Direct Coupling Analysis (DCA)
Direct Coupling Analysis (DCA) is a statistical inference framework used to infer direct co-evolutionary couplings among residue pairs in multiple sequence alignments. A recent formulation of DCA termed mean field DCA (mfDCA), provides the computational power to apply this tool in a high throughput manner to a number of protein and domain families. mfDCA is able to uncover a large number of native intra-domain and inter-domain residue-residue contacts in many domain families.
SMOG: Structure-based Models for Biomolecules: While originally developed for the study of protein folding, over the last 10 years we have worked to extend the applicability of structure-based models to investigate a broad range of biomolecular dynamics, including domain rearrangements in proteins, folding and ligand binding in RNA, and large-scale rearrangements in ribonucleoprotein assemblies.
In collaboration with Gareg Papoiyan at Maryland, the Wolynes lab had made available the AWSEM code (Associative Memory, Water-Mediated Structure and Energy model). Many useful coarse-grained protein force fields require prior knowledge of the native structure for the specific protein target, often with the stated goal of simulating protein folding kinetics and dynamics. These methods, however, cannot be used when the target protein structure is unknown or non-native interactions play a significant role. To address such problems, we have developed the AWSEM potential, and various research groups have successfully demonstrated its broad applications in monomeric protein structure prediction, binding predictions of dimers and multimeric assemblies, folding of membrane proteins, and structural and kinetic studies of protein- DNA comp.
A web platform to simulate and browse the three-dimensional architecture of genomes.
In NDB user can find data for 3D genome structures and also computational tools for simulating the genome. The server is also made for visualization the structures and dynamics of the genome, allowing users to explore the 3D organization of chromosomes from their computer. This platform enables users to visualize and annotate the 3D chromosome structures with experimental tracks from ENCODE or with their own data, allowing for an integrative experience for all genome scientists. NDB uses a novel computational pipeline to create a physics-based model of individual chromosomes from chromatin immunoprecipitation input data. This physical model can be simulated using the GROMACS molecular dynamics package.