| Date |
Time |
Speaker
|
Presentation
|
Other Articles
Reviewed |
|
|
Spring 2025 (January - May 2025)
|
|
| 4/1 |
2:00 PM
|
Isabelle Kwan |
ESSENTIAL INTERFACES: How Complexation Alters Structural Dynamics
|
|
|
| 3/27 |
2:30 PM
|
Matthew Licht |
Overcoming Drug Resistance in Candida Auris
|
|
|
| 3/13 |
2:30 PM
|
Satyaki Saha |
Conformational Sampling of β2AR
|
|
|
| 1/30 |
2:30 PM
|
Diksha Parwana |
From Local Perturbations to Global Dynamics: ENMs for Allostery
|
|
|
| 1/7 |
2:30 PM
|
JiYoung Lee |
Genetic regulation and targeted reversal of lysosomal dysfunction and inflammatory sterol metabolism in pulmonary arterial hypertension
|
|
|
|
Fall 2024 (September - December 2024)
|
|
| 11/21 |
2:30 PM
|
Isabelle Kwan |
Discovering Drug-Target-Pathway Relationship in Clozapine Antipsychotic Efficacy with QuartataWeb
|
|
|
| 11/12 |
9:00 AM
|
Xiaowei Bogetti |
Experimental data guided conformational sampling of protein alternate states
|
|
|
| 11/07 |
2:30 PM
|
Umur Turgut |
Partial Inhibition of the CtaA Chemotaxis Receptor in Pseudomonas Fluorescens increases motility and reduces biofilm formation
|
|
|
| 10/17 |
2:30 PM
|
Anthony Bogetti |
The next frontier in protein structure prediction: pathways and kinetics
|
|
|
|
Spring 2024 (January - May 2024)
|
|
| 7/16 |
3:00 PM
|
JiYoung Lee |
Drug Discovery in collaboration with experimentalists |
|
|
| 7/09 |
2:30 PM
|
Mary Hongying Cheng |
Research Updates |
|
|
| 7/02 |
2:30 PM
|
Anupam Banerjee |
Rhapsody2: Enhanced Prediction and Comprehensive Biophysical Characterization of Pathogenic Missense Variants |
|
|
| 6/25 |
2:30 PM
|
Xiaowei Bogetti |
smFRET and DEER with ProDy |
|
|
| 6/11 |
2:30 PM
|
Anthony Bogetti |
New methods being developed in the Bahar group |
|
|
| 5/21 |
2:30 PM
|
Hoang Nguyen |
Signature Dynamics reveal sequence to dynamic relation |
|
|
| 5/14 |
2:30 PM
|
Haotian (Frank) Zhang |
Exploring Mechanisms of Coproporphyrinogen III oxidase mutations causing Porphyria |
|
|
| 4/16 |
2:30 PM
|
Rostam Razban |
Linking brain structure to function with elastic network theory |
|
|
| 4/02 |
2:30 PM
|
Isabelle Ming Suet Kwan |
Essential Site Scanning Analysis (ESSA) |
|
|
| 3/19 |
2:30 PM
|
Mary Hongying Cheng |
Structural mechanisms for VMAT inhibition by tetrabenazine |
|
|
| 3/12 |
2:30 PM
|
Ivet Bahar |
Bridging Sequence, Structure and Function |
|
|
| 2/20 |
2:30 PM
|
Hoang Nguyen |
Allosteric review on hSERT and dDAT |
|
|
| 2/06 |
2:30 PM
|
Frank Zhang |
Deciphering the Molecular Landscape of Ferroptosis: Drug Interventions and Gene Expression Dynamics |
|
|
| 1/30 |
2:30 PM
|
Carlos Ventura |
Structure Based Mechanistic Approaches for Target Selection of NSCLC for Inducing Ferroptosis |
|
|
| 1/16 |
2:30 PM
|
Anthony Bogetti |
Improving our maps of protein conformational space |
|
|
| 1/02 |
2:30 PM
|
Xiaowei Bogetti |
GNM and ANM analysis reveals the global motions of human V-ATPase |
|
|
|
Fall 2023 (September - December 2023)
|
|
| 12/22 |
2:00 PM
|
Satyaki Saha |
Deciphering the Molecular Mechanism Underlying CIP2A-Mediated Inhibition of PP2A Tumor Suppressor Activity |
|
|
| 12/15 |
2:30 PM
|
Rostam Razban |
Do protein motions constrain enzyme catalysis? |
|
|
| 11/28 |
2:30 PM
|
Diksha Parwana |
GNM analysis on Human V-ATPase |
|
|
| 11/12 |
2:00 PM
|
Hoang Nguyen |
VPS13 and ENM analysis |
|
|
| 10/31 |
2:30 PM
|
Haotian (Frank) Zhang |
Drugs are likely to bind hinge regions |
|
|
| 10/24 |
2:30 PM
|
Xiaowei Bogetti |
Integrating EPR and computational modeling to measure protein structure and dynamics |
|
|
| 10/17 |
2:30 PM
|
Pemra Doruker |
APOP Algorithm for Allosteric Pokcet Prediction |
|
|
| 10/10 |
2:30 PM
|
Anupam Banerjee |
Leveraging Elastic Network Models to Explore the Connectome |
|
|
| 9/12 |
2:30 PM
|
Anthony Bogetti |
Shooting for the moon with weighted ensemble applications |
|
|
|
Spring 2021 (January - May 2021)
|
|
| 3/17 |
11:25 AM
|
James Krieger |
Marie Curie Fellowship |
|
|
| 3/10 |
11:25 AM
|
Burak Kaynak |
2D Rigid Body Extension for MCell |
|
|
| 2/11 |
11:25 AM
|
Hongying (Mary) Chen |
How do mutations in SARS-CoV-2 receptor alter ACE2 binding? |
|
|
| 2/03 |
11:25 AM
|
JiYoung Lee |
Modeling of PAK2-PAK2 dependent on mutation |
|
|
| 1/26 |
11:25 AM
|
Haotian (Frank) Zhang |
Predicting PPI with symmetric logistic matrix fractorization |
|
|
| 1/19 |
11:25 AM
|
Qingya (Hannah) Shi |
Systems level analysis reveals repurposable drugs for COVID-19 |
|
|
| 1/12 |
11:25 AM
|
Ivet Bahar |
Lab Objective for 2021 |
|
|
|
Fall 2020 (September - December 2020)
|
|
| 12/08 |
11:25 AM
|
Yan Zhang |
Mapping a vecotr field of single cells |
|
|
| 12/08 |
11:00 AM
|
Mary Hongying Cheng |
(Short Talk) A pan-coronavirus fusion inhibitor for SARS-CoV2 |
|
|
| 11/17 |
11:00 AM
|
Pemra Doruker |
GPR3/Beta-arr2/Gamma-secretase interplay in Alzeimer's disease |
|
|
| 10/20 |
11:00 AM
|
JiYoung Lee |
Druggability simulations and pharmacophore modeling for PTHR and GLP1R |
|
|
| 10/06 |
11:00 AM
|
Hongchun Li |
Pharmacological suppression of B7-H4 glycosylation restores antitumor immunity in immune-cold breast cancers |
|
|
| 9/29 |
11:00 AM
|
James Krieger |
Inhibiting host proteases involved in SARS-CoV-2 viral entry |
|
|
| 9/15 |
11:00 AM
|
Hannah Shi |
Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis |
|
|
| 9/08 |
11:00 AM
|
Haotian(Frank) Zhang |
Leading Compounds Screening to Target γ-secretase APH-1 subunit |
|
|
|
Summer 2020 (June - August 2020)
|
|
| 8/18 |
11:00 AM
|
Fen Pei |
Predicting large scale protein-protein interactions using symmetric logistic matrix factorization |
|
|
| 8/11 |
11:00 AM
|
Daniel Penaherrera |
Structure-aware context Embeddings for proteins |
|
|
| 8/4 |
11:00 AM
|
She Zhang |
Efficient evaluation of subsystem ENM when the environment is a membrane lattice |
