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ORCIDJeffrey Skolnick
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2020 – today
- 2024
[c6]Vidit Jain, Mukund Rungta, Yuchen Zhuang, Yue Yu, Zeyu Wang, Mu Gao, Jeffrey Skolnick, Chao Zhang:
HiGen: Hierarchy-Aware Sequence Generation for Hierarchical Text Classification. EACL (1) 2024: 1354-1368- [i1]Vidit Jain, Mukund Rungta, Yuchen Zhuang, Yue Yu, Zeyu Wang, Mu Gao, Jeffrey Skolnick, Chao Zhang:
HiGen: Hierarchy-Aware Sequence Generation for Hierarchical Text Classification. CoRR abs/2402.01696 (2024) - 2023
- [j50]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:
Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. Bioinform. 39(8) (2023) - 2021
- [j49]Mu Gao, Jeffrey Skolnick:
A novel sequence alignment algorithm based on deep learning of the protein folding code. Bioinform. 37(4): 490-496 (2021) - [j48]Mu Gao, Jeffrey Skolnick:
A General Framework to Learn Tertiary Structure for Protein Sequence Characterization. Frontiers Bioinform. 1 (2021) - [j47]Hongyi Zhou, Hongnan Cao, Jeffrey Skolnick:
FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening. J. Chem. Inf. Model. 61(4): 2074-2089 (2021) - [j46]Jeffrey Skolnick, Mu Gao, Hongyi Zhou, Suresh Singh:
AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function. J. Chem. Inf. Model. 61(10): 4827-4831 (2021) - [c5]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:
High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function. MLHPC@SC 2021: 46-57
2010 – 2019
- 2018
- [j45]Hongyi Zhou, Hongnan Cao, Jeffrey Skolnick:
FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules. J. Chem. Inf. Model. 58(11): 2343-2354 (2018) - 2017
- [j44]Sam Tonddast-Navaei, Bharath Srinivasan, Jeffrey Skolnick:
On the importance of composite protein multiple ligand interactions in protein pockets. J. Comput. Chem. 38(15): 1252-1259 (2017) - 2016
- [j43]Hongyi Zhou, Jeffrey Skolnick:
A knowledge-based approach for predicting gene-disease associations. Bioinform. 32(18): 2831-2838 (2016) - 2015
- [j42]Ambrish Roy, Jeffrey Skolnick:
LIGSIFT: an open-source tool for ligand structural alignment and virtual screening. Bioinform. 31(4): 539-544 (2015) - [j41]Hui Sun Lee, Sunhwan Jo, Srayanta Mukherjee, Sang-Jun Park, Jeffrey Skolnick, Jooyoung Lee, Wonpil Im:
GS-align for glycan structure alignment and similarity measurement. Bioinform. 31(16): 2653-2659 (2015) - [j40]Ambrish Roy, Bharath Srinivasan, Jeffrey Skolnick:
PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity. J. Chem. Inf. Model. 55(8): 1757-1770 (2015) - 2014
- [j39]Bharath Srinivasan, Hongyi Zhou, Julia Kubanek, Jeffrey Skolnick:
Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders. J. Cheminformatics 6(1): 16 (2014) - [j38]Tadashi Ando, Jeffrey Skolnick:
Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models. PLoS Comput. Biol. 10(12) (2014) - 2013
- [j37]Mu Gao, Jeffrey Skolnick:
APoc: large-scale identification of similar protein pockets. Bioinform. 29(5): 597-604 (2013) - [j36]Hongyi Zhou, Jeffrey Skolnick:
FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach. J. Chem. Inf. Model. 53(1): 230-240 (2013) - [j35]Sunhwan Jo, Hui Sun Lee, Jeffrey Skolnick, Wonpil Im:
Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling. PLoS Comput. Biol. 9(3) (2013) - [j34]Mu Gao, Jeffrey Skolnick:
A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins. PLoS Comput. Biol. 9(10) (2013) - 2012
- [j33]Narendra Kumar, Jeffrey Skolnick:
EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes. Bioinform. 28(20): 2687-2688 (2012) - 2011
- [c4]Wei Guan, Arkadas Ozakin, Alexander G. Gray, Jose Borreguero, Shashi Bhushan Pandit, Anna Jagielska, Liliana Wroblewska, Jeffrey Skolnick:
Learning Protein Folding Energy Functions. ICDM 2011: 1062-1067 - 2010
- [j32]Shashi Bhushan Pandit, Michal Brylinski, Hongyi Zhou, Mu Gao, Adrian K. Arakaki, Jeffrey Skolnick:
PSiFR: an integrated resource for prediction of protein structure and function. Bioinform. 26(5): 687-688 (2010) - [j31]Mu Gao, Jeffrey Skolnick:
iAlign: a method for the structural comparison of protein-protein interfaces. Bioinform. 26(18): 2259-2265 (2010) - [j30]Michal Brylinski, Jeffrey Skolnick:
Q-DockLHM: Low-resolution refinement for ligand comparative modeling. J. Comput. Chem. 31(5): 1093-1105 (2010) - [j29]Michal Brylinski, Jeffrey Skolnick:
Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening. J. Chem. Inf. Model. 50(10): 1839-1854 (2010)
2000 – 2009
- 2009
- [j28]Jeffrey Skolnick, Michal Brylinski:
FINDSITE: a combined evolution/structure-based approach to protein function prediction. Briefings Bioinform. 10(4): 378-391 (2009) - [j27]Adrian K. Arakaki, Ying Huang, Jeffrey Skolnick:
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. BMC Bioinform. 10 (2009) - [j26]Mu Gao, Jeffrey Skolnick:
From Nonspecific DNA-Protein Encounter Complexes to the Prediction of DNA-Protein Interactions. PLoS Comput. Biol. 5(4) (2009) - [j25]Michal Brylinski, Jeffrey Skolnick:
FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling. PLoS Comput. Biol. 5(6) (2009) - [j24]Mu Gao, Jeffrey Skolnick:
A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome. PLoS Comput. Biol. 5(11) (2009) - 2008
- [j23]Shashi Bhushan Pandit, Jeffrey Skolnick:
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score. BMC Bioinform. 9 (2008) - [j22]Ryangguk Kim, Jeffrey Skolnick:
Assessment of programs for ligand binding affinity prediction. J. Comput. Chem. 29(8): 1316-1331 (2008) - [j21]Piotr Rotkiewicz, Jeffrey Skolnick:
Fast procedure for reconstruction of full-atom protein models from reduced representations. J. Comput. Chem. 29(9): 1460-1465 (2008) - [j20]Michal Brylinski, Jeffrey Skolnick:
Q-Dock: Low-resolution flexible ligand docking with pocket-specific threading restraints. J. Comput. Chem. 29(10): 1574-1588 (2008) - 2007
- [j19]Anna Jagielska, Jeffrey Skolnick:
Origin of intrinsic 310-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field. J. Comput. Chem. 28(10): 1648-1657 (2007) - [j18]Liliana Wroblewska, Jeffrey Skolnick:
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking. J. Comput. Chem. 28(12): 2059-2066 (2007) - 2006
- [j17]Yang Zhang, Mark E. DeVries, Jeffrey Skolnick:
Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome. PLoS Comput. Biol. 2(2) (2006) - [j16]Yang Zhang, Mark E. DeVries, Jeffrey Skolnick:
Correction: Structure Modeling of All Identified G Protein-Coupled Receptors in the Human Genome. PLoS Comput. Biol. 2(3) (2006) - 2005
- [j15]Eckart Bindewald, Jeffrey Skolnick:
A scoring function for docking ligands to low-resolution protein structures. J. Comput. Chem. 26(4): 374-383 (2005) - 2004
- [j14]Adrian K. Arakaki, Yang Zhang, Jeffrey Skolnick:
Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment. Bioinform. 20(7): 1087-1096 (2004) - [j13]Yang Zhang, Jeffrey Skolnick:
SPICKER: A clustering approach to identify near-native protein folds. J. Comput. Chem. 25(6): 865-871 (2004) - 2003
- [j12]Michal J. Boniecki, Piotr Rotkiewicz, Jeffrey Skolnick, Andrzej Kolinski:
Protein fragment reconstruction using various modeling techniques. J. Comput. Aided Mol. Des. 17(11): 725-738 (2003) - 2002
- [j11]Marek Wojciechowski, Jeffrey Skolnick:
Docking of small ligands to low-resolution and theoretically predicted receptor structures. J. Comput. Chem. 23(1): 189-197 (2002) - 2001
- [j10]Yury V. Bukhman, Jeffrey Skolnick:
BioMolQuest: integrated database-based retrieval of protein structural and functional information. Bioinform. 17(5): 468-478 (2001) - [j9]Jeffrey Skolnick, Andrzej Kolinski:
Computational studies of protein folding. Comput. Sci. Eng. 3(3): 40-50 (2001) - [j8]Jeffrey Skolnick, Andrzej Kolinski:
Computational studies of protein folding. Comput. Sci. Eng. 3(5): 40-50 (2001) - [j7]Marcos R. Betancourt, Jeffrey Skolnick:
Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions. J. Comput. Chem. 22(3): 339-353 (2001)
1990 – 1999
- 1999
- [c3]Jeffrey Skolnick, Richard H. Lathrop:
Protein Structure Prediction - Session Introduction. Pacific Symposium on Biocomputing 1999: 480-481 - 1998
- [j6]Boris A. Reva, Dmitrii S. Rykunov, Alexei V. Finkelstein, Jeffrey Skolnick:
Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach. J. Comput. Biol. 5(3): 531-538 (1998) - [c2]Boris A. Reva, Alexei V. Finkelstein, Jeffrey Skolnick:
A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. RECOMB 1998: 214-220 - 1997
- [j5]Mariusz Milik, Andrzej Kolinski, Jeffrey Skolnick:
Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates. J. Comput. Chem. 18(1): 80-85 (1997) - 1995
- [c1]Mariusz Milik, Jeffrey Skolnick:
An Object-Oriented Environment for Artifical Evolution of Protein Sequences: The Example of Rational Design of Transmembrane Sequences. Evolutionary Programming 1995: 603-613 - 1994
- [j4]Adam Godzik, Jeffrey Skolnick:
Flexible algorithm for direct multiple alignment of protein structures and sequences. Comput. Appl. Biosci. 10(6): 587-596 (1994) - 1993
- [j3]Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick:
De novo and inverse folding predictions of protein structure and dynamics. J. Comput. Aided Mol. Des. 7(4): 397-438 (1993) - [j2]Maciej Baginki, Lucjan Piela, Jeffrey Skolnick:
The ethylene group as a peptide bond mimicking unit: A theoretical conformational analysis. J. Comput. Chem. 14(4): 471-477 (1993) - [j1]Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick:
Lattice representations of globular proteins: How good are they? J. Comput. Chem. 14(10): 1194-1202 (1993)
Coauthor Index
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last updated on 2024-07-19 18:29 CEST by the dblp team
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