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List of works by Jeffrey J. Gray

"How Do We Do This at a Distance?!" A Descriptive Study of Remote Undergraduate Research Programs during COVID-19

scientific article published in March 2022

A Benchmarking Study of Peptide–Biomineral Interactions

scientific article published in 2018

A Comprehensive, High-Resolution Map of a Gene's Fitness Landscape.

scientific article

A Deep-Dive into the Rosetta Energy Function for Biological Macromolecules

scientific article published in February 2017

A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces

scientific article published on 26 April 2018

A Thermodynamically-Rigorous, Biologically-Driven Energy Function for Membrane Protein Modeling and Design

scientific article published in February 2019

A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.

scientific article published on 7 December 2017

A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19

scientific article

A high throughput mutagenic analysis of yeast sumo structure and function.

scientific article

A humanized yeast system to analyze cleavage of prelamin A by ZMPSTE24

scientific article published on 06 January 2019

AI Models for Protein Design are Driving Antibody Engineering

scientific article published in December 2023

Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint

scientific article

Accurate positioning of functional residues with robotics-inspired computational protein design

scholarly article

Accurately positioning functional residues with robotics-inspired computational protein design

preprint

Acidic C-terminal domains autoregulate the RNA chaperone Hfq

scientific article published on 9 August 2017

Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design

scientific article (publication date: 2013)

Adsorption of Charge-Bidisperse Mixtures of Colloidal Particles

article

Adsorption of colloidal particles by Brownian dynamics simulation: Kinetics and surface structures

article

Allosteric communication occurs via networks of tertiary and quaternary motions in proteins

scientific article

Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability

scientific article

An Integrated Framework Advancing Membrane Protein Modeling and Design

scientific article (publication date: September 2015)

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants

scientific article published on 03 February 2021

Analysis and modeling of the variable region of camelid single-domain antibodies

scientific article

Analysis of protein kinase autophosphorylation using expressed protein ligation and computational modeling

scientific article published on 9 April 2008

Antibody structure prediction using interpretable deep learning

scientific article published on 27 May 2021

Applying linear interaction energy method for rational design of noncompetitive allosteric inhibitors of the sarco- and endoplasmic reticulum calcium-ATPase

scientific article published in April 2005

Benchmarking and analysis of protein docking performance in Rosetta v3.2.

scientific article

Better together: Elements of successful scientific software development in a distributed collaborative community

scientific article published on 04 May 2020

Blind prediction of interfacial water positions in CAPRI

scientific article

CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock

scientific article

Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation.

scientific article

Characterization of Peptides Designed to Control Crystal Nucleation and Growth

scientific article published in January 2015

Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate

scientific article

Chiral switching in biomineral suprastructures induced by homochiral l-amino acid

scientific article published on 01 August 2018

Colicin-mediated transport of DNA through the iron transporter FepA

scientific article published on 11 May 2021

Community-wide assessment of protein-interface modeling suggests improvements to design methodology

scientific article

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

scientific article

Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality

scientific article published on 16 October 2017

Computational Design of High-Resolution Protein Crystals

scientific article published in February 2018

Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel S

scientific article published in April 2023

Computational modeling of membrane proteins

scientific article

Computational predictions of the mutant behavior of AraC.

scientific article published on 23 March 2010

Computed structures of point deletion mutants and their enzymatic activities

scientific article

Computer-based Engineering of Thermostabilized Antibody Fragments

scientific article published on 19 November 2019

Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles

scientific article published on 24 May 2008

Contact rearrangements form coupled networks from local motions in allosteric proteins

scientific article published on April 2008

Contextual protein and antibody encodings from equivariant graph transformers

scientific article published on 29 July 2023

Correction to “The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design”

scientific article published on 06 June 2022

De novo design of peptide-calcite biomineralization systems

scientific article published on September 2010

Deep Learning in Protein Structural Modeling and Design

scientific article published on 12 November 2020

Development and Evaluation of GlycanDock: A Protein–Glycoligand Docking Refinement Algorithm in Rosetta

scientific article published on 16 June 2021

Development of a Broadly Accessible, Computationally Guided Biochemistry Course-Based Undergraduate Research Experience