|
|
| 7/28 |
11:00 AM
|
Fangyuan Chen |
A case of precision medicine approach in treating breast cancer bone metastases |
|
|
| 7/21 |
11:00 AM
|
Cassandra Olivas |
Essential Site Scannig Analysis on Select Multimers |
|
|
| 7/7 |
11:00 AM
|
Burak Kaynak |
Essential Site Scanning Analysis |
|
|
| 6/30 |
11:00 AM
|
Bentley Wingert |
Protein Domain Family Dynamics: SH2 & PDZ |
|
|
|
Spring 2020 (January - May 2020)
|
|
| 2/25 |
2:30 PM
|
Yan Zhang |
From RNA Velocity to Stochastic Dynamics of Cell Fate |
|
|
| 2/17 |
2:30 PM
|
James Krieger |
Dynamics of AMPA-type glutamate receptors and mechanisms of regulation by TARP |
|
|
| 2/4 |
2:30 PM
|
Jiyoung Lee |
Interaction mechanism between beta-arrestin 2 and gamma-secretase related to Alzheimer's disease |
|
|
|
Fall 2019 (September - December 2019)
|
|
| 12/19 |
3:00 PM
|
She Zhang |
Hierarchical organization of chromosomal domains |
|
|
| 12/12 |
4:00 PM
|
Bing Liu |
A platter of data-driven side projects |
|
|
| 11/12 |
11:00 AM
|
Ivet Bahar |
Discussion on projects in the lab |
|
|
| 11/5 |
11:00 AM
|
James Krieger |
Alignment of multi-chain structures in ProDy and results for TRiC/CCT |
|
|
| 10/22 |
11:00 AM
|
Fangyuan Chen |
Transcriptional profiling of breast cancer cell lines at single cell resolution |
|
|
| 10/15 |
11:00 AM
|
Fen Pei |
Predicting large scale protein-protein interactions using symmetric non-negative matrix factorization |
|
|
| 10/8 |
11:00 AM
|
Pemra Doruker & Burak Kaynak |
ENM-based site-scanning, allostery and orthostery - II |
|
|
| 10/1 |
11:00 AM
|
Pemra Doruker & Burak Kaynak |
ENM-based site-scanning, allostery and orthostery - I |
|
|
| 9/24 |
11:00 AM
|
Hongying Cheng |
Regulation of monoamine transporters by small molecules |
|
|
| 9/11 |
3:00 PM
|
Stephanie Aldrich |
Evaluating in silico binding predictions with experimental mutagenesis to identify calcium channel residues involved in the activity of a novel agonist |
|
|
|
Summer 2019 (June - August 2019)
|
|
| 8/14 |
2:30 PM
|
Yan Zhang |
Dynamical Inference From Single Cell RNA-Seq |
|
|
| 8/7 |
2:30 PM
|
Hongchun Li |
Protein ubiquitylation via designed PROTACs or natural protein-protein interactions |
|
|
| 7/31 |
3:00 PM
|
Jiyoung Lee |
Pharmmaker: Pharmacophore modeling and hit identification based on druggability simulations |
|
|
| 7/24 |
2:30 PM
|
She Zhang |
Differences in the intrinsic spatial dynamics of gene loci contribute to cell differentiation |
|
|
| 7/17 |
3:00 PM
|
Bing Liu |
Dopamine transpoter in lipid rafts |
|
|
| 7/10 |
10:30 AM
|
Luca Ponzoni |
Rhapsody: algorithm improvements and applications |
|
|
| 6/19 |
10:30 AM
|
Chen Fangyuan |
RET pathway activation and missense mutations in breast cancer & characterizing highly mobile genes from chromatin dynamics |
|
|
|
Spring 2019 (January - May 2019)
|
|
| 5/29 |
2:30 PM
|
Fen Pei |
Predicting large scale protein-protein interactions using symmetric non-negative matrix factorization |
|
|
| 5/1 |
2:30 PM
|
James Krieger |
Updates to CoMD: application to various systems |
|
|
| 4/24 |
3:30 PM
|
Burak Kaynak |
Protein-ligand complexes as constrained dynamical systems |
|
|
| 4/10 |
2:30 PM
|
Mary Cheng |
Oligomerization in
human dopamine transporter |
|
|
| 2/27 |
1:30 PM
|
Dror Tobi |
Dynamical comparison as a tool to study
proteins: the hemoglobin case |
|
|
| 2/13 |
1:30 PM
|
Ana Ligia Scott |
Self-adaptive collective motions of
macromolecules incorporating structural and environmental effects |
|
|
| 2/6 |
1:30 PM
|
Pemra Doruker |
Conformational dynamics
and interactions of CaMKII |
|
|
|
Fall 2018 (September - December 2018)
|
|
| 12/11 |
1:00 pm
|
Hongchun Li |
Intrinsic dynamics of
toroidal proteins and their behaviors in several biomolecular machineries |
|
|
| 12/4 |
1:00 pm
|
Indira Myers |
Bahar, Kagan and Bayir lab collaborative efforts
|
|
|
| 11/27 |
1:00 pm
|
Balint Dudas |
The activation mechanism of auto-inhibited RalF
|
|
|
| 11/20 |
1:00 pm
|
Yan Zhang/She Zhang |
An improvement to the
system-environment framework when the environment is a lattice |
|
|
| 10/16 |
1:00 pm
|
Ji Young Lee |
A mechanism of channel
pore opening in AMPA receptor related with external domains dynamics |
|
|
| 10/9 |
1:00 pm
|
Ana Ligia Scott |
Structural analysis and searching for allosteric
modulators of dengue virus protease (NS2B / NS3) |
|
|
| 10/2 |
1:00 pm
|
Luca Ponzoni |
Classification of
Single Amino acid Variants (SAVs) |
|
|
| 9/25 |
1:00 pm
|
Bing Liu |
Computational Modeling
Reveals Polypharmacological Strategies for Regulating alpha1-antitrypsin Z Mutant
Protein Disposal |
|
|
|
Summer 2018 (June - August 2018)
|
|
| 8/14 |
1:00 pm
|
Yan Zhang |
CCT Conformational
Space Elucidated by Elastic Network Model Analysis of Cryo-EM Data |
|
|
| 8/7 |
1:00 pm
|
Burak Kaynak |
Towards to rigid body
motions in MCell |
|
|
| 7/24 |
1:00 pm
|
Stephanie Aldrich |
Voltage-gated sodium channel |
|
|
| 7/17 |
1:15 pm
|
She Zhang |
Signature dynamics of
protein families: conserved vs. specific mechanisms of conformational motions |
|
|
| 6/19 |
1:00 pm
|
Hongchun Li |
BalestraWeb 2.0 |
|
|
| 6/12 |
1:00 pm
|
Various Presenters |
Progress report |
|
|
|
Spring 2018 (January - May 2018)
|
|
| 5/15 |
1:00 pm
|
Various Presenters |
ProDy workshop rehearsal |
|
|
| 4/24 |
1:00 pm
|
Jiyoung Lee |
Channel pore in AMPA
receptor |
|
|
| 4/17 |
1:00 pm
|
Karolina Mikulska-Ruminska |
In search of
cardiolipin binding site motif |
|
|
| 4/10 |
1:00 pm
|
Burak Kaynak |
Chapters |
|
|
| 4/3 |
1:00 pm
|
Luca Ponzoni |
State-of-the-art
sequence-based methods for pathogenicity predictions |
|
|
| 3/20 |
1:00 pm
|
Mary Cheng |
Protein complex network
of VCP, PINK1, and P47 |
|
|
| 3/13 |
1:00 pm
|
Bing Liu |
PEBP1-15LO1-LC3
orchestrate autophagic activity to limit ferroptosis |
|
|
