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Section: New Results
SAXS-assisted protein docking
Participants : Gaurav Dhar, Sergei Grudinin.
We have developed an extension of the Pepsi-SAXS method [2] applicable to rescoring of rigid-body protein-protein docking predictions.
Overall Objectives
Research Program
New Software and Platforms
New Results
- Incremental methods for long range interactions
- Adaptive Algorithms for Orbital-Free Density Functional Theory
- As-Rigid-As-Possible molecular interpolation paths
- ART-RRT: As-Rigid-As-Possible Exploration of Ligand Unbinding Pathways
- IM-UFF: extending the Universal Force Field for interactive molecular modeling
- Exploring Chemical Reaction Paths
- Combination of force fields
- Simulating nanomaterials
- Parallel algorithms for adaptive molecular dynamics simulations
- Development of Convex-PL, a scoring function for protein-ligand interactions
- Participation in the D3R Grand Challenge 2 with the Convex-PL scoring function
- Development of a Normal Modes Analysis SAMSON Element
- Development of a Hex SAMSON Element
- Development of RDKit Smiles Manager SAMSON Elements
- Symmetry mate generator for SAMSON
- Development of a symmetry detection software AnAnaS
- Integration of AnAnaS to SAMSON
- Deep Learning for Symmetry detection
- Pepsi-SAXS calculator of small-angle X-ray scattering profiles
- NOLB nonlinear normal modes
- Applications of the NOLB NMA method to structural biology
- Off-grid fitting method
- RapidRMSD library
- SBROD protein quality assessment method
- Symmetry detection methods
- SAXS-assisted protein docking
- Methods for the estimation of collective motions
- Smoothed-force energy optimization
- Adaptively Restrained Molecular Dynamics in LAMMPS
- Single-pass Incremental Force Updates for Adaptively Restrained Molecular Dynamics
- Auto update process for SAMSON & SAMSON-SDK
- SAMSON Elements policies
- Improvements to our software development pipeline
- SAMSON Connect Forum
Partnerships and Cooperations
Bibliography
Overall Objectives
Research Program
New Software and Platforms
New Results
- Incremental methods for long range interactions
- Adaptive Algorithms for Orbital-Free Density Functional Theory
- As-Rigid-As-Possible molecular interpolation paths
- ART-RRT: As-Rigid-As-Possible Exploration of Ligand Unbinding Pathways
- IM-UFF: extending the Universal Force Field for interactive molecular modeling
- Exploring Chemical Reaction Paths
- Combination of force fields
- Simulating nanomaterials
- Parallel algorithms for adaptive molecular dynamics simulations
- Development of Convex-PL, a scoring function for protein-ligand interactions
- Participation in the D3R Grand Challenge 2 with the Convex-PL scoring function
- Development of a Normal Modes Analysis SAMSON Element
- Development of a Hex SAMSON Element
- Development of RDKit Smiles Manager SAMSON Elements
- Symmetry mate generator for SAMSON
- Development of a symmetry detection software AnAnaS
- Integration of AnAnaS to SAMSON
- Deep Learning for Symmetry detection
- Pepsi-SAXS calculator of small-angle X-ray scattering profiles
- NOLB nonlinear normal modes
- Applications of the NOLB NMA method to structural biology
- Off-grid fitting method
- RapidRMSD library
- SBROD protein quality assessment method
- Symmetry detection methods
- SAXS-assisted protein docking
- Methods for the estimation of collective motions
- Smoothed-force energy optimization
- Adaptively Restrained Molecular Dynamics in LAMMPS
- Single-pass Incremental Force Updates for Adaptively Restrained Molecular Dynamics
- Auto update process for SAMSON & SAMSON-SDK
- SAMSON Elements policies
- Improvements to our software development pipeline
- SAMSON Connect Forum
Partnerships and Cooperations
Bibliography