Lista de obras - Lydia Kavraki - Dominio Público Uruguay

A Robotics-Inspired Screening Algorithm for Molecular Caging Prediction

scientific article published on 13 March 2020

A new method for fast and accurate derivation of molecular conformations.

artículo científico publicado en 2002

A review of parameters and heuristics for guiding metabolic pathfinding

artículo científico publicado en 2017

APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations

artículo científico publicado en 2019

Algorithmic issues in modeling motion

Algorithms for structural comparison and statistical analysis of 3D protein motifs.

artículo científico publicado en 2005

An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures

artículo científico publicado en 2003

An algorithm for efficient identification of branched metabolic pathways.

artículo científico publicado en 2011

Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction.

artículo científico publicado en 2010

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

scientific article published on February 2010

Big Data on Robotics

artículo científico publicado en 2016

Binding modes of peptidomimetics designed to inhibit STAT3.

artículo científico publicado en 2012

Call for Papers: Special Issue on Big Data in Robotics

artículo científico publicado en 2016

Call for Papers: Special Issue on Big Data in Robotics

artículo científico publicado en 2016

Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction

artículo científico publicado en 2007

Cavity-aware motifs reduce false positives in protein function prediction.

artículo científico publicado en 2006

Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.

artículo científico publicado en 2017

Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome

artículo científico publicado en 2013

Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

artículo científico publicado en 2007

Computational analysis of complement inhibitor compstatin using molecular dynamics

artículo científico publicado en 2020

Computational models of protein kinematics and dynamics: beyond simulation

artículo científico publicado en 2012

Conformational flexibility models for the receptor in structure based drug design.

artículo científico publicado en 2003

DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach.

artículo científico publicado en 2017

DINC: a new AutoDock-based protocol for docking large ligands.

artículo científico publicado en 2013

Defining Low-Dimensional Projections to Guide Protein Conformational Sampling

artículo científico publicado en 2016

Distributed Computation of the knn Graph for Large High-Dimensional Point Sets

artículo científico publicado en 2007

Electrostatic contributions drive the interaction betweenStaphylococcus aureusprotein Efb-C and its complement target C3d

artículo científico publicado en 2008

Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction

artículo científico publicado en 2007

Finding metabolic pathways using atom tracking

artículo científico publicado en 2010

From coarse-grain to all-atom: toward multiscale analysis of protein landscapes

artículo científico publicado en 2007

General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept

artículo científico publicado en 2018

HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy

artículo científico publicado en 2020

Improving conformational searches by geometric screening.

artículo científico publicado en 2004

Improving protein conformational sampling by using guiding projections

Improving the organization and interactivity of metabolic pathfinding with precomputed pathways

artículo científico publicado en 2020

Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy

artículo científico publicado en 2017

Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests

artículo científico publicado en 2020

Large-Scale Structure-Based Screening of Potential T Cell Cross-Reactivities Involving Peptide-Targets From BCG Vaccine and SARS-CoV-2

artículo científico

Learning Feasibility for Task and Motion Planning in Tabletop Environments

artículo científico publicado en 2019

Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence

scientific article published on 04 October 2023

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

artículo científico publicado en 2006

Machine Learning Guided 3D Printing of Tissue Engineering Scaffolds

scientific article published on 17 September 2020

Machine Learning Guided Atom Mapping of Metabolic Reactions

scientific article published on 14 December 2018

Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods

artículo científico publicado en 2017

Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes

artículo científico publicado en 2020

Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction

artículo científico

Modeling Structures and Motions of Loops in Protein Molecules

article

Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations.

artículo científico publicado en 2006

MotionBenchMaker: A Tool to Generate and Benchmark Motion Planning Datasets

artículo científico publicado en 2022

Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex

artículo científico publicado en 2010

Multiscale characterization of protein conformational ensembles

artículo científico

Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling

artículo científico publicado en 2018

On modeling peptidomimetics in complex with the SH2 domain of Stat3

artículo científico publicado en 2011

On the characterization of protein native state ensembles

artículo científico publicado en 2006

Platform-Independent Benchmarks for Task and Motion Planning

artículo científico publicado en 2018

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

artículo científico publicado en 2008

Probabilistic roadmaps for path planning in high-dimensional configuration spaces

Quantitative comparison of adaptive sampling methods for protein dynamics

scientific article published on 01 December 2018

Randomized Physics-Based Motion Planning for Grasping in Cluttered and Uncertain Environments

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

artículo científico publicado en 2006

Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data

scientific article published on 31 October 2018

Roadmap methods for protein folding

artículo científico publicado en 2008

SIMS: a hybrid method for rapid conformational analysis.

artículo científico publicado en 2013

Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins

article

Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G

scientific article published on 06 November 2020

Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes

artículo científico publicado en 2018

Structure-guided selection of specificity determining positions in the human Kinome

artículo científico publicado en 2016

Targeting the Src Homology 2 (SH2) Domain of Signal Transducer and Activator of Transcription 6 (STAT6) with Cell-Permeable, Phosphatase-Stable Phosphopeptide Mimics Potently Inhibits Tyr641 Phosphorylation and Transcriptional Activity

artículo científico publicado en 2015

The LabelHash algorithm for substructure matching.