| 3/6 |
1:00 pm
|
Ana Ligia Scott |
Some Studies of
Conformational Changes and Functional Movements studies using Full-Atom combined with
Coarse-Grained model |
|
|
| 1/16 |
1:00 pm
|
James Krieger |
Collective MD for
sampling conformational landscapes |
|
|
| 1/9 |
1:00 pm
|
She Zhang |
3D structures of
individual mammalian genomes studied by single-cell Hi-C (paper discussion) |
Stevens, T. J., et al. (2017).
Nature, 544(7648), 59-64. |
|
| 1/2 |
1:00 pm
|
Cihan Kaya |
Projects and Future Ideas |
|
|
|
Fall 2017 (September - December 2017)
|
|
| 12/19 |
1:00 pm
|
Ivet Bahar |
General discussion |
|
|
| 12/12 |
1:00 pm
|
She Zhang |
Studying Chromatin
Dynamics Using the Gaussian Network Model |
|
|
| 11/29 |
11:30 am
|
Hongchun Li |
Druggability analysis
for Trypsin |
|
|
| 11/7 |
1:00 pm
|
Ivet Bahar |
Causality, transfer
entropy, and allosteric communication landscapes in proteins with harmonic
interactions (paper discussion) |
Perturbation-response
scanning (PRS) theory |
|
| 10/4 |
1:00 pm
|
Jiyoung Lee |
ANM/GNM
Druggability MD simulations Pharmacophore modeling of Trypsin |
|
|
| 9/26 |
1:00 pm
|
Yan Zhang |
DNA Condensation
|
|
|
| 9/5 |
10:00 am
|
Bing Liu |
Deciphering
the Dynamics of Cannabinoid Receptor Type 2 |
|
|
|
Summer 2017 (June - August 2017)
|
|
|
|
|
|
|
|
|
| 8/22 |
10:00 am
|
Stephaine Aldrich |
Modeling voltage sensor
movement in the Cav2.1 calcium channel |
|
|
| 8/15 |
10:00 am
|
Various Presenters |
Research Summaries
|
|
|
| 7/18 |
10:00 am
|
Ivet Bahar |
Biomolecular
Systems Dynamics using Elastic Network Models: From Proteins to Chromosomes |
|
|
| 7/5 |
10:00 am
|
Ivet Bahar |
Biomolecular
Systems Dynamics using Elastic Network Models: From Proteins to Chromosomes |
|
|
| 6/30 |
1:00 pm
|
Mary Cheng |
Allosteric Modulation
of Human Dopamine Transporter Activity under Conditions Promoting its Dimerization
|
|
|
| 6/5 |
10:00 am
|
Luca Ponzoni |
Impact
of dynamical features on the classification of missense variants |
|
|
|
Spring 2017 (January - May 2017)
|
|
|
|
|
|
|
|
|
| 5/2 |
10:00 am
|
James Krieger |
Dynamics of ionotropic
glutamate receptors and allosteric potential of their N-terminal domains
(continued) |
meta |
|
| 4/25 |
10:00 am
|
James Krieger |
Dynamics of ionotropic
glutamate receptors and allosteric potential of their N-terminal domains |
R3displacement
R3openning-hres |
|
| 4/19 |
1:00 pm
|
Fen Pei |
Inferring
protein-protein interaction mechanism for HD model based on drug combination data
|
|
|
| 3/21 |
11:00 am
|
She Zhang |
Chromosomal
Dynamics using the GNM |
|
|
| 3/15 |
11:00 am
|
Cihan Kaya |
Activation
triggered subunit exchange in CaMKII |
|
|
| 2/28 |
10:00 am
|
Luca Ponzoni |
Prediction
of functional effects of human nsSNPs |
|
|
| 2/21 |
10:00 am
|
Karolina Mikulska-Ruminska |
MechStiff:
A New Tool for Evaluating Stress-Induced Dynamics |
|
|
| 2/7 |
9:30 am
|
Hongchun Li |
Updates
on the theory of Perturbation Response Scanning (PRS) |
oENM server |
|
| 1/31 |
9:30 am
|
Guangya Hu |
Differences between
thermophilic and mesophilic homologous proteins are mainly from residues with high
interaction degrees |
|
|
|
Fall 2016 (September - December 2016)
|
|
|
|
|
|
|
|
|
| 10/26 |
9:00 am
|
She Zhang |
Adaptability
of protein structures to enable functional interactions and evolutionary implications
(paper discussion) |
Haliloglu T. and Bahar I., Curr. Opin. Struct. Biol 35 (2015) 17 |
|
| 10/26 |
9:15 am
|
Cihan Kaya |
Lab meeting paper
discussion |
|
|
| 10/26 |
9:30 am
|
Hongchun Li |
Lab
meeting paper discussion |
|
|
| 10/10 |
9:00 am
|
Yan Zhang |
Normal
Mode Analysis of TRiC/CCT Based on Cryo-EM Density Map |
|
|
| 10/10 |
9:30 am
|
Hongchun Li |
Dynamic
Modulation of Binding Affinity as a Mechanism to Regulate Interferon Signaling
|
|
|
| 9/14 |
9:00 am
|
Bing Liu |
Tetrad tutorial |
|
|
|
Spring 2016 (January - August 2016)
|
|
|
|
|
|
|
|
|
| 7/21 |
12:30 pm
|
Kliment Ziko |
A
new paradigm of protein allostery: insight through the gaussian network model |
|
|
| 7/14 |
1:15pm
|
Bing Liu |
Computational Modeling
of Redox "Asthmasome" |
|
|
| 6/23 |
1:00pm
|
JiYoung Lee |
ANM analysis of
beta-arrestin-1 |
|
|
| 6/16 |
1:10pm
|
Zuhal Ozcan |
G-protein-coupled
receptors |
|
|
| 6/16 |
12:50pm
|
Pei Fen |
Huntington Disease
Project |
|
|
| 6/16 |
12:30pm
|
She Zhang |
Revealing Chromatin
Dynamics by Gaussian Network Model |
|
|
|
Spring 2015 (January - August 2015)
|
|
|
|
|
|
|
|
|
| 5/20 |
12:30pm
|
Hongchun Li |
Dynamic Modulation of
affinity as a Mechanism to regulate signaling |
|
|
| 4/8 |
12:30pm
|
Indira Srivastava |
Mitochondrial
Dynamics: Fission and Fusion |
|
| 4/1 |
3:30pm
|
Hongchun Li |
Mechanisms
of insertion of tryptophan rich AMPs on membranes |
|
| 3/25 |
3:15pm
|
Guang Hu |
Protein
rings and cages |
|
| 3/18 |
1:30 pm
|
Ivet Bahar |
Projects
in the lab |
|
|
Fall 2014 (September - December 2014)
|
|
|
|
|
|
|
|
|
| 12/17 |
1:00pm
|
Bing Liu |
Autophagy-Apoptosis
Crosstalk |
|
|
| 11/05 |
1:00pm
|
Murat Can Cobanoglu |
Prestwick
Library Screen Analysis |
|
|
| 10/22 |
1:00pm
|
Ivet Bahar |
Learning
from Computational Models and Pharmacology Methods |
|
|
| 10/07 |
3:00pm
|
Filippo Pullara |
Emerging
regulation and functions of autophagy |
|
|
| 09/30 |
4:00pm
|
JiYoung Lee |
Structure
and Dynamics of AMPA Receptor GluA2 in Resting, Pre-Open and Desensitized States
|
|
|
| 09/23 |
4:00pm
|
Mary Cheng |
A
Coarse-grained elastic network atom contact model and its use in the simulation of
protein dynamics and the prediction of the effect of mutations |
|
|
| 09/18 |
4:00pm
|
Kirubakaran Palani |
Computational
identification and invitro validation of novel lead molecules against TOPK and
Tankrase proteins |
|
|
Spring 2014 (January - August 2014)
|
|
|
|
|
|
|
|
| 08/28 |
10:00am
|
Filippo Pullara |
