J. Skolnick

Jeffrey Skolnick, Tadashi Ando, J. Skolnick, 2011, Quantum bioinformatics IV : from quantum information to bio-informatics : Tokyo University of Science, Japan, 10-13 March 2010.

Computational studies of protein folding

Andrzej Kolinski, Jeffrey Skolnick, J. Skolnick, 2001, Comput. Sci. Eng..

Effect of double bonds on the dynamics of hydrocarbon chains

J. Skolnick, A. Kolinski, Y. K. Levine, 1992 .

Accurate reconstruction of all‐atom protein representations from side‐chain‐based low‐resolution models

M Feig, P Rotkiewicz, A Kolinski, 2000, Proteins.

Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates

Mariusz Milik, Andrzej Kolinski, Jeffrey Skolnick, 1997, J. Comput. Chem..

Efficient algorithm for the reconstruction of a protein backbone from the α‐carbon coordinates

Jeffrey Skolnick, Antonio Rey, J. Skolnick, 1992 .

Monte Carlo dynamics study of motions in cis‐unsaturated hydrocarbon chains

Y. K. Levine, J. Skolnick, A. Kolinski, 1991 .

Computer simulations of protein folding with a small number of distance restraints.

J. Skolnick, A. Kolinski, A. Sikorski, 2002, Acta biochimica Polonica.

Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper.

J. Skolnick, A. Kolinski, C. Brooks, 1995, Journal of molecular biology.

Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. II. Alpha-helical motifs.

J Skolnick, J. Skolnick, A. Sikorski, 1990, Journal of molecular biology.

On the emergence of homochirality and life itself

J. Skolnick, M. Gao, 2021, The biochemist.

Faculty Opinions recommendation of LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.

Jeffrey Skolnick, J. Skolnick, 2016 .

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

Jeffrey Skolnick, Shashi Bhushan Pandit, J. Skolnick, 2008, BMC Bioinformatics.

Computer design of idealized β‐motifs

Andrzej Kolinski, Jeffrey Skolnick, J. Skolnick, 1995 .

Neural network system for the evaluation of side-chain packing in protein structures.

A Kolinski, J Skolnick, M Milik, 1995, Protein engineering.

From independent modules to molten globules: observations on the nature of protein folding intermediates.

A Kolinski, J Skolnick, A Godzik, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Method for low resolution prediction of small protein tertiary structure.

A Kolinski, J Skolnick, J. Skolnick, 1997, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Dynamic Monte Carlo Simulations of Globular Protein Folding, Structure and Dynamics

J. Skolnick, A. Kolinski, A. Sikorski, 1990 .

Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders

Hongyi Zhou, Jeffrey Skolnick, Bharath Srinivasan, 2014, Journal of Cheminformatics.

FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach

Hongyi Zhou, Jeffrey Skolnick, J. Skolnick, 2013, J. Chem. Inf. Model..

A Threading-Based Method for the Prediction of DNABinding Proteins with Application to the Human GenomeProteins with Application to the Human Genome

Jeffrey Skolnick, Mu Gao, J. Skolnick, 2009 .

Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment

Yang Zhang, Jeffrey Skolnick, Adrian K. Arakaki, 2004, Bioinform..

TASSER_WT: a protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets.

Jeffrey Skolnick, J. Skolnick, Seung Yup Lee, 2010, Biophysical journal.

Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome

J. Skolnick, Yang Zhang, M. DeVries, 2006, PLoS Comput. Biol..

TASSER‐based refinement of NMR structures

Yang Zhang, Jeffrey Skolnick, J. Skolnick, 2006, Proteins.

A scoring function for docking ligands to low‐resolution protein structures

Eckart Bindewald, Jeffrey Skolnick, J. Skolnick, 2005, J. Comput. Chem..

Scoring function for automated assessment of protein structure template quality

J. Skolnick, Yang Zhang, Yang Zhang, 2004, Proteins.

Numerical estimation of entropy loss on dimerization: improved prediction of the quaternary structure of the GCN4 leucine zipper

J. Skolnick, A. Kolinski, J. Viñals, 2002, physics/0204006.

Differential kinase activity of ACVR1 G328V and R206H mutations with implications to possible TβRI cross-talk in diffuse intrinsic pontine glioma

J. Skolnick, Hongyi Zhou, M. Jin, 2020, Scientific Reports.

ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations

Jeffrey Skolnick, Mu Gao, Hongyi Zhou, 2018, PloS one.

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

Charles L. Brooks, Adrian W. R. Serohijos, John Moult, 2009, Nature Reviews Drug Discovery.

Structure of Proteins : New Approach to Molecular Modeling

J. Skolnick, A. Kolinski, P. Rotkiewicz, 2001 .

Analysis of TASSER‐based CASP7 protein structure prediction results

Seung Yup Lee, Jeffrey Skolnick, Hongyi Zhou, 2007, Proteins.

From genes to protein structure and function: novel applications of computational approaches in the genomic era.

J. Skolnick, J. Fetrow, 2000, Trends in biotechnology.

Scoring function for automated assessment of protein structure template quality

J. Skolnick, Yang Zhang, 2007 .

Q‐DockLHM: Low‐resolution refinement for ligand comparative modeling

Michal Brylinski, Jeffrey Skolnick, J. Skolnick, 2009, J. Comput. Chem..

Phenomenological model of the stress-strain behavior of glassy polymers

J. Skolnick, J. Schaefer, R. Yaris, 1984 .

Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach

Jeffrey Skolnick, Alexei V. Finkelstein, Boris A. Reva, 1998, J. Comput. Biol..

