/9 |
Hod |
progress on thesis |
|
11/16 |
Gabriela |
progress on prot states |
|
11/23 |
--- |
No group meeting |
|
11/30 |
Rebeca Choy |
rotation report |
|
12/7 |
Scott Shell |
guest speaker |
|
12/14 |
Chris McClendon |
rotation report |
|
12/21 |
Jeremy Philips |
rotation report |
Summer 2006
Wednesdays, 10:30-noon
N436A
|
When |
Who |
What |
|
7/5 |
Chris Oostenbrink |
ligand binding affinities |
|
7/12 |
Laura |
MD simulations of phosphorylation |
|
7/19 |
Niu |
druggability |
|
7/26 |
--- |
No group meeting |
|
8/2 |
CK |
progress on alpha-beta barrels |
|
8/9 |
Reina/Dinah |
Summer project final reports |
|
8/16 |
Ben |
loop prediction with imperfect surroundings |
|
8/23 |
Sergio |
last talk?? |
|
8/30 |
Deb Datta |
allostery in caspases |
|
9/6 |
--- |
No group meeting |
|
9/13 |
--- |
No group meeting (ACS) |
Wednesdays, 10:30-noon
N436A
|
When |
Who |
What |
|
3/29 |
Ben/Sergio |
Progress on antibodies |
|
4/5 |
Colin |
Rotation final report |
|
4/12 |
Kat |
Parasite cysteine proteases |
|
4/19 |
Hesper |
Rotation final report |
|
4/26 |
Mike Keiser |
New methods in cheminformatics |
|
5/3 |
Sergio |
Progress towards graduating |
|
5/10 |
Niu |
Druggability, flexibility, ? |
|
5/17 |
--- |
no group meeting |
|
5/24 |
Matt |
Practice talk for faculty lunch |
|
5/31 |
CK |
Progress towards next paper |
|
6/7 |
Vince Voelz |
Protein folding |
|
6/14 |
Gabriela |
Predicting protonation states |
Winter 2006
Tuesdays, 2-3:30 PM
N436A
|
When |
Who |
What |
|
1/5 |
Matt |
State of the Group |
|
1/10 |
--- |
no group meeting |
|
1/17 |
Jerome |
SC MC |
|
1/24 |
Arjun |
2nd practice talk |
|
2/2 (special day & time: 2 PM) |
John Maple |
automated force field development |
|
2/7 |
Nima |
2nd practice talk |
|
2/14 |
John Chodera |
how good are force fields? |
|
2/21 |
--- |
no group meeting |
|
2/28 |
Brian Tuch |
|
|
3/7 |
Jyoti |
talin, pH dependence, etc. |
|
3/14 |
David Mobley |
Ligand binding free energy |
|
3/21 |
Stephen |
rotation final report |
Fall 2005
Thursdays, 10:30-12:00 AM
N436A
|
When |
Who |
What |
|
9/22 |
--- |
no group meeting |
|
9/29 |
--- |
no group meeting |
|
10/6 |
Gabriela Barreiro |
work in Jorgensen group |
|
10/13 |
Banu |
Zipping |
|
10/20 |
Ranyee |
|
|
10/27 |
Niu |
Rescoring with flexibility |
|
11/3 |
CK |
|
|
11/10 |
Sergio |
Progress on flexible loops |
|
11/17 |
Arjun |
First orals practice talk |
|
11/24 |
--- |
No group meeting |
|
12/1 |
Nima |
First orals practice talk |
|
12/8 |
Laura |
Progress on RNA |
|
12/15 |
Kat |
Final talk |
Summer 2005
Wednesdays, 10:30-12:00 AM
N436A
|
When |
Who |
What |
Type |
|
6/22 |
--- |
No group meeting |
|
|
6/29 |
Matt |
What I learned on vacation; how to fix simple PBS problems |
Informal |
|
7/6 |
Kiyoshi Egami |
HPRT and disease |
Visitor |
