Feb 10, 2004 Team Talent Life Sciences: Model Systems for the protein folding problem Jason Crain University of Edinburgh IBM T.J. Watson Research Center.

Slides:

Advertisements

Similar presentations

Dynamics of Social Interactions at Short Timescales G. Bianconi Department of Physics, Northeastern University SAMSI Workshop: Dynamics of networks SAMSI,

Advertisements

ETC Trento Workshop Spectral properties of complex networks

Gelation Routes in Colloidal Systems Emanuela Zaccarelli Dipartimento di Fisica & SOFT Complex Dynamics in Structured Systems Università La Sapienza, Roma.

Diffusion of Interacting Particles in One dimension Deepak Kumar School of Physical Sciences Jawaharlal Nehru University New Delhi IITM, Chennai Nov. 9,

Surface activity profiling: a novel physicochemical tool for the prediction of blood-brain-barrier permeation Paavo K.J. Kinnunen Helsinki Biophysics &

Combining atomic-level Molecular Dynamics with coarse-grained Monte-Carlo dynamics Andrzej Koliński Laboratory of Theory of Biopolymers, Faculty of Chemistry,

Computational methods in molecular biophysics (examples of solving real biological problems) EXAMPLE I: THE PROTEIN FOLDING PROBLEM Alexey Onufriev, Virginia.

Anchored Periplasmic Expression (APEx) A Powerful Technology for Antibody Discovery and Combinatorial Protein Library Screening George Georgiou, Dept.

Screening of Water Dipoles inside Finite-Length Carbon Nanotubes Yan Li, Deyu Lu,Slava Rotkin Klaus Schulten and Umberto Ravaioli Beckman Institute, UIUC.

Presented by ORNL–University Partnerships in Computational Biology Igor B. Jouline (Zhulin) Joint Institute for Computational Sciences The University of.

Protein Rigidity and Flexibility: Applications to Folding A.J. Rader University of Pittsburgh Center for Computational Biology & Bioinformatics.

27803::Systems Biology1CBS, Department of Systems Biology Schedule for the Afternoon 13:00 – 13:30ChIP-chip lecture 13:30 – 14:30Exercise 14:30 – 14:45Break.

Protein folding kinetics and more Chi-Lun Lee ( 李紀倫 ) Department of Physics National Central University.

Schedule for the Afternoon 13:00 – 13:30ChIP-chip lecture 13:30 – 14:30Exercise 14:30 – 14:45Break 14:45 – 15:15Regulatory pathways lecture 15:15 – 15:45Exercise.

Indiana University Bloomington, IN Junguk Hur Computational Omics Lab School of Informatics Differential location analysis A novel approach to detecting.

GTL Facilities Characterization and Imaging of Molecular Machines Lee Makowski.

Water. Buried Water Molecules -Binding -Reactions Surface Water Molecules -Structure -Dynamics -Effect on Protein Motions Water in and on Proteins.

九大数理集中講義 Comparison, Analysis, and Control of Biological Networks (3) Domain-Based Mathematical Models for Protein Evolution Tatsuya Akutsu Bioinformatics.

Max Shokhirev BIOC585 December 2007

Shankar Subramaniam University of California at San Diego Data to Biology.

Structural Bioinformatics R. Sowdhamini National Centre for Biological Sciences Tata Institute of Fundamental Research Bangalore, INDIA.

A computational study of shear banding in reversible associating polymers J. Billen, J. Stegen +, A.R.C. Baljon San Diego State University + Eindhoven.

P-1 Genetically controlled fusion, exocytosis and fission of artificial vesicles E. Boenzli 1, M. Hadorn 1, D. de Lucrezia 2, M. G. Jørgensen 3, P. Eggenberger.

Unconserved Amino Acid Sequences in V3 Domain of gp120 Show No Significant Correlation to Altered Folding and Function Bobak Seddighzadeh Alex George.

BL5203 Molecular Recognition & Interaction Section D: Molecular Modeling. Chen Yu Zong Department of Computational Science National University of Singapore.

Molecular modeling of protein-ligand interactions: Detailed simulations of a biotin-streptavidin complex Prof. Terry P. Lybrand Vanderbilt University Center.

Genetically controlled fusion, exocytosis and fission of artificial vesicles E. Boenzli 1, M. Hadorn 1, D. de Lucrezia 2, M. G. Jørgensen 3, P. Eggenberger.

Simulations of associating polymers under shear J. Billen, M. Wilson, A.R.C. Baljon San Diego State University Funded by:

S1 Entrapment of water by subunit c of ATP synthase. Julie E M McGeoch † & Malcolm W McGeoch* † Department of Molecular and Cellular Biology, Harvard University,

1 Network Motifs in Prebiotic Metabolic Networks Omer Markovitch and Doron Lancet, Department of Molecular Genetics, Weizmann Institute of Science.

