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List of works by Jeffrey Skolnick

A comprehensive survey of small-molecule binding pockets in proteins

scientific article (publication date: October 2013)

A knowledge-based approach for predicting gene-disease associations

scientific article published on 9 June 2016

A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state

scientific article

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

scientific article published in March 2005

A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation

scholarly article

A threading-based method for the prediction of DNA-binding proteins with application to the human genome.

scientific article

APoc: large-scale identification of similar protein pockets

scientific article published on 17 January 2013

Ab initio modeling of small proteins by iterative TASSER simulations

scientific article

Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome

scientific article

Ab initio protein structure prediction using chunk-TASSER

scientific article

Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide- and metal-contaminated subsurface soils

scientific article published in December 2007

Analysis of TASSER-based CASP7 protein structure prediction results.

scientific article

Application of sparse NMR restraints to large-scale protein structure prediction.

scientific article

Are predicted protein structures of any value for binding site prediction and virtual ligand screening?

scientific article published on 14 February 2013

Are protein-protein interfaces special regions on a protein's surface?

scientific article

Assessment of programs for ligand binding affinity prediction

scientific article published in June 2008

Automated structure prediction of weakly homologous proteins on a genomic scale

scientific article

Benchmarking of TASSER in the ab initio limit.

scientific article

Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints

scientific article

Benchmarking of dimeric threading and structure refinement

scientific article published in May 2006

Career accomplishments of Harold A. Scheraga

scientific article

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

scientific article published on 07 September 2018

Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins

article

Comparison of structure-based and threading-based approaches to protein functional annotation

scientific article published on January 2010

Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening ⬇️

scientific article published on October 25, 2010

Comprehensive prediction of drug-protein interactions and side effects for the human proteome

scientific article

Computer simulation of the folding of coiled coils

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

scientific article published in January 2002

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

scientific article published on 24 April 2018

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

scientific article published on 17 February 2006

Cross-Reactivity Virtual Profiling of the Human Kinome by X-ReactKIN: A Chemical Systems Biology Approach ⬇️

scientific article published on November 8, 2010

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion ⬇️

scientific article published on October 11, 2010

DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions

scientific article published on 31 May 2008

DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid

scientific article published in June 2017

Development and benchmarking of TASSER(iter) for the iterative improvement of protein structure predictions.

scientific article

Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm

scientific article

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

scientific article published on 4 January 2008

Development of unified statistical potentials describing protein-protein interactions.

scientific article

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

scientific article published in January 2002

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: algorithm and limitations

scientific article published on September 2013

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

scientific article published on August 24, 2012

EFICAz2: enzyme function inference by a combined approach enhanced by machine learning

scientific article published on 13 April 2009

EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference

scientific article published on December 2004

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

scientific article published on 3 May 2018

ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures

scientific article

Editorial overview

scientific article published on 7 April 2009

Effects of confinement on models of intracellular macromolecular dynamics

scientific article

Efficient algorithm for the reconstruction of a protein backbone from the ?-carbon coordinates

Efficient prediction of nucleic acid binding function from low-resolution protein structures.

scientific article

Electrostatic Persistence Length of a Wormlike Polyelectrolyte

article published in 1977

Experimental validation of FINDSITE(comb) virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders

scientific article

FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs

scientific article

FINDSITE(comb): a threading/structure-based, proteomic-scale virtual ligand screening approach

scientific article

FINDSITE: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

scientific article published on 16 October 2018

FINDSITE: a combined evolution/structure-based approach to protein function prediction

scientific article published on 26 March 2009

FINDSITE: a threading-based approach to ligand homology modeling

scientific article

FINDSITE‐metal: Integrating evolutionary information and machine learning for structure‐based metal‐binding site prediction at the proteome level ⬇️

scientific article published on December 6, 2010

Fast procedure for reconstruction of full-atom protein models from reduced representations.

scientific article

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

scientific article

From nonspecific DNA-protein encounter complexes to the prediction of DNA-protein interactions

scientific article

Further evidence for the likely completeness of the library of solved single domain protein structures

scientific article

GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction

scientific article

GS-align for glycan structure alignment and similarity measurement.

scientific article

High precision multi-genome scale reannotation of enzyme function by EFICAz

scientific article

How Well is Enzyme Function Conserved as a Function of Pairwise Sequence Identity? ⬇️

scientific article published on October 31, 2003

How special is the biochemical function of native proteins?

scientific article

Hurt, tired and queasy: Specific variants in the ATPase domain of the TRAP1 mitochondrial chaperone are associated with common, chronic "functional" symptomatology including pain, fatigue and gastrointestinal dysmotility

scientific article

Identification of metabolites with anticancer properties by computational metabolomics

scientific article published on 17 June 2008

Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function

scientific article

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

scientific article

In quest of an empirical potential for protein structure prediction.

