Overall Objectives
Research Program
Application Domains
New Software and Platforms
New Results
- Algorithms for Orbital-Free Density Functional Theory
- Parallel adaptively restrained particle simulations
- Incremental algorithms for long-range interactions
- Motion planning architecture for nanosystems
- Optimization of transition paths
- As-rigid-as-possible shape interpolation for molecular modeling
- Automatic parameterization for the Universal Force Field
- Interactive modeling with the Universal Force Field
- Error Analysis of Modified Langevin Dynamics
- Algorithmic speed up of the ARPS method
- Numerical analysis for the ARPS method
- New rendering algorithm for secondary structures
- Property models
- Integration of tools in SAMSON
- Development of SAMSON Connect
- Documenting the SAMSON Software Development Kit
- SAMSON SDK Helpers
- Pepsi-SAXS : an adaptive method for rapid and accurate computation of small angle X-ray scattering profiles
- Knodle: a Support Vector Machines-based automatic perception of organic molecules from 3D coordinates
- Symmetry Detection Method
- Pepsi-Dock: fast predictions of putative docking poses using accurate knowledge-based potentials functions to describe interactions between proteins
- Pepsi-Piper: rigid docking predictions using Pepsi potentials into Piper code
- Flex-Dock: towards flexible docking predictions using metaheuristics optimisation methods
- FastRMS: rapid determination of RMSDs corresponding to macromolecular rigid body motions, adding flexibility via collective motions
- SAM : Spherical Polar Fourier Assembly of Protein Complexes with Arbitrary Point Group Symmetry
- KSENIA : Knowledge of Native Protein-Protein Interfaces is Sufficient to Construct Predictive Models for the Selection of Binding Candidates
- Predicting Binding Poses and Affinities in the CSAR 2013–2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential
- Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment
- Convex relaxation for non-convex quadratic optimization problems with applications to side-chain prediction in protein structures
- Critical assessment of protein-ligand docking methods via Drug Design Data Resource (D3R) Challenge 2015
- Towards the development of FFT-accelerated flexible fitting methods
Partnerships and Cooperations
Dissemination
Bibliography
Overall Objectives
Research Program
Application Domains
New Software and Platforms
New Results
- Algorithms for Orbital-Free Density Functional Theory
- Parallel adaptively restrained particle simulations
- Incremental algorithms for long-range interactions
- Motion planning architecture for nanosystems
- Optimization of transition paths
- As-rigid-as-possible shape interpolation for molecular modeling
- Automatic parameterization for the Universal Force Field
- Interactive modeling with the Universal Force Field
- Error Analysis of Modified Langevin Dynamics
- Algorithmic speed up of the ARPS method
- Numerical analysis for the ARPS method
- New rendering algorithm for secondary structures
- Property models
- Integration of tools in SAMSON
- Development of SAMSON Connect
- Documenting the SAMSON Software Development Kit
- SAMSON SDK Helpers
- Pepsi-SAXS : an adaptive method for rapid and accurate computation of small angle X-ray scattering profiles
- Knodle: a Support Vector Machines-based automatic perception of organic molecules from 3D coordinates
- Symmetry Detection Method
- Pepsi-Dock: fast predictions of putative docking poses using accurate knowledge-based potentials functions to describe interactions between proteins
- Pepsi-Piper: rigid docking predictions using Pepsi potentials into Piper code
- Flex-Dock: towards flexible docking predictions using metaheuristics optimisation methods
- FastRMS: rapid determination of RMSDs corresponding to macromolecular rigid body motions, adding flexibility via collective motions
- SAM : Spherical Polar Fourier Assembly of Protein Complexes with Arbitrary Point Group Symmetry
- KSENIA : Knowledge of Native Protein-Protein Interfaces is Sufficient to Construct Predictive Models for the Selection of Binding Candidates
- Predicting Binding Poses and Affinities in the CSAR 2013–2014 Docking Exercises Using the Knowledge-Based Convex-PL Potential
- Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment
- Convex relaxation for non-convex quadratic optimization problems with applications to side-chain prediction in protein structures
- Critical assessment of protein-ligand docking methods via Drug Design Data Resource (D3R) Challenge 2015
- Towards the development of FFT-accelerated flexible fitting methods
Partnerships and Cooperations
Dissemination
Bibliography
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