Outline GB1 chameleon 8-mer Peptide MD GB1 folding pathway Hierarchic folding Conservation scores.

8 years in the lab Outlines Job hunt My future lab.

Protein Properties Function, structure Residue features Targeting Post-trans modifications BIO520 BioinformaticsJim Lund Reading: Chapter , 11.7,

Chymotrypsin Lecture Aims: to understand (1) the catalytic strategies used by enzymes and (2) the mechanism of chymotrypsin.

DAVID Bioinformatics Web Site 2012 – 2015 David Huang, MD LMS/CCR/NCI

10 Feb 2004Team Talent Review1 agenda OPEN SESSION 1300 Introduction & Roadmaps Kenway On-going projects 1305 OGSA-DAIT + Web Services Resource Framework.

Molecular Dynamics Arjan van der Vaart PSF346 Center for Biological Physics Department of Chemistry and Biochemistry Arizona State.

Visually Demonstrating the Principles of Protein Folding Bill McClung, Jeff Schwehm, Greg Wolffe.

Protein Folding recognition with Committee Machine Mika Takata.

ABBIE CHEUNG TERTIARY & QUATERNARY ORGANIZATION. TERTIARY ORGANIZATION The third level in protein organization. Polypeptide chain folded into a three-dimensional.

Brigita Urbanc, Luis Cruz, Shouyong Peng, Jose Borreguero, Alfonso Lam

Molecular Modeling and Visualization Tools in Science Education ChemSenseChemViz Molecular Workbench Virtual Molecular Dynamics Lab NARST Convention Philadelphia,

FOLDING TRANSITION AND „FOLDABILITY”

University of California at San Diego

Simplified picture of the principles used for multiple copy simultaneous search (MCSS) and for computational combinatorial ligand design (CCLD). Simplified.

Permeability of gases in glassy polymers by computer simulation

University of California at San Diego

A first-principles-based theoretical study

Structure-based ligand design toward a selective M3R antagonist.

Nat. Rev. Endocrinol. doi: /nrendo

Blood Volume 92(10): November 15, 1998

Polydactyly L.A. Lettice, et al. Proc. Natl. Acad. Sci. USA 2002; 99(11):

Volume 2, Issue 3, Pages xi-xiii (July 2006)

Simulations capture the experimental force profiles for mutant I27 domains. Simulations capture the experimental force profiles for mutant I27 domains.

MD Studies of LDL and HDL phases of Supercooled Water

Mr. Watson World History

Schedule for the Afternoon

Department of Physics, Fudan University, Shanghai, China

The 3D models in part a are reproduced with permission from Daum, B

Autoinhibition of kinesin-1 motor

Figure 5 Forms of information for programming self-assembly

Protein Folding and Unfolding at Atomic Resolution

Earlier Studies Background: Laminin is one of the basement proteins.

Atomistic Simulations of Viral Insulin Like and Insulin Mimetic Peptides Evan Redfearn and Dr. Harish Vashisth Department of Chemical Engineering, University.

Fig. 3 Phase-contrast imaging.

Interaction of A28-35 with POPG lipid bilayer

Phase transition of nanotube-confined water driven by electric field

Laboratory tests. Laboratory tests. (A) Time lapse of the landing process, refilling process, and subsequent launch. (B) Comparison of position and velocity.

Fig. 2 Emulsion interfacial polymerization mechanism for producing Janus particles. Emulsion interfacial polymerization mechanism for producing Janus particles.

Fig. 5 Classical MD simulations.

Presentation transcript:

Feb 10, 2004 Team Talent Life Sciences: Model Systems for the protein folding problem Jason Crain University of Edinburgh IBM T.J. Watson Research Center (May-October,2004) Feb 10, 2004

Team Talent Do we get hydrophobic / hydrophilic interactions right in simple systems? Transition to hydrophilic exterior is not simple – shows common features B. David Silverman, Ruhong Zhou "Hydrophobic moments of protein structures: Spatially profiling the distribution", Proc. Natl. Acad. Sci. U.S.A. 98, , (2001). IBM –Bioinformatics, Computational Biology + Physical Sciences

Feb 10, 2004 Team Talent Micro-segregation and mesoscale structure in simple aqueous alcohols Dixit & Crain Nature, 2002 Dixit & Crain Europhys. Lett Experiment & simulation (DFT) in Good agreement on local structure(PRL, 2004 submitted) Modifications to water structure (Crain et al. Research Developments in Molecular Physics,2004) 2-phase Percolation (Dougan, Soper & Crain, Nature Submitted 2004) Experiment (iso-sub ND) Simulations (Classical MD)

Feb 10, 2004 Team Talent Toward “real” biology: isomerization of aqueous peptide fragments The Model sysetm – N-methylacetamide - consisting of a single peptide unit –trialanine New IBM Research – Edinburgh project