Experimental
and Simulation Study of Dopamine Receptors, Calmodulin dependent Kinase Type II and
G-proteins |
|
|
| 08/06 |
10:00am
|
Indira Shrivastava |
Hemoglobin
Druggability Simulations |
|
|
| 07/30 |
10:00am
|
Zeynep Kurkcuoglu |
Conformer
Generation with Elastic Network Models |
|
|
| 07/23 |
10:00am
|
Bing Liu |
Modeling
Toll-like Receptor Pathways |
|
|
| 07/09 |
10:00am
|
Cihan Kaya |
Spatiotemporal
modelling of synapses |
|
|
| 06/23 |
10:00am
|
Murat Can Cobanoglu |
BalestraWeb:
Efficient, online drug-target interaction prediction |
|
|
| 06/11 |
12:00pm
|
Feizhuo Kaitlyn Hu |
Drug
predictions and simulations for dopamine transporters |
|
|
| 05/21 |
12:00pm
|
Wenzhi Mao |
Comparative
analysis of sequence co-evolution methods |
|
|
| 05/02 |
01:00pm
|
Mert Gur |
Toward
Gaining a mechanistic understanding of substrate transport by LeuT |
|
|
| 04/24 |
09:30am
|
Filippo Pullara |
Effect
of Protein-Protein Interactions on
Conformational Energy Landscape |
|
|
| 04/17 |
09:00am
|
All lab members |
Paper
discussion of NMDARs |
|
|
| 04/02 |
10:00am
|
All lab members |
Paper
discussion of Leucine transporter |
|
|
| 03/19 |
10:00am
|
All lab members |
Paper vote |
|
|
| 03/12 |
09:30am
|
Ivet Bahar |
Paper
discussion of Synaptic Signaling in Memory and learning |
|
|
| 03/04 |
09:00am
|
All lab members |
Paper
discussion of Synaptic Signaling in Memory and learning |
|
|
| 02/13 |
10:00am
|
Mary Cheng |
Review
of Synaptic signaling |
|
|
| 02/05 |
10:00am
|
Indira Shrivastava |
VDAC
|
|
|
| 01/28 |
9:30am
|
Bing Liu |
Approximation
and Verification Techniques for Biological Pathway Modeling |
|
|
| 01/03 |
3:00pm
|
Ignacio General |
CAMK
II |
|
|
|
Fall 2013 (Sep-Dec 2013)
|
|
|
|
|
|
|
|
| 12/11 |
10:00am
|
Ahmet Bakan |
Applications
of Prody and Drugui |
|
|
| 12/04 |
10:00am
|
Ivet Bahar |
Discussion
of Michael Levitt's research |
|
|
| 11/21 |
10:00am
|
Murat Can Cobanoglu |
Probabilistic
Latent Factor Models for Transformative Drug Discovery |
|
|
| 11/13 |
10:00am
|
Cihan Kaya |
Dynamic
allostery and multiscale modeling |
|
|
| 10/23 |
9:30am
|
Wenzhi Mao |
Comparison
of Performances of Different Protein Coevolution Approaches for Non-interacting
Protein Pairs |
|
|
| 10/09 |
10:00am
|
Chang Liu |
Probabilistic
Matrix Factorization in drug-target interaction prediction |
|
|
| 09/23 |
3:30 pm
|
Filippo Pullara |
what
is missing in single MD simulation |
|
|
| 09/05 |
3:30 pm
|
Mary Cheng |
Pentameric
ligand-gated ion channels |
|
|
|
Spring 2013 (January - August 2013)
|
|
|
|
|
|
|
|
| 08/29 |
3:30 pm
|
Mert Gur
|
Multiscale
Investigation of Biomolecular Systems Dynamics
|
|
|
| 08/08 |
11:00 am
|
Indira Shrivastava
Tim Lezon
Murat Can Cobanoglu
Elia Zomot
|
VDAC:
Voltage Dependent Anion Channel
Computational
Modeling of Spatial Heterogeneity in Growing Tumors
Automated
Hypothesis Generation for Neuroprotective Drugs
Pathway
and mechanism of coupled sodium and substrate binding to outward-facing leucine
transporter, LeuT
|
|
|
| 08/01 |
3:30 pm
|
Ignacio General |
Hsp70's
missing conformer |
|
|
| 06/27 |
3:30 pm
|
Ahmet Bakan |
Modeling
Cytochrome c inhibitors |
|
|
| 06/20 |
3:30 pm
|
Ignacio General |
Protein-Protein
Interactions (or lack thereof) |
|
|
| 05/30 |
10:00 am
|
Wenzhi Mao |
Redundancy
and Diversity of Evolutionary Analysis |
|
|
| 05/23 |
10:00 am
|
Murat Can Cobanoglu |
Predicting
polypharmacology and its applications to drug discovery |
|
|
| 05/17 |
12:30 pm
|
Feizhuo Kaitlyn Hu |
Target
and pathway identification using quantitative systems pharmacology methods |
|
|
| 05/02 |
3:30 pm
|
Anindita Dutta |
Handling
noise in correlated mutation analysis |
Detection
and reduction of evolutionary noise in correlated mutation analysis |
|
| 04/11 |
3:30 pm
|
Filippo Pullara |
Evaluation
of conformational difference between functional and PDB structures |
|
|
| 04/03 |
11:00 am
|
Elia Zomot |
Identification
of conformational transitions in the outward-facing structure of the sodium-coupled
leucine transporter, LeuT |
|
|
| 03/21 |
3:30 pm
|
Mary Cheng |
Coupling
of global and local changes directs substrate binding to a neurotransmitter-sodium
symporter orthologue LeuT |
|
|
| 02/14 |
3:30 pm
|
Mert Gur |
Protein
structures from evolutionary sequence variations: Part 2
|
Hopf
et al, 2012
|
|
| 01/31 |
3:30 pm
|
Tim Lezon |
Protein
structures from evolutionary sequence variations: Part 1
|
Morcos
et al, 2011
Supporting
Information
MaxEnt
Primer
|
|
| 01/03 |
3:30 pm
|
Indira Shrivastava |
Role
of VDAC in Mitochondrial Apoptosis |
|
|
|
Fall 2012 (September - December 2012)
|
|
|
|
|
|
|
|
| 12/13 |
3:30 pm
|
Anindita Dutta |
ProDy
EVOL: Sequence and Dynamics Comparison Tool |
|
|
| 12/06 |
3:45 pm
|
Ivet Bahar |
Protein
Dynamics and Relevance to Sequence Evolution and Drug Discovery |
|
|
| 11/15 |
3:30 pm
|
Ignacio General |
Allosteric
signal transmission in the nucleotide-binding of 70-kDa heat shock protein (Hsp70)
molecular chaperones |
|
|
| 10/25 |
3:30 pm
|
Ahmet Bakan |
Structure-Based
Drug Discovery |
|
|
| 10/18 |
3:30 pm
|
Kristina Paris |
Hitting
a moving target: Druggability, flexibility, and stability in c-Myc inhibitor
design |
|
|
| 09/27 |
3:30 pm
|
Murat Can Cobanoglu |
Repurposing
a known drug for Alpha 1-Antitrypsin Deficiency |
|
|
| 09/20 |
3:30 pm
|
Ahmet Bakan |
Virtual
Screening for Cyt c Inhibitor Discovery |
|
|
| 09/13 |
3:30 pm
|
Elia Zomot |
A
conformational switch in a partially unwound helix selectively determines the pathway
for substrate release from the carnitine/gamma-butyrobetaine antiporter CaiT |
|
|
|
Spring/Summer 2012 (January - August 2012)
|
|
|
|
|
|
|
|
| 08/23 |
3:30 pm
|
Mary Cheng |
Investigation
of Sodium-coupled Neurotransmitter Transporters |
|
|
| 08/16 |
3:30 pm
|
Fei Lu |
Molecular