|
7/13 |
Ben |
Progress on antibodies |
Informal |
|
7/20 |
Jerome |
Progress on MC |
Informal |
|
7/27 |
Dan |
Final data for phospho H-bond paper |
Formal |
|
8/3 |
CK/Nima/Sergio |
Results for enolases, prior to program project meeting |
Informal |
|
8/10 |
Elaine Meng |
New Features of Chimera |
Visitor |
|
8/17 |
Dinah Zaghi |
Final report on summer research |
Visitor |
|
8/24 |
Laura Dominguez |
Prior work |
Visitor |
|
8/31 |
--- |
No group meeting |
|
|
9/7 |
Eli |
Computational and experimental work on phosphorylation |
Informal |
|
9/14 |
Kat |
Update on docking against homology models |
|
Spring 2005
Wednesdays, 10:30-12:00 AM
N436A
|
When |
Who |
What |
Type |
|
3/30 |
Ben/Sergio |
Progress on antibodies |
Formal |
|
4/6 |
Dan |
Rotation Report |
Formal |
|
4/13 |
Hod |
Progress report |
Informal |
|
4/20 |
Kat |
Screening contest paper |
Informal |
|
4/27 |
Eli/Arjun |
Final results for phospho-loop paper |
Informal |
|
5/4 |
Niu |
|
|
|
5/11 |
Alan Graves |
Model binding sites |
Guest |
|
5/18 |
Ray Nagatani |
|
Guest |
|
5/25 |
--- |
No group meeting |
|
|
6/1 |
Greg Friedland |
|
Guest |
|
6/8 |
Kat |
rescoring with polarizability |
Informal |
|
6/15 |
CK |
docking against enolase HM |
Informal |
Winter 2005
Wednesdays, 10:30-12:00 AM
N436A
|
When |
Who |
What |
Type |
|
1/5 |
Eli |
Second practice oral exam |
Formal |
|
1/12 |
Matt |
State of the Group |
Informal |
|
1/19 |
Jerome |
Second practice oral exam |
Formal |
|
1/26 |
Victor Kenyon |
Practice talk |
Formal |
|
2/2 |
open slot |
|
Informal |
|
2/9 |
Nima/CK/Sergio |
Progress on enolases |
Informal |
|
2/16 |
Kat |
|
Informal |
|
2/23 |
--- |
Probably no group meeting |
--- |
|
3/2 |
Niu/CK |
Anything related to AIDS grant |
Informal |
|
3/9 |
Terry Lang |
|
Informal |
|
3/16 |
Matt |
Practice Talk |
Formal |
|
3/23 |
No group meeting |
|
|
Fall 2004
Thursdays, 10-11:30 AM
N436A
|
When |
Who |
What |
Type |
|
9/9 |
No group meeting |
|
|
|
9/16 |
No group meeting |
|
|
|
9/23 |
Matt |
|
Informal |
|
9/30 |
Ben |
First practice oral exam |
Formal |
|
10/7 |
Eli |
First practice oral exam |
Formal |
|
10/14 |
Jerome |
First practice oral exam |
Formal |
|
10/21 |
Kat |
Docking against HM |
Formal |
|
10/28 |
Ilya |
|
Informal |
|
11/4 |
No group meeting |
|
|
|
11/11 |
Hod |
|
Informal |
|
11/18 |
No group meeting |
|
|
|
11/25 |
No group meeting |
|
|
|
12/2 |
Arjun |
|
Informal |
|
12/9 |
Ben |
Second practice oral exam |
Formal |
|
12/16 |
Sergio |
|
Informal |
|
12/23 |
No group meeting |
|
|
|
12/30 |
No group meeting |
|
|
Summer 2004
Thursdays, 10-11:30 AM
N436A
|
When |
Who |
What |
Journal Watch |
|
6/24 |
Eli |
Me: Proteins |
|
|
7/1 |
Ilya |
Limitations of implicit solvent |
Eli: JMB |
|
7/8 |
Michael |
CDK2/GTPase docking |
Kat: Prot Sci |
