NANO-D - 2015 - Annual activity report

NANO-D

NANO-D - 2015

Project-Team Nano-d

Members

Overall Objectives

Overview
Research axes

Research Program

The need for practical design of nanosystems
Challenges of practical nanosystem design
Current simulation approaches
Research axes

Application Domains

Overview
Structural Biology
Pharmaceutics and Drug Design
Nano-engineering

Highlights of the Year

New Software and Platforms

SAMSON

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

Regional Initiatives
National Initiatives
European Initiatives
International Initiatives
International Research Visitors

Dissemination

Promoting Scientific Activities
Teaching - Supervision - Juries
Popularization
Participation to conferences, seminars

Bibliography

Publications of the year
References in notes

Previous |

Home | Next next

Section: New Results

Numerical analysis for the ARPS method

Participants : Zofia Trstanova, Gabriel Stoltz, Stephane Redon.

Previous works have led to understanding of the choice of optimal parameters for the ARPS dynamics. The interest lies in achieving the highest percentage of restrained particles, while minimizing the modification of the variance and the systematic error. We study discretization schemes of the ARPS-Langevin dynamics, such that the systematic error remains of second order in the time step size and we introduce a Metropolis step in order to stabilize the simulations and hence to allow "a sharper" choice of the ARPS parameters, which lead to better algorithmic speed-ups.

Previous |

Home | Next next