De novo and inverse folding predictions of protein structure and dynamics. - Adam Godzik; Andrzej Kolinski; Jeffrey Skolnick (J. Comput. Aided Mol. Des., 1993)

The ethylene group as a peptide bond mimicking unit: A theoretical conformational analysis. - Maciej Baginki; Lucjan Piela; Jeffrey Skolnick (J. Comput. Chem., 1993)

Lattice representations of globular proteins: How good are they? - Adam Godzik; Andrzej Kolinski; Jeffrey Skolnick (J. Comput. Chem., 1993)

Flexible algorithm for direct multiple alignment of protein structures and sequences. - Adam Godzik; Jeffrey Skolnick (Comput. Appl. Biosci., 1994)

An Object-Oriented Environment for Artifical Evolution of Protein Sequences: The Example of Rational Design of Transmembrane Sequences. - Mariusz Milik; Jeffrey Skolnick (Evolutionary Programming, 1995)

Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates. - Mariusz Milik; Andrzej Kolinski; Jeffrey Skolnick (J. Comput. Chem., 1997)

A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. - Boris A. Reva; Alexei V. Finkelstein; Jeffrey Skolnick (RECOMB, 1998)

Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach. - Boris A. Reva; Dmitrii S. Rykunov; Alexei V. Finkelstein; Jeffrey Skolnick (J. Comput. Biol., 1998)

Protein Structure Prediction - Session Introduction. - Jeffrey Skolnick; Richard H. Lathrop (Pacific Symposium on Biocomputing, 1999)

BioMolQuest: integrated database-based retrieval of protein structural and functional information. - Yury V. Bukhman; Jeffrey Skolnick (Bioinform., 2001)

Computational studies of protein folding. - Jeffrey Skolnick; Andrzej Kolinski (Comput. Sci. Eng., 2001)

Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions. - Marcos R. Betancourt; Jeffrey Skolnick (J. Comput. Chem., 2001)

Docking of small ligands to low-resolution and theoretically predicted receptor structures. - Marek Wojciechowski 004; Jeffrey Skolnick (J. Comput. Chem., 2002)

Protein fragment reconstruction using various modeling techniques. - Michal J. Boniecki; Piotr Rotkiewicz; Jeffrey Skolnick; Andrzej Kolinski (J. Comput. Aided Mol. Des., 2003)

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. - Adrian K. Arakaki; Yang Zhang 040; Jeffrey Skolnick (Bioinform., 2004)

SPICKER: A clustering approach to identify near-native protein folds. - Yang Zhang 040; Jeffrey Skolnick (J. Comput. Chem., 2004)

A scoring function for docking ligands to low-resolution protein structures. - Eckart Bindewald; Jeffrey Skolnick (J. Comput. Chem., 2005)

Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome. - Yang Zhang 040; Mark E. DeVries; Jeffrey Skolnick (PLoS Comput. Biol., 2006)

Correction: Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome. - Yang Zhang 040; Mark E. DeVries; Jeffrey Skolnick (PLoS Comput. Biol., 2006)

Origin of intrinsic 310-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field. - Anna Jagielska; Jeffrey Skolnick (J. Comput. Chem., 2007)

Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking. - Liliana Wroblewska; Jeffrey Skolnick (J. Comput. Chem., 2007)

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. - Shashi Bhushan Pandit; Jeffrey Skolnick (BMC Bioinform., 2008)

Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. - Michal Brylinski; Jeffrey Skolnick (J. Comput. Chem., 2008)

Assessment of programs for ligand binding affinity prediction. - Ryangguk Kim; Jeffrey Skolnick (J. Comput. Chem., 2008)

Fast procedure for reconstruction of full-atom protein models from reduced representations. - Piotr Rotkiewicz; Jeffrey Skolnick (J. Comput. Chem., 2008)

FINDSITE: a combined evolution/structure-based approach to protein function prediction. - Jeffrey Skolnick; Michal Brylinski (Briefings Bioinform., 2009)

EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. - Adrian K. Arakaki; Ying Huang; Jeffrey Skolnick (BMC Bioinform., 2009)

FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling. - Michal Brylinski; Jeffrey Skolnick (PLoS Comput. Biol., 2009)

From Nonspecific DNA-Protein Encounter Complexes to the Prediction of DNA-Protein Interactions. - Mu Gao; Jeffrey Skolnick (PLoS Comput. Biol., 2009)

A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome. - Mu Gao; Jeffrey Skolnick (PLoS Comput. Biol., 2009)

iAlign: a method for the structural comparison of protein-protein interfaces. - Mu Gao; Jeffrey Skolnick (Bioinform., 2010)

