List of works - Lydia E. Kavraki

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.

scientific article

A review of parameters and heuristics for guiding metabolic pathfinding

scientific article published on 15 September 2017

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

scientific article published on 02 March 2019

Algorithmic issues in modeling motion

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

scientific article

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

scientific article published on 01 February 2003

An algorithm for efficient identification of branched metabolic pathways.

scientific article

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

scientific article

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

scientific article published on February 2010

Big Data on Robotics

scientific article

Binding modes of peptidomimetics designed to inhibit STAT3.

scientific article

Call for Papers: Special Issue on Big Data in Robotics

scientific article

Call for Papers: Special Issue on Big Data in Robotics

scientific article published on 01 March 2016

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

scientific article published on April 2007

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

scientific article published in January 2006

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

scientific article

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

scientific article

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

scientific article

Computational analysis of complement inhibitor compstatin using molecular dynamics

scientific article published on 12 August 2020

Computational models of protein kinematics and dynamics: beyond simulation

scientific article published on 9 April 2012

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

scientific article

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

scientific article published in November 2017

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

scientific article

Defining Low-Dimensional Projections to Guide Protein Conformational Sampling

scientific article published on 28 November 2016

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

scientific article published on March 2007

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

scientific article

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

scientific article published on 01 June 2007

Finding metabolic pathways using atom tracking

scientific article

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

scientific article

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

scientific article published on 12 March 2018

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

scientific article published on 01 July 2020

Improving conformational searches by geometric screening.

scientific article

Improving protein conformational sampling by using guiding projections

Improving the organization and interactivity of metabolic pathfinding with precomputed pathways

scientific article published on 10 January 2020

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

scientific article published on 4 October 2017

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

scientific article published on 22 July 2020

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

scientific article published on 13 January 2022

Learning Feasibility for Task and Motion Planning in Tabletop Environments

scientific article published on 23 January 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

scholarly article

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

scientific article published on 16 October 2017

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

scientific article published on 12 November 2020

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

scientific article published on January 2008

Modeling Structures and Motions of Loops in Protein Molecules

article

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

scientific article published in October 2006

MotionBenchMaker: A Tool to Generate and Benchmark Motion Planning Datasets

scientific article published in 2022

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

scientific article

Multiscale characterization of protein conformational ensembles

scientific article published on September 2009

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

scientific article published on 24 March 2018

On modeling peptidomimetics in complex with the SH2 domain of Stat3

scientific article published on 01 January 2011

On the characterization of protein native state ensembles

scientific article published on 8 December 2006

Platform-Independent Benchmarks for Task and Motion Planning

scientific article published in 2018

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

scientific article

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

scientific article published on 2 May 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

scientific article published on January 2008

SIMS: a hybrid method for rapid conformational analysis.

scientific article

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

scientific article published on 01 January 2018

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

scientific article

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

scientific article published on 27 October 2015

The LabelHash algorithm for substructure matching.

scientific article

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

scientific article published on 8 June 2011

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

scientific article published in July 2007

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

scientific article published in 2018

Tracing conformational changes in proteins

scientific article

Understanding protein flexibility through dimensionality reduction

scientific article published on 01 January 2003

Understanding the challenges of protein flexibility in drug design.

scientific article published on 28 September 2015

Unfolding the fold of cyclic cysteine-rich peptides

scientific article

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

List of works by Lydia E. 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