artículo científico publicado en 2010

The LabelHash server and tools for substructure-based functional annotation.

artículo científico publicado en 2011

The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs

artículo científico publicado en 2007

The Task-Motion Kit: An Open Source, General-Purpose Task and Motion-Planning Framework

artículo científico publicado en 2018

Tracing conformational changes in proteins

artículo científico publicado en 2010

Understanding protein flexibility through dimensionality reduction

artículo científico publicado en 2003

Understanding the challenges of protein flexibility in drug design.

artículo científico

Unfolding the fold of cyclic cysteine-rich peptides

artículo científico publicado en 2008

Unix Philosophy and the Real World: Control Software for Humanoid Robots

Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins

scientific article published on 05 September 2019

Lista de obras de Lydia Kavraki

A Robotics-Inspired Screening Algorithm for Molecular Caging Prediction

A new method for fast and accurate derivation of molecular conformations.

A review of parameters and heuristics for guiding metabolic pathfinding

APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations

Algorithmic issues in modeling motion

Algorithms for structural comparison and statistical analysis of 3D protein motifs.

An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures

An algorithm for efficient identification of branched metabolic pathways.

Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction.

Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides

Big Data on Robotics

Binding modes of peptidomimetics designed to inhibit STAT3.

Call for Papers: Special Issue on Big Data in Robotics

Call for Papers: Special Issue on Big Data in Robotics

Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction

Cavity-aware motifs reduce false positives in protein function prediction.

Coarse-Grained Conformational Sampling of Protein Structure Improves the Fit to Experimental Hydrogen-Exchange Data.

Combinatorial clustering of residue position subsets predicts inhibitor affinity across the human kinome

Composite motifs integrating multiple protein structures increase sensitivity for function prediction.

Computational analysis of complement inhibitor compstatin using molecular dynamics

Computational models of protein kinematics and dynamics: beyond simulation

Conformational flexibility models for the receptor in structure based drug design.

DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach.

DINC: a new AutoDock-based protocol for docking large ligands.

Defining Low-Dimensional Projections to Guide Protein Conformational Sampling

Distributed Computation of the knn Graph for Large High-Dimensional Point Sets

Electrostatic contributions drive the interaction betweenStaphylococcus aureusprotein Efb-C and its complement target C3d

Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction

Finding metabolic pathways using atom tracking

From coarse-grain to all-atom: toward multiscale analysis of protein landscapes

General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept

HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy

Improving conformational searches by geometric screening.

Improving protein conformational sampling by using guiding projections

Improving the organization and interactivity of metabolic pathfinding with precomputed pathways

Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy

Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests

Large-Scale Structure-Based Screening of Potential T Cell Cross-Reactivities Involving Peptide-Targets From BCG Vaccine and SARS-CoV-2

Learning Feasibility for Task and Motion Planning in Tabletop Environments

Leveraging Large Language Models for Predicting Microbial Virulence from Protein Structure and Sequence

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

Machine Learning Guided 3D Printing of Tissue Engineering Scaffolds

Machine Learning Guided Atom Mapping of Metabolic Reactions

Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods

Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes

Matching of structural motifs using hashing on residue labels and geometric filtering for protein function prediction

Modeling Structures and Motions of Loops in Protein Molecules

Modeling protein conformational ensembles: from missing loops to equilibrium fluctuations.

MotionBenchMaker: A Tool to Generate and Benchmark Motion Planning Datasets

Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex

Multiscale characterization of protein conformational ensembles

Native State of Complement Protein C3d Analysed via Hydrogen Exchange and Conformational Sampling

On modeling peptidomimetics in complex with the SH2 domain of Stat3

On the characterization of protein native state ensembles

Platform-Independent Benchmarks for Task and Motion Planning

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids.

Probabilistic roadmaps for path planning in high-dimensional configuration spaces

Quantitative comparison of adaptive sampling methods for protein dynamics

Randomized Physics-Based Motion Planning for Grasping in Cluttered and Uncertain Environments

Recurrent use of evolutionary importance for functional annotation of proteins based on local structural similarity

Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data

Roadmap methods for protein folding

SIMS: a hybrid method for rapid conformational analysis.

Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins

Structural Modeling and Molecular Dynamics of the Immune Checkpoint Molecule HLA-G

Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes

Structure-guided selection of specificity determining positions in the human Kinome

Targeting the Src Homology 2 (SH2) Domain of Signal Transducer and Activator of Transcription 6 (STAT6) with Cell-Permeable, Phosphatase-Stable Phosphopeptide Mimics Potently Inhibits Tyr641 Phosphorylation and Transcriptional Activity

The LabelHash algorithm for substructure matching.

The LabelHash server and tools for substructure-based functional annotation.

The MASH pipeline for protein function prediction and an algorithm for the geometric refinement of 3D motifs

The Task-Motion Kit: An Open Source, General-Purpose Task and Motion-Planning Framework

Tracing conformational changes in proteins

Understanding protein flexibility through dimensionality reduction

Understanding the challenges of protein flexibility in drug design.

Unfolding the fold of cyclic cysteine-rich peptides

Unix Philosophy and the Real World: Control Software for Humanoid Robots

Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins