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Computational Research in Molecular Chemistry
McCammon Lab Seminars

Weekly Meetings [archived]

Weekly meetings are held biweekly on Wednesdays from 11:30 AM to 1:00 PM in Urey Hall 2205 (Keck II). Catering is provided.

Current seminars

Date Speaker Title
January 8, 2014-No Group Meeting
January 15, 2014Ferran FeixasPlaying with reaction mechanisms, drug discovery, and protein folding: A brief overview of two years in the lab
January 22, 2014Changsun EunSequential enzyme reactions and electrostatic channeling
January 29, 2014Nuo WangA better mean field model: SMPB and its application to lipid bilayers
February 5, 2014-No Group Meeting
February 12, 2014Vince MetzgerInsights from molecular simulations and multi-scale biological modeling
February 19, 2014-No Group Meeting
February 26, 2014Pat BlachlyChanges in [4Fe-4S] coordination in the IspH catalytic cycle: Implications for drug design
March 5, 2014Leonardo BoechiDiscussing the role of water molecules in protein-ligand binding
March 12, 2014Andreas GoetzDipeptide aggregarion in aqueous solution: Performance of current force fields
March 19, 2014-No Group Meeting
March 26, 2014Ole AndersenElucidating the inhibitory mechanism of the serpin alpha-1 antitrypsin
April 2, 2014Chris McClendonDynamic architecture of a protein kinase
April 9, 2014Pete Kekenes-HuskeyDiffusional control of biochemical oscillations: A precedent for biological signaling
April 16, 2014Olivia KimCalculation of pH-dependent free energy of binding of host-guest complexes
April 23, 2014Gary HuberEfficient implementation of AGBNP implicit solvent force field for Brownian dynamics
April 30, 2014Steffen LindertFinding novel anticancer and antibacterial drug leads using CADD: Farnesyl diphosphate synthase (FPPS) and undecaprenyl diphosphate synthase (UPPS) inhibitors from in silico screening
May 7, 2014-No Group Meeting
May 14, 2014Adam van WartWISP: A computational approach towards research in allostery
May 21, 2014Pete Kekenes-HuskeyAn open discussion on the faculty job search and transition
May 28, 2014Victoria FeheraMD on T4 lysozyme cavity mutants: Observations of cavity fluidity, conformational selection, and ligand gating
June 4, 2014-No Group Meeting
June 11, 2014Joe KausComputer-aided drug design: Methods and applications
June 16, 2014Johannes SchonebergReaction-Diffusion Dynamics in Biological Systems: Theory, computation, modeling and simulation. Application to the visual cascade and the synaptic vesicle cycle
June 18, 2014-No Group Meeting
June 25, 2014Alisha CalimanExploring and characterizing the conformational spaces of S1pR1 and A2AAR for the treatment of multiple sclerosis
July 2, 2014-No Group Meeting
July 9, 2014Dahlia GoldfeldStudies of the muscarinic acetylcholine receptor (M2)
July 16, 2014-No Group Meeting
July 25, 2014Joanna TrylskaThe dynamics of ribosomal RNA as a tool to understand the specificity of ribosome inhibitors
July 30, 2014-No Group Meeting
August 6, 2014-No Group Meeting
August 13, 2014-No Group Meeting
August 20, 2014-No Group Meeting
August 27, 2014-No Group Meeting
September 3, 2014Nuo WangHow well can mean-field methods predict the ion distribution near biomolecules?
September 10, 2014-No Group Meeting
September 17, 2014Yinglong MiaoLigand binding of muscarinic G-protein coupled receptor
September 24, 2014-No Group Meeting
October 1, 2014-No Group Meeting
October 8, 2014Pekka PostilaMembrane and neurotransmitters
October 15, 2014Christopher LeeThings I'm working on: Passive membrane permeability, influenza virulence, and more
October 22, 2014-No Group Meeting
October 29, 2014-No Group Meeting
November 5, 2014Gary HuberContinuum-particulate methods in finding rates of reaction
November 12, 2014-No Group Meeting
November 19, 2014Ozlem Demirp53 Reactivation as a cancer therapy: Drugging a novel cryptic pocket
November 26, 2014-No Group Meeting
December 3, 2014Steffen LindertIterative cryoEM-guided molecular dynamics: Rosetta protein structure refinement protocol
December 10, 2014-No Group Meeting
December 17, 2014-No Group Meeting
December 24, 2014-No Group Meeting
December 31, 2014-No Group Meeting
January 7, 2015Steffen LindertThe power of computation in biology: Elucidation of atomic resolution protein structures from sparse experimental data and discovery of potent antibiotics against resistant bacteria
January 14, 2015-No Group Meeting
January 21, 2015Alisha CalimanCharacterizing and targeting sphingolipid receptor specificity
January 28, 2015-No Group Meeting
February 4, 2015-No Group Meeting
February 11, 2015Joe KausSampling in free energy calculations: How to deal with multiple binding poses in alchemical relative binding free energy calculations
February 18, 2015Yinglong MiaoIntegrative simulation and experimental studies of the cytochrome p450 and G-protein coupled receptor: From dynamics to function and drug design
February 25, 2015-No Group Meeting
March 4, 2015Nuo WangSubstrate channeling between the Human dihydrofolate reductase and thymidylate synthase
March 11, 2015Clarisse RicciFunctional aspects of peroxisome proliferator-activated receptors (PPARs) investigated by computational methods
March 18, 2015-No Group Meeting
March 25, 2015-No Group Meeting
April 1, 2015Christopher LeeEstimating the local diffusivity tensor: model building and validation
April 8, 2015-No Group Meeting
April 15, 2015Olivia KimIntegrating conformational and protonation equilibria in biomolecular modeling
April 22, 2015-No Group Meeting
April 29, 2015-No Group Meeting
May 6, 2015-No Group Meeting
May 13, 2015Mindy HuangComputational modeling of biomolecular systems: Insights into protein dynamics, free energy and peptide/ligand binding
May 20, 2015-No Group Meeting
May 27, 2015Niel HenriksenValidation of high-precision computational calorimetry approach for studying host-guest binding
June 3, 2015Gary HuberHybrid particle-continuum method for diffusing charged particles
June 10, 2015-No Group Meeting
June 17, 2015Alisha CalimanTargeting the sphingosine-11-phosphate receptor using virtual screening methods
June 24, 2015-No Group Meeting
July 1, 2015Yinglong MiaoGaussian accelerated molecular dynamics: Simultaneous unconstrained enhanced sampling and free energy calculation
July 8, 2015-No Group Meeting
July 15, 2015Nuo WangPredicting Binding Free Energy by Continuum Methods
July 22, 2015-No Group Meeting
July 29, 2015Ozlem DemirElucidating the Binding Interface Between Human Apobec3f and HIV-1 Vif
August 5, 2015-No Group meeting
August 12, 2015Clarisse RicciMolecular dynamics investigation of Plasmodium vivax GGPPS: principal motions and implications for computer-aided drug discovery
August 19, 2015-No Group Meeting
August 26, 2015-No Group Meeting
September 2, 2015Tavina ClaiborneProtein Kinases Dynamics and its Impact on Structure-based Drug Discovery
September 9, 2015-No Group Meeting
September 16, 2015Rob SwiftTraining Structure-Based Ensembles for Docking Profit
September 23, 2015-No Group Meeting
September 30, 2015-No Group Meeting
October 7, 2015Jamie SchifferDefining the dynamic structure of proteins by integrating computation and experiment
October 14, 2015-No Group Meeting
October 21, 2015-No Group Meeting
October 28, 2015Sophia HirakisInvestigating the sub-cellular dynamics of Calcium Induced Calcium Release in cardiac myocytes
November 4, 2015Bryn TaylorInvestigation of CCR2 druggability via in silico dynamics
November 11, 2015-No Group Meeting - Veterans Day
November 18, 2015-No Group Meeting
November 25, 2015-No Group Meeting - Eat lots of Turkey
December 2, 2015Jeffrey WagnerPOVME
December 9, 2015NBCR Seminar - Holst GroupReformulating Molecular Dynamics for Improved Efficiency and Error Quantification
December 16, 2015-No Group Meeting
December 23, 2015-No Group Meeting
December 30, 2015-No Group Meeting
January 6, 2016Yinglong MiaoComputer-Aided Drug Design and Improved Methodology for Biomolecular Modeling
January 13, 2016-No Group Meeting
January 20, 2016Jacob DurrantComputer-Aided Drug Design: From Basic Science to Clinical Applications
January 27, 2016-No Group Meeting