scientific article published on 30 December 2020

Diverse Scientific Benchmarks for Implicit Membrane Energy Functions

scientific article published on 26 July 2021

Diverse scientific benchmarks for implicit membrane energy functions

scientific article published on 24 June 2020

Docking and Design of Oligosaccharides, Glycoproteins, and Glycolipids

scientific article published in January 2015

Effect of trisodium citrate treatment on hybridoma cell viability

Efficient Flexible-Backbone Docking of Challenging Protein Complexes

scientific article published in February 2018

Efficient flexible backbone protein-protein docking for challenging targets

article

Engineering immunity with quantitative tools

scholarly article

Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks

scientific article published on 29 November 2021

Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics

scientific article published on 23 July 2012

Evolution of CDR H3 Flexibility at an Immunomic Scale

scientific article published in February 2018

Expanding the toolkit for membrane protein modeling in Rosetta

scientific article published on 22 December 2016

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27

scientific article

FLAb: Benchmarking deep learning methods for antibody fitness prediction

scientific article published on 15 January 2024

Fast Implicit Potentials for Accurate Prediction and Design of Membrane Protein Structures

scientific article published in February 2018

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

scientific article published on 25 April 2023

Fate and Efficacy of Engineered Allogeneic Stem Cells Targeting Cell Death and Proliferation Pathways in Primary and Brain Metastatic Lung Cancer

scientific article published on 14 July 2023

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer

scientific article published in July 2023

Flexible backbone assembly and refinement of symmetrical homomeric complexes

scientific article published on 6 September 2018

Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to Hirschsprung disease liability

scientific article

Generative language modeling for antibody design

scientific article published on 14 December 2021

Geometric Potentials from Deep Learning Improve Prediction of CDR H3 Loop Structures

scientific article published on 10 February 2020

Glycoengineering of Esterase Activity through Metabolic Flux-Based Modulation of Sialic Acid.

scientific article published on 20 February 2017

Hallucinating structure-conditioned antibody libraries for target-specific binders

scientific article published on 6 June 2022

High-resolution protein-protein docking

scientific article

Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance

scientific article

IgLM: Infilling language modeling for antibody sequence design

scientific article published on 15 November 2023

Implicit model to capture electrostatic features of membrane environment

scientific article published on 27 June 2023

Improved antibody structure prediction by deep learning of side chain conformations

scientific article published on 22 September 2021

Improved prediction of antibody VL-VH orientation

scientific article published on 8 June 2016

Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12.

scientific article published in December 2007

Induced fit with replica exchange improves protein complex structure prediction

scientific article published on 03 June 2022

Induced fit with replica exchange improves protein complex structure prediction

scientific article published on 10 December 2021

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

scientific article published on 25 April 2016

Local motions in a benchmark of allosteric proteins

scientific article published in May 2007

Macromolecular modeling and design in Rosetta: recent methods and frameworks

scientific article published on 01 June 2020

Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2

scientific article

Microstructure Formation and Kinetics in the Random Sequential Adsorption of Polydisperse Tethered Nanoparticles Modeled as Hard Disks

Modeling and docking antibody structures with Rosetta

scientific article published on 16 August 2016

Modeling and docking of antibody structures with Rosetta.

scientific article published on 26 January 2017

Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35.

scientific article published on 26 September 2016

Modeling the structure of mAb 14B7 bound to the anthrax protective antigen

scientific article published in January 2008

Modulation of calcium oxalate dihydrate growth by phosphorylated osteopontin peptides

scientific article published on 17 July 2018

Modulation of calcium oxalate dihydrate growth by selective crystal-face binding of phosphorylated osteopontin and polyaspartate peptide showing occlusion by sectoral (compositional) zoning

scientific article

Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell.

scientific article

Neutron reflectometry studies of the adsorbed structure of the amelogenin, LRAP.