Dynamics Simulation of Phenazine Biosynthetic enzyme PhzF |
|
|
| 08/09 |
3:30 pm
|
Mert Gur |
Transition
pathways of proteins explored by Monte Carlo sampling of collective modes coupled with
MD |
|
|
| 08/02 |
12:00 pm
|
Tim Lezon |
A
hilbert space formalism to analysis of high content screening data |
|
|
| 07/05 |
3:30 pm
|
Indira Shrivastava |
HIV-Envelope
Protein gp120 |
|
|
| 05/31 |
3:30 pm
|
Anindita Dutta |
Druggability
of iGluR NTDs |
|
|
| 05/24 |
3:30 pm
|
Ignacio General |
Interdomain
Allostery of Heat Shock Protein 70 |
|
|
| 04/26 |
3:30 pm
|
Kristina Paris |
Flexibility,
Stability, and Druggability: Implications for c-Myc-Max inhibitor design |
|
|
| 04/12 |
3:30 pm
|
Elia Zomot |
Activation
mechanism of the beta2-adrenergic receptor |
Dror
et al. PNAS 2011
Rasmussen
et al. Nature 2011 |
|
| 03/29 |
3:30 pm
|
Ahmet Bakan |
Prediction
of Drug Combinations by Integrating Molecular and Pharmacological Data |
Zhao
et al.PlosCompBio 2011 |
|
| 03/15 |
3:30 pm
|
Murat Can Cobanoglu |
Drug
Target Interaction Discovery using Active Learning |
|
|
| 03/01 |
3:30 pm
|
Mert Gur |
The
Substrate-Driven Transition of Dopamine Transporter |
Shan
et al.Plos One 2011 |
|
| 02/16 |
4:00 pm
|
Hagai Meirovitch |
Calculation
of the Absolute Free Energy of Binding of Protein-Ligand Complexes |
|
|
| 02/09 |
4:00 pm
|
Tim Lezon |
Drug
Sensitivity Encoded in Population Heterogeneity |
Singh
et al. Mol Sys Biol 2010 |
|
| 01/27 |
11:00 am
|
Ignacio General |
Binding
Free Energy of the Avidin-Biotin System |
|
|
|
Fall 2011 (September - December 2011)
|
|
|
|
|
|
|
|
| 12/15 |
11:00 am
|
Indira Shrivastava |
|
Vijayan
et al. PCCP 2011 |
|
| 12/01 |
11:00 am
|
Murat Can Cobanoglu |
Predicting
Polypharmacology |
|
|
| 11/10 |
11:00 am
|
Kristina Paris |
FEP/H-REMD
for Absolute Ligand Binding Free Energy Calculations |
Jiang
and Roux. JCTC 2010
Sugita
and Okamoto. ChemPhysLett 1999
Wang
et al. Biophys J. 2006 |
|
| 10/03 |
11:00 am
|
Anindita Dutta |
Thesis Proposal Practice Talk |
|
|
| 10/27 |
11:00 am
|
Elia Zomot |
Pathway
and Mechanism of Drug Binding to G-protein-coupled Receptors |
Dror
et al. PNAS 2011 |
|
| 09/29 |
11:00 am
|
Ahmet Bakan |
The
Importance of Discerning Shape in Molecular Pharmacology |
Yera
et al. J Med Chem 2011
Kortagere
et al. TIPS 2008 |
|
| 09/22 |
10:30 am
|
Ying Liu |
Thesis Defense Practice |
|
|
|
Spring/Summer 2011 (January - August 2011)
|
|
|
|
|
|
|
|
| 04/21 |
9:30 am
|
Lin Liu |
|
Morcos
et al.PlosCompBio 2010.pdf |
|
| 04/14 |
9:30 am
|
Lidio Meireles |
CG-NMA
for Modeling Protein Conformational Changes upon Ligand Binding |
|
|
| 03/31 |
9:30 am
|
Anindita Dutta |
Computational
methods for identifying a layered allosteric regulatory mechanism for ALS-causing
mutations of Cu-Zn superoxide dismutase 1 |
Schuyler
et al. Proteins 2010 |
|
| 03/10 |
9:30 am
|
|
Discuss Lab Showcase |
|
|
| 03/03 |
9:30 am
|
Elia Zomot |
Microsecond
simulations of the aspartate transporter GltPh on the ANTON machine |
|
|
| 02/17 |
9:30 am
|
Ying Liu |
Deformation
Modes of Protein Families |
Orozco
et al Structure 2010
Orozco
et al BMC Bioinformatics 2009 |
|
| 02/10 |
9:30 am
|
Ahmet Bakan |
A
ML-based method to improve docking scoring functions and its application to drug
repurposing |
ML_Docking_Bourne_JCIM_2011
|
|
| 02/03 |
9:30 am
|
Divesh Bhatt |
Proteome-wide
study of PTS1-Pexp5 affinities |
Ghosh&Berg
JACS 2010 |
|
| 01/20 |
9:30 am
|
Mert Gur |
Finding
Transition Pathways Using the String Method with Swarms of Trajectories |
Roux
et al J.Phys.Chem. 2008 |
|
| 01/13 |
9:30 am
|
Muratcan Cobanoglu |
Predicting
Drug-Target Interactions
Classification
of GPCRs Using Family Specific Motifs |
|
|
|
Fall 2010 (September - December 2010)
|
|
|
|
|
|
|
|
| 12/22 |
1:30 pm
|
Tim Lezon |
Is
Protein Folding Sub-Diffusive? |
Sergei
Krivov, PLoS 2010. |
|
| 12/15 |
1:30 pm
|
Indira Shrivastava |
Combining
an Elastic Network with a Coarse-Grained Molecular Force Field: Structure, Dynamics,
and Intermolecular Recognition |
J.
Chem. Theory Comput. 2009 |
|
| 11/17 |
1:30 pm
|
Lin Liu |
Self-Guided
Langevin Dynamics Simulation Method (SGLD) |
Self-guided
Langevin Dynamics (Wu and Brooks, 2003) Self-guided
MD simulation (Wu and Wang, 1998) |
|
| 11/10 |
3:00 pm
|
Anindita Dutta |
Dynamics
of Lactose Permease (LacY) and other MFS proteins |
SGLD-Brooks
|
|
| 11/04 |
1:00 pm
|
Lidio Meireles |
Fragment-Based
Design of Molecular Mimicry |
|
|
| 10/06 |
1:30 pm
|
Elia Zomot |
Protonation
of Glutamate-208 Induces the Release of Agmatine in Outward-Facing Conformation of
Arginine/Agmatine Antiporter (AdiC) |
|
|
| 9/29 |
1:30 pm
|
Ying Liu |
Residue
Mobility and Function |
Lunde
et al. (2007)
Yogurtcu et al. (2008) |
|
| 9/23 |
4:00 pm
|
Ahmet Bakan |
Prody Demo |
|
|
| 9/15 |
1:30 pm
|
Divesh Bhatt |
Path
Sampling |
|
|
|
|
|
|
|
|
|
| 9/1 |
11:30 am
|
Ahmet Bakan
|
NMWiz
Tutorial |
|
|
|
|
|
|
|
|
|
Spring/Summer 201
0 (January
- August
2010)
|
|
|
|
|
|
|
| 8/18 |
1:00 pm
|
Tim Lezon
|
Statistical
Analysis of Protein Structural Dynamics (cont'd)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 8/11 |
11:00 am
|
Tim Lezon
|
Statistical
Analysis of Protein Structural Dynamics
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 7/28 |
11:00 am
|
Lin Liu |
Motions
extracted from MD simulations are robust
|
Senet
et al. (2008) Liu
et al. (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 7/19 |
11:30 am
|
I. Shrivastava |
Single
Molecule Dynamics of Gating in a Neurotransmitter Transporter Homolog
|
Zhao
et al. (2010)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 6/16 |
11:00 am
|
Anindita Dutta |
Coarse-grained
modeling of protein receptors
|
Balabin
et al. (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 6/2 |
11:00 am
|
Lidio Meireles |
Recore
|
Maass
et al. (2007) |
|
|
|
|
