List of works - Robert L Jernigan

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining

scientific article

A DNA-Centric Look at Protein-DNA Complexes

article

A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models

scientific article published on 01 January 2021

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

scientific article

A role for CH…O interactions in protein-DNA recognition ⬇️

scientific article published on April 17, 1998

Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics.

scientific article published on 27 May 2015

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

An enhanced elastic network model to represent the motions of domain-swapped proteins

scientific article published on 01 April 2006

Characterization of protein-protein interfaces

scientific article

Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes

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

Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model for Protein Residue-Level Structural Fluctuations ⬇️

scientific article published on January 8, 2013

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

scientific article published on June 2009

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

scientific article

Comparison of tRNA motions in the free and ribosomal bound structures

scientific article published on 19 August 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

Comparisons of experimental and computed protein anisotropic temperature factors

scientific article published on July 2009

Computational and experimental characterization of RNA cubic nanoscaffolds

scientific article

Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM)

scientific article

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model ⬇️

scientific article published on January 27, 1998

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

scientific article published on 22 June 2019

Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli ⬇️

scientific article published on February 24, 2011

Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport ⬇️

scientific article published on September 23, 2010

Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change

scientific article published in April 2017

Distance matrix-based approach to protein structure prediction

scientific article

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

scientific article published on December 2015

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

scientific article

Dynamics of large proteins through hierarchical levels of coarse-grained structures.

scientific article

Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome

scientific article published in September 2008

Elastic network models capture the motions apparent within ensembles of RNA structures

scientific article (publication date: June 2014)

Elastic network normal modes provide a basis for protein structure refinement

scientific article

Entropies Derived from the Packing Geometries within a Single Protein Structure

scientific article published in 2022

Exploration of the relationship between topology and designability of conformations

scientific article published on June 2011

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

scientific article

Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model

scientific article published on August 2009

Fold-specific sequence scoring improves protein sequence matching

scientific article

Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys

scientific article published in July 2007

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

scientific article

Functional clustering of yeast proteins from the protein-protein interaction network

scientific article

Functional motions can be extracted from on‐lattice construction of protein structures ⬇️

scientific article published on November 1, 2003

GOR V server for protein secondary structure prediction

scientific article

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

article

Global ribosome motions revealed with elastic network model

scientific article

How do side chains orient globally in protein structures?

scientific article published on November 2005

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

scientific article

How well can we understand large-scale protein motions using normal modes of elastic network models?

scientific article published on 4 May 2007

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

scientific article

Ideal amino acid exchange forms for approximating substitution matrices

scientific article published in November 2007

Ideal architecture of residue packing and its observation in protein structures ⬇️

scientific article published on October 1, 1997

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

Immunoglobulin Structure Exhibits Control over CDR Motion

scientific article

Inferring ideal amino acid interaction forms from statistical protein contact potentials

scientific article published on April 2005

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

scientific article published on 6 March 2017

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

Loop motions of triosephosphate isomerase observed with elastic networks.

scientific article published in January 2006

MAVENs: motion analysis and visualization of elastic networks and structural ensembles

scientific article

Models to Approximate the Motions of Protein Loops

scientific article

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

scientific article

Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

scientific article published on 19 April 2011

Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron

scientific article published on November 2008

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

scientific article published on June 2012

PIDD: database for Protein Inter-atomic Distance Distributions.

scientific article

Packing regularities in biological structures relate to their dynamics

scientific article

Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials ⬇️

scientific article

Predicting DNA-binding sites of proteins from amino acid sequence

scientific article

Predicting Designability of Small Proteins from Graph Features of Contact Maps

scientific article

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

scientific article

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

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

Predicting the order in which contacts are broken during single molecule protein stretching experiments

scientific article

Prediction of RNA binding sites in proteins from amino acid sequence

scientific article

Prediction of protein secondary structure by mining structural fragment database

scientific article published on May 2005

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

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

Protein elastic network models and the ranges of cooperativity

scholarly article

Protein flexibility: coordinate uncertainties and interpretation of structural differences

scientific article published on 22 October 2009

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

RNABindR: a server for analyzing and predicting RNA-binding sites in proteins

scientific article (publication date: 8 May 2007)

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

scientific article published in December 2005

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

scientific article published on July 2007

Relating molecular flexibility to function: a case study of tubulin

scientific article

Revealing rotational modes of functionalized gold nanorods on live cell membranes

scientific article published in November 2012

Ribosome Mechanics Informs about Mechanism.