E. coli DHFR complex with inhibitor AMPQD

J. Skolnick, Hongyi Zhou, H. Cao, 2018 .

The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release

J. Skolnick, Hongyi Zhou, H. Cao, 2018, Communications Biology.

EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes

Jeffrey Skolnick, Narendra Kumar, J. Skolnick, 2012, Bioinform..

On the apparent radius of gyration of linear polymers and the experimental determination of the excluded-volume parameter

A. J. Barrett, J. Skolnick, 1988 .

Docking of small ligands to low‐resolution and theoretically predicted receptor structures

Marek Wojciechowski, Jeffrey Skolnick, J. Skolnick, 2002, J. Comput. Chem..

Development of a physics-based force field for the scoring and refinement of protein models.

Liliana Wroblewska, Jeffrey Skolnick, Anna Jagielska, 2008, Biophysical journal.

The protein folding problem: a biophysical enigma.

A Kolinski, J Skolnick, J. Skolnick, 2002, Current pharmaceutical biotechnology.

Effects of confinement on models of intracellular macromolecular dynamics

Jeffrey Skolnick, Edmond Chow, J. Skolnick, 2015, Proceedings of the National Academy of Sciences.

DESTINI: A deep-learning approach to contact-driven protein structure prediction

Hongyi Zhou, Jeffrey Skolnick, Mu Gao, 2019, Scientific Reports.

Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model.

J. Skolnick, A. Kolinski, P. Romiszowski, 2003, Biophysical journal.

Application of a high coordination lattice model in protein structure prediction

J. Skolnick, A. Kolinski, P. Rotkiewicz, 1998 .

Monte Carlo Models of Spontaneous Insertion of Peptides into Lipid Membranes

J. Skolnick, M. Milik, 1996 .

Monte-Carlo Simulation

J. Skolnick, Sitao Wu, Yang Zhang, 2022 .

Learning Protein Folding Energy Functions

Alexander G. Gray, Wei Guan, Jeffrey Skolnick, 2011, 2011 IEEE 11th International Conference on Data Mining.

Segment assembly, structure alignment and iterative simulation in protein structure prediction

J. Skolnick, Yang Zhang, 2013, BMC Biology.

TASSER_low‐zsc: An approach to improve structure prediction using low z‐score–ranked templates

Jeffrey Skolnick, Shashi B Pandit, J. Skolnick, 2010, Proteins.

Ab initio protein structure prediction using chunk-TASSER.

J. Skolnick, Hongyi Zhou, 2007, Biophysical journal.

A unified approach to the prediction of protein structure and function

Andrzej Kolinski, Jeffrey Skolnick, J. Skolnick, 2002 .

WeFold: A coopetition for protein structure prediction

George A. Khoury, Adam K. Sieradzan, Tomasz K. Wirecki, 2014, Proteins.

Q‐Dock: Low‐resolution flexible ligand docking with pocket‐specific threading restraints

J. Skolnick, M. Brylinski, Michal Brylinski, 2008, J. Comput. Chem..

Improving threading algorithms for remote homology modeling by combining fragment and template comparisons

Jeffrey Skolnick, Hongyi Zhou, J. Skolnick, 2010, Proteins.

Genomic‐scale comparison of sequence‐ and structure‐based methods of function prediction: Does structure provide additional insight?

J. Skolnick, J. Fetrow, N. Siew, 2001, Protein science : a publication of the Protein Society.

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Jerry M. Parks, Russell B. Davidson, J. Skolnick, 2023, Bioinform..

Correction: Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome

J. Skolnick, Yang Zhang, M. DeVries, 2006, PLoS Comput. Biol..

J. Skolnick, K. McKernan, Hongyi Zhou, 2015, Mitochondrion.

Bioinformatics Applications Note Structural Bioinformatics Psifr: an Integrated Resource for Prediction of Protein Structure and Function

J. Skolnick, Hongyi Zhou, S. Pandit, 2022 .

LeMeDISCO is a computational method for large-scale prediction & molecular interpretation of disease comorbidity

J. Skolnick, Hongyi Zhou, B. Ilkowski, 2022, Communications Biology.

Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs

J. Skolnick, Hongyi Zhou, Ambrish Roy, 2018, Medicinal research reviews.

Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants.

J. Skolnick, E. Shakhnovich, João V. Rodrigues, 2017, ACS chemical biology.

EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes

J. Skolnick, Narendra Kumar, 2012, Bioinform..

Identification of metabolites with anticancer properties by computational metabolomics

J. Skolnick, A. Arakaki, Ying Huang, 2008, Molecular Cancer.

Spontaneous insertion of polypeptide chains into membranes: a Monte Carlo model.

J Skolnick, M Milik, J. Skolnick, 1992, Proceedings of the National Academy of Sciences of the United States of America.

Monte Carlo Study of Local Orientational Order in a Semiflexible Polymer Melt Model

J. Skolnick, A. Kolinski, R. Yaris, 1986 .

Polymer Melt Model

J. Skolnick, A. Kolinski, R. Yaris, 2001 .

A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition.

Dominik Gront, Andrzej Kolinski, Jeffrey Skolnick, 2003, Biopolymers.

Colligative Properties of Helical Polyelectrolytes

J. Skolnick, 1979 .

Atovaquone and Pibrentasvir Inhibit the SARS-CoV-2 Endoribonuclease and Restrict Infection In Vitro but Not In Vivo

J. Skolnick, Hongyi Zhou, Joshy Jacob, 2023, Viruses.

Generalized Fokker-Planck Approach to the Coupling Model and Comparison with Computer Simulations

J. Skolnick, S. L. Peng, K. Ngai, 1992 .

Theory of the helix-coil transition in singly crosslinked, two-chain coiled coils. 2. Role of mismatched states

C. L. Chen, J. Skolnick, 1986 .