Jeffrey Skolnick
Orcid: 0000-0002-1877-4958
According to our database1,
Jeffrey Skolnick
authored at least 55 papers
between 1993 and 2024.
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Bibliography
2024
Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics, 2024
2023
Predicted structural proteome of <i>Sphagnum divinum</i> and proteome-scale annotation.
Bioinform., August, 2023
2021
J. Chem. Inf. Model., 2021
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function.
J. Chem. Inf. Model., 2021
A General Framework to Learn Tertiary Structure for Protein Sequence Characterization.
Frontiers Bioinform., 2021
A novel sequence alignment algorithm based on deep learning of the protein folding code.
Bioinform., 2021
High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function.
Proceedings of the IEEE/ACM Workshop on Machine Learning in High Performance Computing Environments, 2021
2018
FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules.
J. Chem. Inf. Model., 2018
2017
On the importance of composite protein multiple ligand interactions in protein pockets.
J. Comput. Chem., 2017
2016
Bioinform., 2016
2015
<i>PoLi</i>: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity.
J. Chem. Inf. Model., 2015
Bioinform., 2015
2014
Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models.
PLoS Comput. Biol., 2014
Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders.
J. Cheminformatics, 2014
2013
Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling.
PLoS Comput. Biol., 2013
PLoS Comput. Biol., 2013
FINDSITE<sup>comb</sup>: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach.
J. Chem. Inf. Model., 2013
2012
EFICAz<sup>2.5</sup>: application of a high-precision enzyme function predictor to 396 proteomes.
Bioinform., 2012
2011
Proceedings of the 11th IEEE International Conference on Data Mining, 2011
2010
Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening.
J. Chem. Inf. Model., 2010
J. Comput. Chem., 2010
Bioinform., 2010
Bioinform., 2010
2009
A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome.
PLoS Comput. Biol., 2009
From Nonspecific DNA-Protein Encounter Complexes to the Prediction of DNA-Protein Interactions.
PLoS Comput. Biol., 2009
PLoS Comput. Biol., 2009
EFICAz<sup>2</sup>: enzyme function inference by a combined approach enhanced by machine learning.
BMC Bioinform., 2009
FINDSITE: a combined evolution/structure-based approach to protein function prediction.
Briefings Bioinform., 2009
2008
Fast procedure for reconstruction of full-atom protein models from reduced representations.
J. Comput. Chem., 2008
J. Comput. Chem., 2008
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints.
J. Comput. Chem., 2008
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score.
BMC Bioinform., 2008
2007
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking.
J. Comput. Chem., 2007
Origin of intrinsic 3<sub>10</sub>-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field.
J. Comput. Chem., 2007
2006
Correction: Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome.
PLoS Comput. Biol., 2006
Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome.
PLoS Comput. Biol., 2006
2005
J. Comput. Chem., 2005
2004
J. Comput. Chem., 2004
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment.
Bioinform., 2004
2003
J. Comput. Aided Mol. Des., 2003
2002
Docking of small ligands to low-resolution and theoretically predicted receptor structures.
J. Comput. Chem., 2002
2001
Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions.
J. Comput. Chem., 2001
BioMolQuest: integrated database-based retrieval of protein structural and functional information.
Bioinform., 2001
1999
Proceedings of the 4th Pacific Symposium on Biocomputing, 1999
1998
Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach.
J. Comput. Biol., 1998
A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins.
Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998
1997
Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates.
J. Comput. Chem., 1997
1995
An Object-Oriented Environment for Artifical Evolution of Protein Sequences: The Example of Rational Design of Transmembrane Sequences.
Proceedings of the Fourth Annual Conference on Evolutionary Programming, 1995
1994
Flexible algorithm for direct multiple alignment of protein structures and sequences.
Comput. Appl. Biosci., 1994
1993
J. Comput. Chem., 1993
The ethylene group as a peptide bond mimicking unit: A theoretical conformational analysis.
J. Comput. Chem., 1993
J. Comput. Aided Mol. Des., 1993