scientific article published on 12 March 2013

Non-H3 CDR template selection in antibody modeling through machine learning

scientific article published on 11 January 2019

Nonequilibrium Phase Behavior during the Random Sequential Adsorption of Tethered Hard Disks

scientific article published in Physical Review Letters

Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI Rounds 37–45

scientific article published on 30 August 2019

Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37-45

scientific article published on 19 November 2019

Partial high-resolution structure of phosphorylated and non-phosphorylated leucine-rich amelogenin protein adsorbed to hydroxyapatite

scientific article

Phosphorylation-dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage

scientific article

Plasma Cells Are the Most Abundant Gluten Peptide MHC-expressing Cells in Inflamed Intestinal Tissues From Patients With Celiac Disease

scientific article published on 26 December 2018

Prediction of calcite morphology from computational and experimental studies of mutations of a de novo-designed peptide

scientific article published on 22 August 2011

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Protein Docking and Steered Molecular Dynamics Reveal Alternative Regulatory Sites on the SERCA Calcium Transporter

scientific article published on 20 December 2019

Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane

scientific article published on 14 March 2020

Protein structure prediction and design in a biologically-realistic implicit membrane

scientific article published on 8 May 2019

Protein-protein docking predictions for the CAPRI experiment

scientific article (publication date: July 2003)

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

scientific article (publication date: August 2003)

Pushing the Backbone in Protein-Protein Docking.

scientific article

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design

scientific article published on 16 April 2021

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

scientific article

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules

scientific article (publication date: 2011)

Rapid calculation of protein pKa values using Rosetta

scientific article

Real-time PyMOL visualization for Rosetta and PyRosetta

scientific article

Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange

scientific article published on 25 November 2023

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification.

scientific article

Residue-centric modeling and design of saccharide and glycoconjugate structures

scientific article

Robustification of RosettaAntibody and Rosetta SnugDock

scientific article published on 25 March 2021

RosettaAntibody: antibody variable region homology modeling server

scientific article published on 20 May 2009

Scientific benchmarks for guiding macromolecular energy function improvement

scientific article (publication date: 2013)

Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE)

scientific article (publication date: 2013)

Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking

scientific article published on 19 April 2016

Shotgun scanning glycomutagenesis: a simple and efficient strategy for constructing and characterizing neoglycoproteins

scientific article published on 29 June 2020

Simultaneous prediction of antibody backbone and side-chain conformations with deep learning

scientific article published in 2022

SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models

scientific article

Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system

scientific article published on April 2009

Structural Diversity in the Type IV Pili of Multidrug-resistant Acinetobacter

scientific article

Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2

scientific article published on 27 June 2020

Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis

scientific article published in March 2006

Structurally distinct toxicity inhibitors bind at common loci on β-amyloid fibril

scientific article

Structure prediction of domain insertion proteins from structures of individual domains.

scientific article

Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite

scientific article published on 12 October 2007

Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level

scientific article published on 15 March 2023

Structure-Based Prediction of Polypeptide Substrate Specificities of Glycosyltransferases

scholarly article

Structure-based cross-docking analysis of antibody-antigen interactions

scientific article published on 15 August 2017

Structure-based design of supercharged, highly thermoresistant antibodies

scientific article published on April 2012

Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex

scientific article published on 13 May 2013

Targeted DNA methylation using an artificially bisected M.HhaI fused to zinc fingers

scientific article

Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors

scientific article published on 4 January 2018

The Human Ganglioside Interactome in Live Cells Revealed Using Clickable Photoaffinity Ganglioside Probes

scientific article published on 18 June 2024

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

scientific article published on 21 April 2017

The RosettaDock server for local protein-protein docking

scientific article

The interaction of proteins with solid surfaces

scientific article published on February 2004

The structure of the colorectal cancer-associated enzyme GalNAc-T12 reveals how nonconserved residues dictate its function

scientific article published on 23 September 2019

Thermostability Enhancement of GH 62 α- l -Arabinofuranosidase by Directed Evolution and Rational Design

scientific article published on 14 February 2024

Toward Accurate Prediction and Design of Kinked Alpha Helices in Membrane Proteins

scholarly article

Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction

scientific article

Toward computational design of protein crystals with improved resolution

scientific article published on 2 June 2019

Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking

scientific article

Toward the computational design of protein crystals with improved resolution

scientific article published on 01 November 2019

Truncation of the caspase-related subunit (Gpi8p) of Saccharomyces cerevisiae GPI transamidase: dimerization revealed

scientific article

Using the RosettaSurface algorithm to predict protein structure at mineral surfaces.

scientific article

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).

scientific article

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