List of works - Robert L Jernigan

Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses

scientific article

The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality

scientific article published on 31 December 2013

RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access

scientific article published on November 15, 1998

Packing regularities in biological structures relate to their dynamics

scientific article

Refinement of NMR-determined protein structures with database derived mean-force potentials

scientific article published on July 2007

Refinement of NMR-determined protein structures with database derived distance constraints

scientific article published in December 2005

Ideal amino acid exchange forms for approximating substitution matrices

scientific article published in November 2007

A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly

scientific article

Revealing rotational modes of functionalized gold nanorods on live cell membranes

scientific article published in November 2012

Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

scientific article (publication date: October 2015)

Diversity of function-related conformational changes in proteins: coordinate uncertainty, fragment rigidity, and stability

scientific article

Identifying interaction sites in "recalcitrant" proteins: predicted protein and RNA binding sites in rev proteins of HIV-1 and EIAV agree with experimental data

scientific article

Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.

scientific article

Elastic network normal modes provide a basis for protein structure refinement

scientific article

Protein flexibility: coordinate uncertainties and interpretation of structural differences

scientific article published on 22 October 2009

Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape.

scientific article

Distributions of experimental protein structures on coarse-grained free energy landscapes.

scientific article published on December 2015

Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics.

scientific article published on 27 May 2015

PIDD: database for Protein Inter-atomic Distance Distributions

scientific article

Structural interpretation of protein-protein interaction network

scientific article

Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics

scientific article published on 20 June 2018

Ribosome Mechanics Informs about Mechanism.

scientific article

Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.

scientific article published on 4 January 2008

Exploration of the relationship between topology and designability of conformations

scientific article published on June 2011

How do side chains orient globally in protein structures?

scientific article published on November 2005

Comparisons of Protein Dynamics from Experimental Structure Ensembles, Molecular Dynamics Ensembles, and Coarse-Grained Elastic Network Models.

scientific article published on 27 January 2018

A DNA-Centric Look at Protein-DNA Complexes

article

Factors correlating with significant differences between X-ray structures of myoglobin

scientific article

Shape-dependent designability studies of lattice proteins

scientific article published on July 2007

The use of experimental structures to model protein dynamics

scientific article

Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices

article

Knowledge-based entropies improve the identification of native protein structures.

scientific article published on 6 March 2017

Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change

scientific article published in April 2017

Prediction of side chain orientations in proteins by statistical machine learning methods

scientific article

How noise in force fields can affect the structural refinement of protein models?

scientific article

Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites

scientific article published on 22 June 2019

Statistical measures on residue-level protein structural properties

scientific article published on 31 March 2011

Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable

scientific article

Altered dynamics upon oligomerization corresponds to key functional sites.

scientific article published on 6 April 2017

An analysis of conformational changes upon RNA-protein binding

article

P.R.E.S.S.--an R-package for exploring residual-level protein structural statistics

scientific article published on June 2012

Models to Approximate the Motions of Protein Loops

scientific article

Short paths in protein structure space originate in graph structure

scientific article published on 14 December 2009

Immunoglobulin Structure Exhibits Control over CDR Motion

scientific article

Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement

scientific article published in April 2008

Loop folds in proteins and evolutionary conservation of folding nuclei

scientific article published on 01 December 2002

Volumes and surface areas: geometries and scaling relationships between coarse- grained and atomic structures

scientific article published on January 2014

Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information

scientific article

Clusters of Structurally Similar MHC I HLA-A2 Molecules, Found with a New Method, Suggest Mechanisms of T-Cell Receptor Avidity

scientific article published on 24 November 2015

Entropies Derived from the Packing Geometries within a Single Protein Structure

scientific article published in 2022

List of works by Robert L Jernigan

Combining statistical potentials with dynamics-based entropies improves selection from protein decoys and docking poses

The critical role of the loops of triosephosphate isomerase for its oligomerization, dynamics, and functionality

RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access

Packing regularities in biological structures relate to their dynamics

Refinement of NMR-determined protein structures with database derived mean-force potentials

Refinement of NMR-determined protein structures with database derived distance constraints

Ideal amino acid exchange forms for approximating substitution matrices

A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly

Revealing rotational modes of functionalized gold nanorods on live cell membranes

Bridging between NMA and Elastic Network Models: Preserving All-Atom Accuracy in Coarse-Grained Models

Diversity of function-related conformational changes in proteins: coordinate uncertainty, fragment rigidity, and stability

Identifying interaction sites in "recalcitrant" proteins: predicted protein and RNA binding sites in rev proteins of HIV-1 and EIAV agree with experimental data

Free energies for coarse-grained proteins by integrating multibody statistical contact potentials with entropies from elastic network models.

Elastic network normal modes provide a basis for protein structure refinement

Protein flexibility: coordinate uncertainties and interpretation of structural differences

Molecular determinants of cadherin ideal bond formation: Conformation-dependent unbinding on a multidimensional landscape.

Distributions of experimental protein structures on coarse-grained free energy landscapes.

Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics.

PIDD: database for Protein Inter-atomic Distance Distributions

Structural interpretation of protein-protein interaction network

Protein dynamic communities from elastic network models align closely to the communities defined by molecular dynamics

Ribosome Mechanics Informs about Mechanism.

Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.

Exploration of the relationship between topology and designability of conformations

How do side chains orient globally in protein structures?

Comparisons of Protein Dynamics from Experimental Structure Ensembles, Molecular Dynamics Ensembles, and Coarse-Grained Elastic Network Models.

A DNA-Centric Look at Protein-DNA Complexes

Factors correlating with significant differences between X-ray structures of myoglobin

Shape-dependent designability studies of lattice proteins

The use of experimental structures to model protein dynamics

Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices

Knowledge-based entropies improve the identification of native protein structures.

Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change

Prediction of side chain orientations in proteins by statistical machine learning methods

How noise in force fields can affect the structural refinement of protein models?

Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites

Statistical measures on residue-level protein structural properties

Use of machine learning algorithms to classify binary protein sequences as highly-designable or poorly-designable

Altered dynamics upon oligomerization corresponds to key functional sites.

An analysis of conformational changes upon RNA-protein binding

P.R.E.S.S.--an R-package for exploring residual-level protein structural statistics

Models to Approximate the Motions of Protein Loops

Short paths in protein structure space originate in graph structure

Immunoglobulin Structure Exhibits Control over CDR Motion

Knowledge-based versus experimentally acquired distance and angle constraints for NMR structure refinement

Loop folds in proteins and evolutionary conservation of folding nuclei

Volumes and surface areas: geometries and scaling relationships between coarse- grained and atomic structures

Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information

Clusters of Structurally Similar MHC I HLA-A2 Molecules, Found with a New Method, Suggest Mechanisms of T-Cell Receptor Avidity

Entropies Derived from the Packing Geometries within a Single Protein Structure