scientific article

Shape-dependent designability studies of lattice proteins

scientific article published on July 2007

Short paths in protein structure space originate in graph structure

scientific article published on 14 December 2009

Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches ⬇️

scientific article published on November 1, 1997

Statistical measures on residue-level protein structural properties

scientific article published on 31 March 2011

Structural Compliance - A New Metric for Protein Flexibility

scientific article published on 17 June 2020

Structural interpretation of protein-protein interaction network

scientific article

The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

scientific article published on January 2006

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

scientific article published on 31 December 2013

The energy profiles of atomic conformational transition intermediates of adenylate kinase

scientific article

The importance of slow motions for protein functional loops

scientific article published on 07 February 2012

The origin and extent of coarse-grained regularities in protein internal packing

scientific article

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

scientific article published on 24 November 2008

The transfer matrix method for lattice proteins—an application with cooperative interactions

The use of experimental structures to model protein dynamics

scientific article

Understanding the recognition of protein structural classes by amino acid composition ⬇️

scientific article published on October 1, 1997

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

scientific article

Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms 1 1Edited by I. Tinoco ⬇️

scientific article published on September 4, 1998

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

scientific article published on January 2014

List of works by Robert L Jernigan

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining

A DNA-Centric Look at Protein-DNA Complexes

A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models

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

A role for CH…O interactions in protein-DNA recognition ⬇️

Aldolases Utilize Different Oligomeric States To Preserve Their Functional Dynamics.

Altered dynamics upon oligomerization corresponds to key functional sites.

An analysis of conformational changes upon RNA-protein binding

An enhanced elastic network model to represent the motions of domain-swapped proteins

Characterization of protein-protein interfaces

Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes

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

Coarse Grained Normal Mode Analysis vs. Refined Gaussian Network Model for Protein Residue-Level Structural Fluctuations ⬇️

Collective dynamics of the ribosomal tunnel revealed by elastic network modeling

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

Comparison of tRNA motions in the free and ribosomal bound structures

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

Comparisons of experimental and computed protein anisotropic temperature factors

Computational and experimental characterization of RNA cubic nanoscaffolds

Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM)

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model ⬇️

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

Crystal structure of the CusBA heavy-metal efflux complex of Escherichia coli ⬇️

Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport ⬇️

Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change

Distance matrix-based approach to protein structure prediction

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

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

Dynamics of large proteins through hierarchical levels of coarse-grained structures.

Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome

Elastic network models capture the motions apparent within ensembles of RNA structures

Elastic network normal modes provide a basis for protein structure refinement

Entropies Derived from the Packing Geometries within a Single Protein Structure

Exploration of the relationship between topology and designability of conformations

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

Focused functional dynamics of supramolecules by use of a mixed-resolution elastic network model

Fold-specific sequence scoring improves protein sequence matching

Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys

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

Functional clustering of yeast proteins from the protein-protein interaction network

Functional motions can be extracted from on‐lattice construction of protein structures ⬇️

GOR V server for protein secondary structure prediction

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

Global ribosome motions revealed with elastic network model

How do side chains orient globally in protein structures?

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

How well can we understand large-scale protein motions using normal modes of elastic network models?

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

Ideal amino acid exchange forms for approximating substitution matrices

Ideal architecture of residue packing and its observation in protein structures ⬇️

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

Immunoglobulin Structure Exhibits Control over CDR Motion

Inferring ideal amino acid interaction forms from statistical protein contact potentials

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

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

Loop folds in proteins and evolutionary conservation of folding nuclei

Loop motions of triosephosphate isomerase observed with elastic networks.

MAVENs: motion analysis and visualization of elastic networks and structural ensembles

Models to Approximate the Motions of Protein Loops

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

Multibody coarse-grained potentials for native structure recognition and quality assessment of protein models

Orientational distributions of contact clusters in proteins closely resemble those of an icosahedron

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

PIDD: database for Protein Inter-atomic Distance Distributions.

Packing regularities in biological structures relate to their dynamics

Potentials 'R' Us web-server for protein energy estimations with coarse-grained knowledge-based potentials ⬇️

Predicting DNA-binding sites of proteins from amino acid sequence

Predicting Designability of Small Proteins from Graph Features of Contact Maps

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

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

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

Predicting the order in which contacts are broken during single molecule protein stretching experiments

Prediction of RNA binding sites in proteins from amino acid sequence

Prediction of protein secondary structure by mining structural fragment database

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

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

Protein elastic network models and the ranges of cooperativity

Protein flexibility: coordinate uncertainties and interpretation of structural differences

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