|
|
|
|
|
|
|
|
|
| 5/18 |
11:00 am
|
Elia Zomot |
AdiC1:
a system for extrusion of protons |
Gao
et al. (2009) Gao
et al. (2010) |
|
|
|
|
|
|
|
|
|
|
|
|
|
| 4/21 |
11:00 am
|
Literature Club |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 4/14 |
11:00 am
|
I. Shrivastava |
Structure
of an AMPA-Subtype Glutamate Receptor
|
Sobolevsky
et al. (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 4/7 |
11:00 am
|
Ahmet Bakan |
ProDy
Introduction |
ProDy
Documentation Download
ProDy
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 3/31 |
11:00 am
|
Ying Liu |
the
Relation between Intrinsic Dynamics and Sequence Variation
|
Mittermaier
et al. (2003)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 3/24 |
11:00 am
|
Anindita Dutta
Lidio Meireles
Ying Liu
Lin Liu
J. DeChancie
|
Overview
Substrate
Binding Site
Inhibition
Mechnism of LeuT and GltPh
Gating
Mechnism of LeuT and GltPh
|
Krishnamurthy
et al. (2009)
Gouaux
(2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 3/10 |
11:00 am
|
Ahmet Bakan
Elia Zomot
I. Shrivastava
Tim Lezon
|
LeuT-vSGLT
alignment
Neurotransmitter
Transporters
Symmetry
in Topology of SSS and NSS transporters
>Incorporating
membrane effects into ANM
|
Krishnamurthy
et al. (2009)
Gouaux
(2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 3/3 |
11:00 am
|
Lin Liu |
Analysis
of Sub-τc and Supra-τc Motions in Protein GB1
|
Bui
et al. (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 2/17 |
11:00 am
|
J. DeChancie |
Simulation
of GltPh Gate Opening
|
Reyes
et al. (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 2/3 |
11:00 am
|
Tim Lezon |
Random
Matrix
|
Potestio
et al. (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1/20 |
12:00 am
|
Bahar Group |
General
Discussion
|
|
|
|
|
|
|
|
|
Fall 200
9 (August
- December
2009)
|
|
|
|
|
|
| 12/16 |
11:30 am
|
Ivet Bahar |
Lecture on
Elastic Network Models and Normal Mode Analysis: Historic Remark
and Theretical Basis |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 12/9 |
11:30 am
|
Nicki Zevola |
Diagnosing
and exploiting cancer's addiction to blocks in apoptosis through the
Bcl-2 pathway |
Letai
(2008)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 12/2 |
11:30 am
|
Ahmet Bakan |
Ph.D. Thesis Defense
Rehearsal |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 11/4 |
11:30 am
|
Anindita Dutta |
Protein
Dynamism and Evolvability |
Tokuriki
and Tawfik (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 10/28 |
11:30 am
|
Lidio Meireles |
Fragment-Based Drug Discovery |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 10/14 |
11:30 am
|
I. Shrivastava |
Inherent
Dynamics of Acid Sensing Ion Channel |
Yang
et al. (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 10/7 |
11:30 am
|
Elia Zomot |
Computational
Analysis of vSGLT
|
Faham
et al. (2008)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 9/29 |
4:00 pm
|
Ying Liu |
Dynamics-Based
Alignment
Derivation
of Equation (4) CATH
|
Zen
et al. (2008) Zen
et al. (2009)
Hinsen
et al. (2000)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 9/23 |
11:30 am
|
Lin Liu |
Kinetic
Studies of Domain Swapped Proteins
|
Samson
and Levitt (2008)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 9/16 |
11:30 am
|
Tim Lezon |
Non-uniqueness
of the Protein Structure
|
Burra
et al. (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 9/2 |
11:30 am
|
J. DeChancie |
Structure
of a Na-independent AA Transporter
|
Shaffer
et al. (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 8/26 |
12:30 pm
|
Anindita Dutta |
Metal-binding
residues are distinguished by lower mobilities and efficient
signal propagation
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Spring 200
9 (January
- April
2009)
|
|
|
|
|
| 8/19 |
12:30 pm
|
Ahmet Bakan |
Binding
Site Detection and Druggability
Index from First Principles
|
Seco
et al. (2009)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 7/22 |
2:00 pm
|
Zheng Yang |
Thesis
Defense Rehearsal
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
| 6/24 |
9:30 pm
|
Group Discussion |
Summary1
Summary
2
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
| 6/17 |
12:30 pm
|
Elia Zomot
|
Substrate
Binding and the Occluded State in the Leucine Transporter
|
Celik
et al. (2008) Singh
et al. (2008)
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
| 5/27 |
12:30 pm
|
Lee-wei Yang |
Intrinsic
Dynamic Domains
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
| 5/20 |
12:30 pm
|
Tim Lezon
|
Optimizing
GNM Spring Constants
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| 5/12 |
10:30 pm
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Lin Liu
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Computational
Studies of Domain Swapping
|
Sirota
et al. (2008)
Ding
and et al. (2006) |
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| 5/6 |
12:00 am
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Ying Liu
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Central
Residues Crucial to Maintain Short Paths in Network Communication
|
del
Sol et al. (2006)
Watts
and Strogatz (1998) |
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| 4/29 |
12:30 pm
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J. DeChancie
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Structural
Basis for Sulfhydryl Oxidase Ero1p Regulation |
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| 4/15 |
12:30 pm
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Ahmet Bakan
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MAP
Kinase Phosphatase Family |
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| 4/1 |
12:30 pm
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I. Shrivastava
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Glutamate
Transporter: Gltph |
