Novel methods that perform local moves such as the gaussian bias or Con-certed Rotation with Angles, increase the exploration of the conformationalphase space. These methods have been applied successfully to small systems,and have proved to be more efficient than the classical Monte Carlo method.The main aim of my work was to study and include backbone movesfor proteins, such as the Concerted Rotation with Angle (CRA) and thegaussian bias in the ProtoMS package. The CRA was then applied to severalsystems of biological interest to compute relative binding free energies andconformational changes to obtain insights into the binding mode and systemflexibility.The CRA algorithm has been used to sample biological systems suchas lysozyme L99A muta...
This thesis introduces the first global parametric model of protein loops amenable to effective samp...
Proteins are chemically simple molecules, being unbranched polymers of uncomplicated organic compoun...
Every organism contains a few hundred to thousands of proteins. A protein is made of a sequence of m...
Computational protein design is a method to modify proteins and obtain new properties, using their 3...
Proteins are essential molecules in living organisms that perform a broad scope of functionalities, ...
Over the past two decades the field of computational protein design has produced striking successes,...
Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides an...
Successfully incorporating backbone flexibility into the computational modeling and design of protei...
AbstractWe propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for ...
This thesis presents an amalgamation of high performance computing techniques to get better insight ...
Normal mode methods are becoming a popular alternative to sample the conformational landscape of pro...
Protein structure and motion plays an essential role in nearly all forms of life. Understanding both...
International audienceAbstract Flexible loops are paramount to protein functions, with action modes ...
Conformational changes associated with protein function often occur beyond the time scale currently ...
Understanding the structural, dynamical and energetic basis of protein-protein interactions (PPIs) i...
This thesis introduces the first global parametric model of protein loops amenable to effective samp...
Proteins are chemically simple molecules, being unbranched polymers of uncomplicated organic compoun...
Every organism contains a few hundred to thousands of proteins. A protein is made of a sequence of m...
Computational protein design is a method to modify proteins and obtain new properties, using their 3...
Proteins are essential molecules in living organisms that perform a broad scope of functionalities, ...
Over the past two decades the field of computational protein design has produced striking successes,...
Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides an...
Successfully incorporating backbone flexibility into the computational modeling and design of protei...
AbstractWe propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for ...
This thesis presents an amalgamation of high performance computing techniques to get better insight ...
Normal mode methods are becoming a popular alternative to sample the conformational landscape of pro...
Protein structure and motion plays an essential role in nearly all forms of life. Understanding both...
International audienceAbstract Flexible loops are paramount to protein functions, with action modes ...
Conformational changes associated with protein function often occur beyond the time scale currently ...
Understanding the structural, dynamical and energetic basis of protein-protein interactions (PPIs) i...
This thesis introduces the first global parametric model of protein loops amenable to effective samp...
Proteins are chemically simple molecules, being unbranched polymers of uncomplicated organic compoun...
Every organism contains a few hundred to thousands of proteins. A protein is made of a sequence of m...