MMM: A toolbox for integrative structure modeling

MMM: a sequence-to-structure alignment protocol

MOTIVATION Accurate alignment of a target sequence to a template structure continues to be a bottleneck in producing good quality comparative protein structure models. RESULTS Multiple Mapping Method (MMM) is a comparative protein structure modeling server with an emphasis on a novel alignment optimization protocol. MMM takes inputs from five profile-to-profile based alignment methods. The al...

Electromembrane Processes, a Toolbox for Advanced Separations

A MATLAB toolbox for structural kinetic modeling

SUMMARY Structural kinetic modeling (SKM) enables the analysis of dynamical properties of metabolic networks solely based on topological information and experimental data. Current SKM-based experiments are hampered by the time-intensive process of assigning model parameters and choosing appropriate sampling intervals for Monte-Carlo experiments. We introduce a toolbox for the automatic and effi...

Integrative modeling for prediction

This is a synopsis of the presentation that I gave at the MIT LIDS Paths Ahead symposium in November 2009.

3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.

Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough...