Jeffrey Skolnick

62 papers A* 1B 1Misc 1Journal 56Unranked 3

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	GlueFinder: A Data-Driven Framework for the Rational Discovery of Molecular Glues. J. Chem. Inf. Model. Jeffrey Skolnick, Bharath Srinivasan, Hongyi Zhou
2026	J	`jnl`	MENDELSEEK: An algorithm that predicts mendelian genes and elucidates what makes them special. PLoS Comput. Biol. Hongyi Zhou, Brice Edelman, Jeffrey Skolnick
2026	J	`jnl`	Scalable discovery and validation of order-specific electronic health record event trajectories for interpretable adverse-outcome risk estimation. J. Biomed. Informatics Brice Edelman, Hannah Kim, Jeffrey Skolnick
2025	J	`jnl`	AF3Complex yields improved structural predictions of protein complexes. Bioinform. Jonathan Feldman, Jeffrey Skolnick
2025	J	`jnl`	Entabolons: How Metabolites Modify the Biochemical Function of Proteins and Cause the Correlated Behavior of Proteins in Pathways. J. Chem. Inf. Model. Jeffrey Skolnick, Bharath Srinivasan, Samuel Skolnick, Brice Edelman, Hongyi Zhou
2025	J	`jnl`	Valsci: an open-source, self-hostable literature review utility for automated large-batch scientific claim verification using large language models. BMC Bioinform. Brice Edelman, Jeffrey Skolnick
2024	—	`conf`	HiGen: Hierarchy-Aware Sequence Generation for Hierarchical Text Classification. EACL (1) Vidit Jain, Mukund Rungta, Yuchen Zhuang, Yue Yu, Zeyu Wang, Mu Gao, Jeffrey Skolnick, Chao Zhang
2024	J	`jnl`	HiGen: Hierarchy-Aware Sequence Generation for Hierarchical Text Classification. CoRR Vidit Jain, Mukund Rungta, Yuchen Zhuang, Yue Yu, Zeyu Wang, Mu Gao, Jeffrey Skolnick, Chao Zhang
2023	J	`jnl`	Predicted structural proteome of Bioinform. 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
2021	J	`jnl`	A General Framework to Learn Tertiary Structure for Protein Sequence Characterization. Frontiers Bioinform. Mu Gao, Jeffrey Skolnick
2021	J	`jnl`	A novel sequence alignment algorithm based on deep learning of the protein folding code. Bioinform. Mu Gao, Jeffrey Skolnick
2021	J	`jnl`	AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function. J. Chem. Inf. Model. Jeffrey Skolnick, Mu Gao, Hongyi Zhou, Suresh Singh
2021	J	`jnl`	FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening. J. Chem. Inf. Model. Hongyi Zhou, Hongnan Cao, Jeffrey Skolnick
2021	—	`conf`	High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function. MLHPC@SC 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, Wael R. Elwasif, Nicholas Quentin Haas, Jeffrey Skolnick, Jianlin Cheng, Ada Sedova
2018	J	`jnl`	FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules. J. Chem. Inf. Model. Hongyi Zhou, Hongnan Cao, Jeffrey Skolnick
2017	J	`jnl`	On the importance of composite protein multiple ligand interactions in protein pockets. J. Comput. Chem. Sam Tonddast-Navaei, Bharath Srinivasan, Jeffrey Skolnick
2016	J	`jnl`	A knowledge-based approach for predicting gene-disease associations. Bioinform. Hongyi Zhou, Jeffrey Skolnick
2015	J	`jnl`	GS-align for glycan structure alignment and similarity measurement. Bioinform. Hui Sun Lee, Sunhwan Jo, Srayanta Mukherjee, Sang-Jun Park, Jeffrey Skolnick, Jooyoung Lee, Wonpil Im
2015	J	`jnl`	LIGSIFT: an open-source tool for ligand structural alignment and virtual screening. Bioinform. Ambrish Roy, Jeffrey Skolnick
2014	J	`jnl`	Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. J. Cheminformatics Bharath Srinivasan, Hongyi Zhou, Julia Kubanek, Jeffrey Skolnick
2014	J	`jnl`	Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models. PLoS Comput. Biol. Tadashi Ando, Jeffrey Skolnick
2013	J	`jnl`	A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins. PLoS Comput. Biol. Mu Gao, Jeffrey Skolnick
2013	J	`jnl`	APoc: large-scale identification of similar protein pockets. Bioinform. Mu Gao, Jeffrey Skolnick
2013	J	`jnl`	FINDSITE J. Chem. Inf. Model. Hongyi Zhou, Jeffrey Skolnick
2013	J	`jnl`	Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling. PLoS Comput. Biol. Sunhwan Jo, Hui Sun Lee, Jeffrey Skolnick, Wonpil Im
2012	J	`jnl`	EFICAz Bioinform. Narendra Kumar, Jeffrey Skolnick
2011	A*	`conf`	Learning Protein Folding Energy Functions. ICDM Wei Guan, Arkadas Ozakin, Alexander G. Gray, Jose Borreguero, Shashi Bhushan Pandit, Anna Jagielska, Liliana Wroblewska, Jeffrey Skolnick
2010	J	`jnl`	Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening. J. Chem. Inf. Model. Michal Brylinski, Jeffrey Skolnick
2010	J	`jnl`	PSiFR: an integrated resource for prediction of protein structure and function. Bioinform. Shashi Bhushan Pandit, Michal Brylinski, Hongyi Zhou, Mu Gao, Adrian K. Arakaki, Jeffrey Skolnick
2010	J	`jnl`	Q-Dock J. Comput. Chem. Michal Brylinski, Jeffrey Skolnick
2010	J	`jnl`	iAlign: a method for the structural comparison of protein-protein interfaces. Bioinform. Mu Gao, Jeffrey Skolnick
2009	J	`jnl`	A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome. PLoS Comput. Biol. Mu Gao, Jeffrey Skolnick
2009	J	`jnl`	EFICAz BMC Bioinform. Adrian K. Arakaki, Ying Huang, Jeffrey Skolnick
2009	J	`jnl`	FINDSITE PLoS Comput. Biol. Michal Brylinski, Jeffrey Skolnick
2009	J	`jnl`	FINDSITE: a combined evolution/structure-based approach to protein function prediction. Briefings Bioinform. Jeffrey Skolnick, Michal Brylinski
2009	J	`jnl`	From Nonspecific DNA-Protein Encounter Complexes to the Prediction of DNA-Protein Interactions. PLoS Comput. Biol. Mu Gao, Jeffrey Skolnick
2008	J	`jnl`	Assessment of programs for ligand binding affinity prediction. J. Comput. Chem. Ryangguk Kim, Jeffrey Skolnick
2008	J	`jnl`	Fast procedure for reconstruction of full-atom protein models from reduced representations. J. Comput. Chem. Piotr Rotkiewicz, Jeffrey Skolnick
2008	J	`jnl`	Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinform. Shashi Bhushan Pandit, Jeffrey Skolnick
2008	J	`jnl`	Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J. Comput. Chem. Michal Brylinski, Jeffrey Skolnick
2007	J	`jnl`	Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking. J. Comput. Chem. Liliana Wroblewska, Jeffrey Skolnick
2007	J	`jnl`	Origin of intrinsic 3 J. Comput. Chem. Anna Jagielska, Jeffrey Skolnick
2006	J	`jnl`	Correction: Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome. PLoS Comput. Biol. Yang Zhang, Mark E. DeVries, Jeffrey Skolnick
2006	J	`jnl`	Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome. PLoS Comput. Biol. Yang Zhang, Mark E. DeVries, Jeffrey Skolnick
2005	J	`jnl`	A scoring function for docking ligands to low-resolution protein structures. J. Comput. Chem. Eckart Bindewald, Jeffrey Skolnick
2004	J	`jnl`	Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinform. Adrian K. Arakaki, Yang Zhang, Jeffrey Skolnick
2004	J	`jnl`	SPICKER: A clustering approach to identify near-native protein folds. J. Comput. Chem. Yang Zhang, Jeffrey Skolnick
2003	J	`jnl`	Protein fragment reconstruction using various modeling techniques. J. Comput. Aided Mol. Des. Michal J. Boniecki, Piotr Rotkiewicz, Jeffrey Skolnick, Andrzej Kolinski
2002	J	`jnl`	Docking of small ligands to low-resolution and theoretically predicted receptor structures. J. Comput. Chem. Marek Wojciechowski, Jeffrey Skolnick
2001	J	`jnl`	BioMolQuest: integrated database-based retrieval of protein structural and functional information. Bioinform. Yury V. Bukhman, Jeffrey Skolnick
2001	J	`jnl`	Computational studies of protein folding. Comput. Sci. Eng. Jeffrey Skolnick, Andrzej Kolinski
2001	J	`jnl`	Computational studies of protein folding. Comput. Sci. Eng. Jeffrey Skolnick, Andrzej Kolinski
2001	J	`jnl`	Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions. J. Comput. Chem. Marcos R. Betancourt, Jeffrey Skolnick
1999	Misc	`conf`	Protein Structure Prediction - Session Introduction. Pacific Symposium on Biocomputing Jeffrey Skolnick, Richard H. Lathrop
1998	B	`conf`	A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. RECOMB Boris A. Reva, Alexei V. Finkelstein, Jeffrey Skolnick
1998	J	`jnl`	Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach. J. Comput. Biol. Boris A. Reva, Dmitrii S. Rykunov, Alexei V. Finkelstein, Jeffrey Skolnick
1997	J	`jnl`	Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates. J. Comput. Chem. Mariusz Milik, Andrzej Kolinski, Jeffrey Skolnick
1995	—	`conf`	An Object-Oriented Environment for Artifical Evolution of Protein Sequences: The Example of Rational Design of Transmembrane Sequences. Evolutionary Programming Mariusz Milik, Jeffrey Skolnick
1994	J	`jnl`	Flexible algorithm for direct multiple alignment of protein structures and sequences. Comput. Appl. Biosci. Adam Godzik, Jeffrey Skolnick
1993	J	`jnl`	De novo and inverse folding predictions of protein structure and dynamics. J. Comput. Aided Mol. Des. Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick
1993	J	`jnl`	Lattice representations of globular proteins: How good are they? J. Comput. Chem. Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick
1993	J	`jnl`	The ethylene group as a peptide bond mimicking unit: A theoretical conformational analysis. J. Comput. Chem. Maciej Baginki, Lucjan Piela, Jeffrey Skolnick