Jeffrey Skolnick

Protein Engineering vol.10 no.10 pp.1123–1130, 1997 Recognition of protein structure on coarse lattices with residue–residue energy functions (2009)

Boris A. Reva, Alexei V. Finkelstein, Michel Sanner, Arthur J. Olson, Jeffrey Skolnick

2To whom correspondence should be addressed We suggest and test potentials for the modeling of protein structure on coarse lattices. The coarser the lattice, the more complete and faster is the...

FINDSITE: a combined evolution/structure-based approach to protein function prediction (2009)

Skolnick, Jeffrey, Brylinski, Michal

A key challenge of the post-genomic era is the identification of the function(s) of all the molecules in a given organism. Here, we review the status of sequence and structure-based approaches to...

TM-align: A protein structure alignment algorithm based on TM-score (2008)

Yang Zhang, Jeffrey Skolnick

TM-score

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score (2008)

Pandit, Shashi, Skolnick, Jeffrey

Abstract Background Protein tertiary structure comparisons are employed in various fields of contemporary structural biology. Most structure comparison methods involve generation of an initial seed...

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score (2008)

Pandit, Shashi Bhushan, Skolnick, Jeffrey

Identification of metabolites with anticancer properties by computational metabolomics (2008)

Arakaki, Adrian K, Mezencev, Roman, Bowen, Nathan J, Huang, Ying, McDonald, John F, Skolnick, Jeffrey

Abstract Background Certain endogenous metabolites can influence the rate of cancer cell growth. For example, diacylglycerol, ceramides and sphingosine, NAD + and arginine exert this effect by acting...

Identification of metabolites with anticancer properties by computational metabolomics (2008)

Arakaki, Adrian K., Mezencev, Roman, Bowen, Nathan J., Huang, Ying, McDonald, John F., Skolnick, Jeffrey

DBD-Hunter: a knowledge-based method for the prediction of DNA protein interactions (2008)

The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria (2008)

Thomas, Sara H., Wagner, Ryan D., Arakaki, Adrian K., Skolnick, Jeffrey, Kirby, John R., Shimkets, Lawrence J., ...

Introduction A Scoring Function for Docking Ligands to Low-Resolution Protein Structures (2008)

Eckart Bindewald, Jeffrey Skolnick

Algorithm for Rapid Reconstruction of Protein Backbone from Alpha Carbon Coordinates (2008)

Mariusz Milik, Andrzej Kolinski, Jeffrey Skolnick

Introduction SPICKER: A Clustering Approach to Identify Near-Native Protein Folds (2008)

Yang Zhang, Jeffrey Skolnick

DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions (2008)

Molecular Cancer BioMed Central (2008)

The structures of DNA–protein complexes have illuminated the diversity of DNA–protein binding mechanisms shown by different protein families. This lack of generality could pose a great challenge...

Adrian K Arakaki, Roman Mezencev, Nathan J Bowen, Ying Huang, John F Mcdonald, Jeffrey Skolnick, ...

Identification of metabolites with anticancer properties by computational metabolomics

COMMUNICATION Functional Analysis of the Escherichia coli Genome Using the Sequence-to-Structure-to-Function Paradigm: Identification of Proteins Exhibiting the (2007)

Oxidoreductase Activity, Jacquelyn S. Fetrow, Adam Godzik, Jeffrey Skolnick

One goal of the genome sequencing projects is to determine the sequence of the human genome and that of a number of experimentally important organisms. These projects have been quite successful, with...

Research Horizons [Volume 24, Number 2, Winter/Spring 2007] (2007)

Sanders, Jane M., Meek, Gary, Robinson, Rick, Arkin, Ronald C., Toon, John, Skolnick, Jeffrey, ...

Ab initiomodeling of small proteins by iterative TASSER simulations (2007)

Wu, Sitao, Skolnick, Jeffrey, Zhang, Yang

Abstract Background Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier...

Ab initio modeling of small proteins by iterative TASSER simulations (2007)

Wu, Sitao, Skolnick, Jeffrey, Zhang, Yang

By (2007)

Hongyi Zhou, Jeffrey Skolnick

This un-edited manuscript has been accepted for publication in Biophysical Journal and is freely available on BioFast at

High precision multi-genome scale reannotation of enzyme function by EFICAz (2006)

Arakaki, Adrian K, Tian, Weidong, Skolnick, Jeffrey

Abstract Background The functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to...

High precision multi-genome scale reannotation of enzyme function by EFICAz (2006)

Arakaki, Adrian K., Tian, Weidong, Skolnick, Jeffrey

All-atom ab initio folding of a diverse set of proteins (2006)

Yang, Jae Shick, Chen, William W., Skolnick, Jeffrey, Shakhnovich, Eugene I.

Natural proteins fold to a unique, thermodynamically dominant state. Modeling of the folding process and prediction of the native fold of proteins are two major unsolved problems in biophysics. Here,...

Correction: Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome (2006)

Yang Zhang, Mark E. DeVries, Jeffrey Skolnick

Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome (2006)

Yang Zhang, Mark E. DeVries, Jeffrey Skolnick

G protein–coupled receptors (GPCRs), encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction...

Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome (2006)

Zhang, Yang, DeVries, Mark E., Skolnick, Jeffrey

Efficient prediction of nucleic acid binding function from low-resolution protein structures (2006)

András Szilágyi, Jeffrey Skolnick

Structural genomics projects aim to solve the experimental structures of all existing protein folds. The rationale behind these projects is that knowing a protein’s structure will help with...