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| 3/25 |
12:30 pm
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Nicki Zevola
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Structure
of BH3 Domains |
Day et al. (2008) |
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| 2/25 |
12:30 pm
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Enrique Marcos
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Intermediates
in Phosphoryl Transfer Reactions
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Marcos
et al (2008)
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| 2/18 |
12:30 pm
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Anindita Dutta
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Zheng
et al (2007)
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| 2/11 |
12:30 pm
|
Ying Liu
|
A
Hierarchy of Timescales in Protein Dynamics
|
Henzler-Wildman
et al (2007a)
Henzler-Wildman
et al (2007b)
>
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| 2/4 |
12:30 pm
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Lin Liu
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Comparative
Analysis of the Equilibrium Dynamics of Designed Protein
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| 1/28 |
12:30 pm
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Tim Lezon
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Estimating
the absolute time scales of ANM
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| 1/21 |
12:30 pm
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Zheng Yang
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Allosteric
Transitions of Supramolecular Systems |
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| 1/14 |
12:30 pm
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Yan Gu |
Dynamics
from RDC-Derived Ubiquitin Ensemble
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Lange
et al (2008) |
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| 1/6 |
11:30
am
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J. DeChancie |
Milestones
in the Activation of a GPCR
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Chipot
(2008) |
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Fall 2008
(September -
December 2008)
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| 12/18 |
3:30
pm
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Ahmet Bakan
|
Normal Mode
Analysis in Molecular Docking
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| 12/2 |
11:00
am
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Yan Gu
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I-TASSER
Server
|
Yang
Zhang (2008)
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| 11/25 |
10:30
am
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I. Shrivastava |
Convergence
of MD Simulations of Membrane Proteins
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Grossfield
et al. (2007)
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| 11/18 |
3:30
pm
|
Ying Liu
Zheng Yang
|
Evolutionary
Trace Method
Min
Action Path
|
Lichtarge
et al. (1996)
Franklin
er al. (2007)
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| 11/11 |
11:30
am
|
Ivet Bahar |
Guidelines
and Review
|
Eyal
and Bahar (2008) |
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Lin Liu |
Topological
Determinants of Protein Domain Swapping
|
Ding
and et al. (2006)
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Spring 2008 (January
-
April 2008)
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| 5/8 |
4:30pm |
Suvrajit Maji |
Formal
Analysis of
Gene Regulatory Network |
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| 5/1 |
4:00pm |
Ying Liu
|
Hsp
Project
Progress Report |
Swain
et
al. (2007) Dunn
et al. (2007)
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| 4/24 |
3:30pm |
Ivet Bahar
Ahmet Bakan
Basak Isin |
NMA
in Drug Discovery |
Floquet
et
al. (2006) Cavasotto
et al. (2004)
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| 4/10 |
3:30pm |
Eran Eyal |
Anisotropic
Response of Proteins to External Forces |
Eyal
and Bahar (2008) |
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| 4/3 |
3:30pm |
Yan Gu
|
A
Putative
Aspartate Permission Pathway |
Liu
et
al. (2008)
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| 3/20 |
3:30pm |
|
List of Papers to be
Discussed
|
Ivetac
et al. (2007) Fares
et
al. (2006) Qian_et
al. (2004)
Aden
and Wolf-Watz. (2007) Liu
et
al. (2008) Floquet
et
al. (2006)
Dyer_et
al. (2007) Zheng
et al. (2007)
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| 3/6 |
3:30pm |
Rakesh Mishra
|
Rotation Project:
Conformational Flexibilities
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| 2/28 |
3:30pm |
Zheng Yang
|
Spherical
Proteins Studied by Elasticity
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| 2/21 |
3:30pm |
Lin Liu
|
Comparison
of NMR and X-Ray Data
|
Yang
et
al. (2007)
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| 2/14 |
3:30
pm
|
Basak Isin
I. Shrivastava
Ahmet Bakan
|
Combining
Conformational Sampling and ENM
|
Schroder
et al. (2007)
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| 2/7 |
3:30
pm
|
Ivet Bahar |
Guidelines
|
Link
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Fall 2007 (September - December 2007)
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12/19
|
3:30pm
|
Basak Isin
|
Allosteric Pathways
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11/26
|
3:30
pm
|
Zheng Yang |
Spherical_Proteins
|
Coccia
et al. (1998) |
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11/5
|
3:30
pm
|
Yan Gu |
Research
Description |
Wang
et al. (2006) |
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10/29
|
3:30
pm
|
I. Shrivastava |
Electrostatic
Basis for Enzyme Catalysis |
Warshel
et al.
