Classification of Heterogeneous Particles in Cryo-EM Reconstructions

CVC Seminar Wed Sept 21 1:15-2:30pm ACES 4.304

Speaker: E. Greg Daniel

Title: Classification of Heterogeneous Particles in Cryo-EM Reconstructions

Abstract: One of the common approaches in single particle reconstruction of viruses is Cryo-Electron Microscopy. In this approach, a large sample of particles (with unknown orientations) are produced, and then an electron micrograph is created . . . → Read More: Classification of Heterogeneous Particles in Cryo-EM Reconstructions

CVC Seminar Wed Sept 14 1:15-2:30pm ACES 4.304

Speaker: Qiming Yuan

Title: Learning Parameters in F2Dock

Abstract: Choosing parameters for a scoring function plays an important role in protein-protein docking prediction. Some previous approaches only rely on empirical statistics, positive examples or average negative examples. We formulate a learning framework for deriving parameters for scoring function based on observed . . . → Read More:

VolumeRover updates

Some newer binaries were posted not long ago for Mac OSX, Windows and Linux. Also, automatic twitter updates from svn commits broke earlier this summer but are now working again. Check it out!   Note, if the commit message is longer than ~134 characters, it will be silently ignored and not posted to twitter.  Will . . . → Read More: VolumeRover updates

Polyhedron Separation

CVC Seminar Wed Sept 7 1:15-2:30pm ACES 4.304

Speaker: John Edwards

Title: Polyhedron Separation

Abstract: A polyhedron K is said to separate polyhedra P and Q if any path from any point on the surface of Q to any point on the surface of P passes through the surface of K. An optimal separating polyhedron among all K . . . → Read More: Polyhedron Separation

Parallelizing molecular energy and force calculations using cilk++ and CUDA

CVC Seminar Wed Aug 31 1:15-2:30pm ACES 4.304

Deukhyun Cha

Parallelizing molecular energy and force calculations using cilk++ and CUDA

Parallelization is an obvious tool for accelerating serial algorithms, but effective results often require a further treatment of the algorithm. Many commodity PCs provide high performance multi-threading environment including multi-core CPUs and programmable GPUs. In this talk, I will . . . → Read More: Parallelizing molecular energy and force calculations using cilk++ and CUDA

Code Review: TexMol and VolRover

CVC Seminar: Wednesday, August 24 1:15-2:30pm Room TBA

Alex Rand

Code Review: TexMol and VolRover

In our first seminar of the semester, we will review the current status of our primary graphical user applications, TexMol and VolRover. We will discuss currently implemented features, work in progress and give a short tutorial on how to quickly add new features to . . . → Read More: Code Review: TexMol and VolRover

Flexible Fitting of Crystal Structures into Density Maps

CVC Seminar: Wed June 1 10:00-11am ACES 4.402

Radhakrishna Bettadapura

Flexible Fitting of Crystal Structures into Density Maps

In flexible fitting, the crystal structure P of a protein is deformed to maximize a pre-determined correlation measure with a cryo-EM density map M of the same protein. All flexible fitting algorithms ask, and answer, three questions: 1) How can . . . → Read More: Flexible Fitting of Crystal Structures into Density Maps

A Reduced Flexibility Model and Improved Scoring Scheme For Lead Optimization In Computational Drug Design

CVC Seminar: Wed June 1 1:30-3pm ACES 4.304

Maysam Moussalem

A Reduced Flexibility Model and Improved Scoring Scheme For Lead Optimization In Computational Drug Design

Virtual drug screening and design offer a much faster and cheaper alternative to the the process of testing tens of thousands of drugs, one by one, in the laboratory. Computational drug design can be . . . → Read More: A Reduced Flexibility Model and Improved Scoring Scheme For Lead Optimization In Computational Drug Design

Sampling macromolecular recognition landscapes using Fast Fourier Transforms based approaches and their generalizations.

CVC Seminar: Wed May 11 1:30-3pm ACES 4.304

Dima Kozakov

Sampling macromolecular recognition landscapes using Fast Fourier Transforms based approaches and their generalizations.

Sampling energy landscape of macromolecular interactions is a challenging problem of computational biology. Classical approaches like Molecular Dynamics and Monte Carlo are not always optimal for these applications due to large configurational space of . . . → Read More: Sampling macromolecular recognition landscapes using Fast Fourier Transforms based approaches and their generalizations.

Centroidal Voronoi Tessellation vs. Optimal Delaunay Triangulation

CVC Seminar – Wed May 4 1:30-3pm ACES 4.304

Dr. Wenping Wang

Centroidal Voronoi Tessellation vs. Optimal Delaunay Triangulation

Abstract:
We present a comparative study on CVT (Centroidal Voronoi Tessellation) and ODT (Optimal Delaunay Triangulation), which are two closely related optimization-based methods for mesh generation. While CVT is relatively well understood and widely applied, ODT has only recently been proposed . . . → Read More: Centroidal Voronoi Tessellation vs. Optimal Delaunay Triangulation