February 3, 2016Gary HuberHydrodynamic Interactions Among Complex Bodies Using Bead Models
February 10, 2016-No Group Meeting
February 17, 2016Giulia PalermoUnraveling the mechanistic basis of protein/nucleic acid systems via computational methods
February 24, 2016-No Group Meeting
March 2, 2016-No Group Meeting
March 9, 2016Siti AzmaEnsemble Docking to Nuclear Hormone Receptors
March 16, 2016-No Group Meeting
September 21, 2016Robert MalmstromAn ensemble view of protein-ligand interactions in a canonical signaling domain
September 28, 2016-No Group Meeting
October 5, 2016Clarisse RicciCoarse-graining solvation energies: the Martini-VISM method and future directions
October 12, 2016-No Group Meeting
October 19, 2016-No Group Meeting
October 26, 2016Emilia Pecora de BarrosElectrostatic interactions as mediators in the allosteric activation of PKA RIalpha
November 2, 2016--No Group Meeting
November 9, 2016-No Group Meeting
November 16, 2016--No Group Meeting
November 30, 2016--No Group Meeting
December 7, 2016Yinglong MiaoAccelerated Computer Simulations: Method Development and Applications in Drug Discovery
December 14, 2016Giulia PalermoUnraveling the mechanistic function of the CRISPR/Cas9 system via computational methods: progresses and novel ideas
December 21, 2016--No Group Meeting
December 28, 2016--No Group Meeting
January 4, 2017--No Group Meeting
January 11, 2017Christopher LeeInvestigating Transport Properties with Multi-Scale Computable Mesh Models from Heterogeneous Structural Datasets
January 18, 2017--No Group Meeting
January 25, 2017Sophia HirakisParticle-based approaches to clearing calcium: a protein landscape model of the Sarco/Endoplasmic reticulum Calcium-ATPase (SERCA) pump for sub-cellular stochastic models
February 1, 2017--No Group Meeting
February 8, 2017Alisha CalimanExploring and Characterizing the Conformational Spaces of A2AAR and S1PR1 for the Treatment of Immunological Diseases
February 15, 2017--No Group Meeting
February 22, 2017Tavina OffuttDynamics of the R175H Mutant in the Full-Length p53 Tetramer System
March 1, 2017--No Group Meeting
March 8, 2017Gary HuberBrownye 2.0: more flexible software
March 15, 2017--No Group Meeting
March 22, 2017Ozlem DemirDynamics of Apobec3b Enzyme
March 29, 2017--No Group Meeting
April 5, 2017--No Group Meeting
April 12, 2017Lorenzo CasalinoRNA splicing: A Computational Journey from Ribozymes to Spliceosome
April 19, 2017--No Group Meeting
April 26, 2017Mindy HuangLigand association and dissociation: Case of p38 kinase
May 3, 2017--No Group Meeting
May 10, 2017Jeffrey WagnerEverything you wanted to know about APOBEC, but were too afraid to ask
May 17, 2017--No Group Meeting
May 24, 2017--Cancelled
May 31, 2017Frank NoeFrom all-atom molecular kinetics beyond the seconds timescale to cellular signal transduction
June 7, 2017--Cancelled
June 14, 2017Dan MermelsteinFast, accurate pH dependent alchemical free energy calculations towards rational drug design
June 21, 2017--No Group Meeting
June 28, 2017Ashay PatelStructure and dynamics of acyl carrier proteins and their partner proteins
July 5, 2017--No Group Meeting
July 12, 2017Mattia BernettiCharacterization of protein-ligand binding pathways via computational methods
July 19, 2017--No Group Meeting
July 26, 2017--No Group Meeting
August 2, 2017--No Group Meeting
August 9, 2017Ben JaggerQuantitative Ranking of Small Molecule Off Rates for the Beta-Cyclodextrin Host System using SEEKR
August 16, 2017--No Group Meeting
August 23, 2017Bryn TaylorDifferential Dynamics and Druggability of Chemokine Receptor CCR2
August 30, 2017--No Group Meeting
September 6, 2017Terra SztainStructure and Dynamics of Acyl Carrier Proteins
September 13, 2017--No Group Meeting
September 20, 2017Jamie SchifferTBD
September 27, 2017--No Group Meeting
October 4, 2017Clarisse RicciCurrent progress (and future directions) on the Variational Implicit Solvent Method (VISM)
October 11, 2017Christopher LeeWorking Towards GAMer 2.0: Adaptive Mesh Generation for Biological Datasets
October 18, 2017--No Group Meeting
October 25, 2017--No Group Meeting
November 1, 2017Emilia Pecora de BarrosMD in protein design: insights from simulations of designed ligand-binding proteins
November 8, 2017--No Group Meeting
November 15, 2017--No Group Meeting
November 22, 2017--No Group Meeting
November 29, 2017Sarah KochanekWhole-Virion Simulation of Influenza Reveals Novel Druggable Pockets on Surface Glycoproteins
December 6, 2017--No Group Meeting
December 13, 2017Pek IeongMechanistic insight on LpxH Cap Dynamic and Regulation
December 20, 2017--No Group Meeting
December 27, 2017--No Group Meeting
January 3, 2018--No Group Meeting
January 10, 2018Giulia PalermoMolecular mechanism and rational design of the CRISPR-Cas9 system via computational methods
January 17, 2018--No Group Meeting
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