PSiFR: an integrated resource for prediction of protein structure and function. - Shashi Bhushan Pandit; Michal Brylinski; Hongyi Zhou; Mu Gao; Adrian K. Arakaki; Jeffrey Skolnick (Bioinform., 2010)

Q-DockLHM: Low-resolution refinement for ligand comparative modeling. - Michal Brylinski; Jeffrey Skolnick (J. Comput. Chem., 2010)

Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening. - Michal Brylinski; Jeffrey Skolnick (J. Chem. Inf. Model., 2010)

Learning Protein Folding Energy Functions. - Wei Guan 002; Arkadas Ozakin; Alexander G. Gray; Jose Borreguero; Shashi Bhushan Pandit; Anna Jagielska; Liliana Wroblewska; Jeffrey Skolnick (ICDM, 2011)

EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. - Narendra Kumar; Jeffrey Skolnick (Bioinform., 2012)

APoc: large-scale identification of similar protein pockets. - Mu Gao; Jeffrey Skolnick (Bioinform., 2013)

FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach. - Hongyi Zhou; Jeffrey Skolnick (J. Chem. Inf. Model., 2013)

A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins. - Mu Gao; Jeffrey Skolnick (PLoS Comput. Biol., 2013)

Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling. - Sunhwan Jo; Hui Sun Lee; Jeffrey Skolnick; Wonpil Im (PLoS Comput. Biol., 2013)

Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. - Bharath Srinivasan; Hongyi Zhou; Julia Kubanek; Jeffrey Skolnick (J. Cheminformatics, 2014)

Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models. - Tadashi Ando; Jeffrey Skolnick (PLoS Comput. Biol., 2014)

GS-align for glycan structure alignment and similarity measurement. - Hui Sun Lee; Sunhwan Jo; Srayanta Mukherjee; Sang-Jun Park; Jeffrey Skolnick; Jooyoung Lee; Wonpil Im (Bioinform., 2015)

LIGSIFT: an open-source tool for ligand structural alignment and virtual screening. - Ambrish Roy; Jeffrey Skolnick (Bioinform., 2015)

PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity. - Ambrish Roy; Bharath Srinivasan; Jeffrey Skolnick (J. Chem. Inf. Model., 2015)

A knowledge-based approach for predicting gene-disease associations. - Hongyi Zhou; Jeffrey Skolnick (Bioinform., 2016)

On the importance of composite protein multiple ligand interactions in protein pockets. - Sam Tonddast-Navaei; Bharath Srinivasan; Jeffrey Skolnick (J. Comput. Chem., 2017)

FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules. - Hongyi Zhou; Hongnan Cao; Jeffrey Skolnick (J. Chem. Inf. Model., 2018)

High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function. - Mu Gao; Peik Lund-Andersen; Alex Morehead; Sajid Mahmud; Chen Chen; Xiao Chen; Nabin Giri; Raj S. Roy; Farhan Quadir; T. Chad Effler; Ryan Prout; Subil Abraham; et al. (MLHPC@SC, 2021)

A novel sequence alignment algorithm based on deep learning of the protein folding code. - Mu Gao; Jeffrey Skolnick (Bioinform., 2021)

A General Framework to Learn Tertiary Structure for Protein Sequence Characterization. - Mu Gao; Jeffrey Skolnick (Frontiers Bioinform., 2021)

AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function. - Jeffrey Skolnick; Mu Gao; Hongyi Zhou; Suresh Singh (J. Chem. Inf. Model., 2021)

FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening. - Hongyi Zhou; Hongnan Cao; Jeffrey Skolnick (J. Chem. Inf. Model., 2021)

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. - Russell B. Davidson; Mark Coletti; Mu Gao; Bryan Piatkowski; Avinash Sreedasyam; Farhan Quadir; David J. Weston; Jeremy Schmutz; Jianlin Cheng; Jeffrey Skolnick; Jerry M. Parks; Ada Sedova (Bioinform., 2023)

HiGen: Hierarchy-Aware Sequence Generation for Hierarchical Text Classification. - Vidit Jain; Mukund Rungta; Yuchen Zhuang; Yue Yu 001; Zeyu Wang; Mu Gao; Jeffrey Skolnick; Chao Zhang 014 (EACL (1), 2024)

Entabolons: How Metabolites Modify the Biochemical Function of Proteins and Cause the Correlated Behavior of Proteins in Pathways. - Jeffrey Skolnick; Bharath Srinivasan; Samuel Skolnick; Brice Edelman; Hongyi Zhou (J. Chem. Inf. Model., 2025)

Valsci: an open-source, self-hostable literature review utility for automated large-batch scientific claim verification using large language models. - Brice Edelman; Jeffrey Skolnick (BMC Bioinform., 2025)