|
7/15 |
Kat |
Model binding sites: initial results |
CK: J Med Chem |
|
7/22 |
??? |
Reserved for CASP |
|
|
7/29 |
No group meeting |
|
|
|
8/5 |
Hod |
Automated identification of fragments in electron density |
Ben: PNAS |
|
8/12 |
Ben |
Antibody modeling |
Ilya: JCP |
|
8/19 |
??? |
Reserved for CASP |
|
|
8/26 |
Sergio |
Loop flexibility |
Sergio: JPC B |
|
9/2 |
CK |
|
Me: F1000 selections |
|
9/9 |
No group meeting |
|
|
Spring 2004
Thursdays, 10-11:30 AM
N436A
|
When |
Who |
What |
Journal Watch |
|
4/1 |
Arjun |
Me: Proteins |
|
|
4/8 |
Michael |
Eli: JMB |
|
|
4/15 |
Ben |
Progress on antibodies |
Jerome: J Comp Chem |
|
4/22 |
No group meeting |
|
|
|
4/29 |
Ilya |
|
CK: J Med Chem |
|
5/6 |
Eli |
|
Kat: Prot Sci |
|
5/13 |
Jerome |
|
Ben: PNAS |
|
5/20 |
CK |
|
Ilya: JCP |
|
5/27 |
Kat |
|
Sergio: JPC B |
|
6/3 |
Matt |
cyclic peptides |
|
|
6/10 |
Probably no group meeting |
|
|
|
6/17 |
David |
Me: F1000 selections |
Winter 2004
Tuesdays, 2-3:30 PM
N436A
|
When |
Who |
What |
|
1/6 |
Matt |
Goals for quarter, scheduling, etc. |
|
1/13 |
CK and/or Kat |
DHFR |
|
1/20 |
Ben |
literature talk |
|
1/27 |
Ilya |
progress on docking and/or nonpolar solvation |
|
2/3 |
Sergio |
First “practice talk” for orals |
|
2/10 |
Eli |
??? |
|
2/17 |
Niu |
progress on automated docking (possibly CK and/or Kat can also discuss rescoring results) |
|
2/24 |
Hod |
progress on fragment fitting |
|
3/2 |
Sergio |
Second practice talk for orals |
|
3/9 |
Jerome |
progress on antibodies |
|
3/16 |
Arjun |
Rotation final report |
|
3/23 |
CK |
Practice talk for ACS |
|
3/30 |
No group meeting |
ACS National Meeting |
Summer/Fall 2003
Thursdays, 10-11:30 AM
N436A
|
When |
Who |
What |
|
7/22 |
Matt |
Introduce new people, overview of projects |
|
7/29 |
Ilya |
Prior work at UCSC |
|
8/5 |
Nima |
Rotation final report |
|
8/12 |
CK |
|
|
8/19 |
Brian |
|
|
8/26 |
Ben |
Rotation final report |
|
9/2 |
Matt |
Goals for Fall; the guts of PLOP |
|
9/11 |
Matt |
More “guts” |
|
9/18 |
No group meeting |
"paternity leave" : ) |
|
9/25 |
Matt/Eli |
Matt: pKa prediction; Eli: PIBS practice talk |
|
10/2 |
No group meeting |
I’m giving a lecture in Wendell’s class |
|
10/9 |
Sergio |
Phosphopeptide simulations |
|
10/16 |
Kat |
|
|
10/23 |
Hod |
Progress on automated xtal structure building |
|
10/30 |
Eli |
CDK2 |
|
11/6 |
Jeremy |
Homology modeling of antibodies |
|
11/13 |
Ilya |
Solvent-separated H-bonds and implicit solvent models |
|
11/20 |
CK |
Progress on rescoring protein-ligand complexes |
|
11/27 |
No group meeting |
Thanksgiving |
|
12/4 |
No group meeting |
|
|
12/11 |
Ben |
Rescoring protein-protein complexes |
|
12/18 |
Matt |
TBA |
|
12/25 |
No group meeting |
|
|
1/1 |
No group meeting |
|
|
1/8 |
Matt |
Goals for the quarter |