(1989) Warshel
et al. (2006) |
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10/22
|
3:30
pm
|
C.Chennubhotla |
Allosteric
Changes in Conformations |
Ming_wall_prl (2005)
Ming_wall_prl_erratum (2006)
Ming_wall_jmb
(2006) Zheng_Brooks
(2005)
Handout1
Handout2
Handout3
|
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| 10/19 |
4:00
pm
|
Ying Liu |
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10/8
|
3:30
pm
|
Eran Eyal |
Correlated
Mutations and the Applications |
Halperin
et al.
(2006) |
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10/1
|
3:30
pm
|
Tim Lezon |
Promiscuity
of Drugs |
Agoston
et al.
(2005) Hopkins
et al. (2006) |
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9/24
|
3:30
pm
|
C.Chennubhotla
Suvrajit Maji |
Protein-Protein
Interaction Networks II |
Batada
et al. (2006)
Han
et al. (2004)
Bertin
et
al. (2007)
|
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| 9/10 |
3:30
pm
|
Ahmet Bakan
Ivet Bahar |
Alchemy
v.s. Umbrella: A Review
Umbrella
Sampling |
Torrie
et al. (1976) |
|
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| 9/4 |
3:30
pm
|
Lin Liu |
Study of
PRL-2 Phosphatease as a Drug Target
|
Stephens
et al. (2005) |
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8/27
|
3:30
pm
|
Ahmet Bakan
|
Predicting
Absolute Ligand Binding Free Energies |
Mobley
et al. (2007) |
|
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|
Suvrajit Maji
|
Protein-Protein
Interaction Networks I
|
Han
et al. (2004) Bertin
et
al. (2007)
|
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I. Shrivastava
|
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Hermann
et al.
(2007) |
|
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|
Ying Liu
|
Evolutionary Noise
Detection |
Noivirt
et al. (2005) |
|
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|
Fall/Spring 2006
|
|
9/29
|
12
:
00
pm
|
Ivet Bahar
|
(Continued
from 9/15)
|
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9/15
|
12
:
00
pm
|
Ivet Bahar
|
MD Trajectory Analysis
|
Garcia (1992) Hess (2000) Hess (2002) Flyvbjerg and Petersen (1989)
|
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9/8
|
12:00
pm
|
Dror Tobi
|
(Ch. 3, Linssen, 1998) Essential Dynamics
|
Amadei
et al.
(1993) van Aalten (1995)
|
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5/5
|
10
:00
am
|
I. Shrivastava
Basak Isin
|
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5/3
|
12
:
15
pm
|
Dr.
T Haliloglu
|
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4/18
|
2:00
pm
|
Chakra
Chennubhotla
|
Finding
Pathways of Allosteric Com-munication: Static and Dynamic Views
|
Can Conformational Changes
Be Described by Only a
Few Normal Modes. Petrone & Pande (2006)
|
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|
4/11
|
2
:
00
pm
|
Eran Eyal
|
(Continued
from last week)
|
((2) Comparing
protein-ligand docking programs Cole et al (2005) |
Presentation (Chuang)(3)
Hemagluttinin Presentation (Zheng)
|
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|
4/5
|
12
:
15
pm
|
Eran Eyal
|
ANM: evaluation, improvement and a new
web-based visualization tool
|
1) Receptor flexibility in
ligand docking through
normal modes Cavasotto et al (2005) |
Presentation (Basak)
|
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|
3/29
|
12
:
15
pm
|
Xiong Liu
|
Conservation profiles based on
n-gram patterns
|
Fight AIDS@Home - AUTODOCK
(The Scripps Institute) Presentation (Ahmet)
|
|
|
3/22
|
12
:
15
pm
|
Yingyu Wang
|
Comparison of dynamics characterized
by X-ray, NMR and GNM
|
Discovery of a novel class
of reversible
non-peptide caspase inhibitors via a structure-based approach. Fatturoso et al (2005) |
Presentation (Zerrin)
|
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|
3/15
|
12
:
15
pm
|
Lee-Wei Yang
|
Comparison of dynamics characterized by
X-ray, NMR and computations
|
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|
|
3/8
|
12
:
15
pm
|
Dror Tobi
|
(Continued
from last week)
|
Essential motions in a
fungal lipase with bound
substrate, inhibitor and product. Peters & Bywater (2002) |
Presentation (Zerrin)
|
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|
3/1
|
12
:
15
pm
|
Dror
Tobi
Indira Shrivastava
|
Identification of protein functionally
important regions using unique 3-grams
|
(1)
Protein dynamics and conformational transitions in allosteric proteins.
target="_blank">Jardetzky (1996) (2)
Energetics of Ion Conduction through the K+ Channel. Bernèche & Roux (2001) Presentation .. (Indira)
|
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|
2/24
|
3
:
15
pm
|
Tural Aksel
|
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|
2/17
|
2
:
30
pm
|
Chuang Wu
|
Topological basis of signal integration in
yeast transcription regulatory network
|
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|
2/1
|
12
:
15
pm
|
Zheng Yang
|
Update: Study of Virus Capsids
|
|
|
|
1/25
|
12
:
15
pm
|
Ahmet Bakan
|
Screening Chemical Libraries for
Compoundswith Cdc25B Activity
|
Characterization
of topological structure on
complex networks. Nakamura (2003)(Zerrin)
|
|
|
1/17
|
12
:
00
pm
|
Zerrin Bagci
|
Roles of Cooperativity and Nitric Oxide in
Regulating Apoptotic Response
|
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|