scientific article

Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis

scientific article published on 28 May 2015

Insights into the slow-onset tight-binding inhibition of Escherichia coli dihydrofolate reductase: detailed mechanistic characterization of pyrrolo [3,2-f] quinazoline-1,3-diamine and its derivatives as novel tight-binding inhibitors

scientific article

Interplay of physics and evolution in the likely origin of protein biochemical function

scientific article

Krylov subspace methods for computing hydrodynamic interactions in Brownian dynamics simulations ⬇️

scientific article published on August 14, 2012

LIGSIFT: an open-source tool for ligand structural alignment and virtual screening

scientific article

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

scientific article

Learning Protein Folding Energy Functions

scientific article published on December 2011

Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding.

scientific article

M-TASSER: an algorithm for protein quaternary structure prediction

scientific article

MEDICASCY: A Machine Learning Approach for Predicting Small-Molecule Drug Side Effects, Indications, Efficacy, and Modes of Action

scientific article published on 02 April 2020

MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading

scientific article

Memories of Harold Scheraga

scientific article published on 17 March 2021

Metabolomics identifies the intersection of phosphoethanolamine with menaquinone-triggered apoptosis in an in vitro model of leukemia

scientific article

Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q.

scientific article published on May 2004

Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome

scientific article

New benchmark metrics for protein‐protein docking methods ⬇️

scientific article published on March 1, 2011

Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper

scientific article

On the importance of composite protein multiple ligand interactions in protein pockets

scientific article

On the importance of hydrodynamic interactions in lipid membrane formation

scientific article published on 8 January 2013

On the origin and highly likely completeness of single-domain protein structures.

scientific article

On the role of physics and evolution in dictating protein structure and function

scientific article

Origin of intrinsic 3(10)-helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field

scientific article

PSiFR: an integrated resource for prediction of protein structure and function.

scientific article

Performance of the Pro-sp3-TASSER server in CASP8

scientific article

Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules

scientific article

PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity.

scientific article

Pocket detection and interaction-weighted ligand-similarity search yields novel high-affinity binders for Myocilin-OLF, a protein implicated in glaucoma

scientific article

Prediction of physical protein-protein interactions

scientific article

Protein Folding and Dynamics─An Overview on the Occasion of Harold Scheraga’s 100th Birthday

scientific article published in 2023

Protein fragment reconstruction using various modeling techniques

scientific article published on November 2003

Protein model quality assessment prediction by combining fragment comparisons and a consensus C(alpha) contact potential

scientific article

Protein model refinement using an optimized physics-based all-atom force field

scientific article

Protein structure prediction by pro-Sp3-TASSER.

scientific article

Putting the pathway back into protein folding

scientific article

Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.

scientific article

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

scientific article published on July 2008

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

scientific article published on 19 May 2017

Reply to Zimmerman et al.: The space of single domain protein structures is continuous and highly connected.

scientific article published on 14 December 2009

Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers

scientific article published on 16 January 2018

Repurposing FDA-approved drugs for anti-aging therapies

scientific article published on 02 August 2016

Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling

scientific article

SPICKER: a clustering approach to identify near-native protein folds

scientific article

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

scientific article

Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models

scientific article

Structural space of protein–protein interfaces is degenerate, close to complete, and highly connected ⬇️

scientific article published on December 13, 2010

Structure modeling of all identified G protein-coupled receptors in the human genome

scientific article

TASSER-Lite: an automated tool for protein comparative modeling

scientific article

TASSER-based refinement of NMR structures

scientific article published on May 2006

TASSER: an automated method for the prediction of protein tertiary structures in CASP6.

scientific article published in January 2005

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

scientific article published on November 3, 2010

TASSER_low-zsc: an approach to improve structure prediction using low z-score-ranked templates

scientific article

TM-align: a protein structure alignment algorithm based on the TM-score

scientific article

TOUCHSTONE II: a new approach to ab initio protein structure prediction

scientific article

TOUCHSTONE: a unified approach to protein structure prediction.

scientific article

TOUCHSTONEX: protein structure prediction with sparse NMR data.

scientific article

Template-based protein structure modeling using TASSER(VMT.).

scientific article

Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins

scientific article

The PDB is a covering set of small protein structures

scientific article published in December 2003

The continuity of protein structure space is an intrinsic property of proteins

scientific article

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

scientific article published in 2018

The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation ⬇️

scientific article published on February 21, 2012

The mosaic genome of Anaeromyxobacter dehalogenans strain 2CP-C suggests an aerobic common ancestor to the delta-proteobacteria

scientific article

The protein structure prediction problem could be solved using the current PDB library

scientific article

The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement

scientific article

Theory and simulation

scientific article published in April 2013

Tribute to Harold A. Scheraga

scientific article published on 23 October 2020

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

scientific article

Use of residual dipolar couplings as restraints in ab initio protein structure prediction.

scientific article

WeFold: a coopetition for protein structure prediction

scientific article

What is the relationship between the global structures of apo and holo proteins?

scientific article

Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods?

scientific article

Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function ⬇️

scientific article published on June 8, 2011

iAlign: a method for the structural comparison of protein-protein interfaces

scientific article

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