TM-align: a protein structure alignment algorithm based on the TM-score (2005)

TM-align: a protein structure alignment algorithm based on the TM-score (2005)

EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference (2004)

We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is...

Tian, Weidong, Arakaki, Adrian K., Skolnick, Jeffrey

Large scale assessment of the utility of low resolution protein structures for biochemical function assignment (2004)

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

Motivation: Several protein function prediction methods employ structural features captured in three-dimensional descriptors of biologically relevant sites. These methods are successful when applied...

EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference (2004)

Tian, Weidong, Arakaki, Adrian K., Skolnick, Jeffrey

EFICAz (Enzyme Function Inference by Combined Approach) is an automatic engine for large-scale enzyme function inference that combines predictions from four different methods developed and optimized...

Large scale assessment of the utility of low resolution protein structures for biochemical function assignment (2004)

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

Motivation: Several protein function prediction methods employ structural features captured in three-dimensional descriptors of biologically relevant sites. These methods are successful when applied...

Development of unified statistical potentials describing protein-protein interactions (2003)

Hui Lu, Long Lu, Jeffrey Skolnick

ABSTRACT A residue-based and a heavy atom-based statistical pair potential are developed for use in assessing the strength of protein-protein interactions. To ensure the quality of the potentials, a...

TOUCHSTONE II: A new approach to ab initio protein structure prediction (2003)

Yang Zhang, Andrzej Kolinski, Jeffrey Skolnick

ABSTRACT We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting Ca atoms, with attached Cb atoms and...

Multimeric Threading-Based Prediction of Protein-Protein Interactions on a Genomic Scale: Application to the Saccharomyces cerevisiae Proteome (2003)

Lu, Long, Arakaki, Adrian K., Lu, Hui, Skolnick, Jeffrey

MULTIPROSPECTOR, a multimeric threading algorithm for the prediction of protein–protein interactions, is applied to the genome of Saccharomyces cerevisiae. Each possible pairwise interaction among...

Numerical estimation of entropy loss on dimerization: improved prediction of the quaternary structure of the GCN4 leucine zipper (2002)

Vinals, Jorge, Kolinski, Andrzej, Skolnick, Jeffrey

A lattice based model of a protein is used to study the dimerization equilibrium of the GCN4 leucine zipper. Replica exchange Monte Carlo is used to determine the free energy of both the monomeric...

Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures (2001)

Computational studies of protein folding (2001)

Skolnick, Jeffrey, Kolinski, Andrzej

©2001 IEEE. Personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale...

Enhanced functional annotation of protein sequences via the use of structural descriptors (2001)

Naomi Siew, Brian T. Hoffman, Li Zhang, Jeffrey Skolnick, Lorna I. Neilson, ...

In order to circumvent limitations of sequence based methods in the process of making functional predictions for proteins, we have developed a methodology that uses a...

Marcos R. Betancourt, Jeffrey Skolnick, The Donald, Danforth Plant

Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight? (2001)

Fetrow, Jacquelyn S., Siew, Naomi, Di Gennaro, Jeannine A., Martinez-Yamout, Maria, Dyson, H. Jane, Skolnick, Jeffrey

A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method...

BioMolQuest: integrated database-based retrieval of protein structural and functional information (2001)

Bukhman, Yury V., Skolnick, Jeffrey

Motivation: Information about a particular protein or protein family is usually distributed among multiple databases and often in more than one entry in each database. Retrieval and organization of...

Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures (2000)

Gront, Dominik, Kolinski, Andrzej, Skolnick, Jeffrey

Access the most recent version at doi: 10.1110/ps.49201 References (2000)

Jacquelyn S. Fetrow, Naomi Siew, Maria Martinez-yamout, H. Jane Dyson, Jeffrey Skolnick, ...

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

Dynamics and thermodynamics of �-hairpin assembly: Insights from various simulation techniques (1999)

Andrzej Kolinski, Bartosz Ilkowski, Jeffrey Skolnick

ABSTRACT Small peptides that might have some features of globular proteins can provide important insights into the protein folding problem. Two simulation methods, Monte Carlo Dynamics (MCD), based...

Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α / β proteins (1998)

Kolinski, Andrzej, Galazka, Wojciech, Skolnick, Jeffrey

Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins (1998)

Angel R. Ortiz, Andrzej Kolinski, Jeffrey Skolnick

By incorporating predicted secondary and tertiary restraints into ab initio folding simulations, low resolution tertiary structures of a test set of 20 nonhomologous proteins have been predicted....

Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactions (1997)

Kolinski, Andrzej, Skolnick, Jeffrey

Does a backwardly read protein sequence have a unique native state? (1996)

Olszewski, Krzysztof A., Kolinski, Andrzej, Skolnick, Jeffrey

Amino acid sequences of native proteins are generally not palindromic. Nevertheless, the protein molecule obtained as a result of reading the sequence backwards, i.e. a retro-protein, obviously has...

Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions (1996)

DeBolt, Stephen E., Skolnick, Jeffrey

Two atomic level knowledge-based mean force interaction potentials (KBPs), a centrosymmetric burial position term and a long-range pairwise term, were developed. These were tested by comparing...

Predicting leucine zipper structures from sequence (1996)

Hirst, Jonathan D., Vieth, Michal, Skolnick, Jeffrey, Brooks, Charles L.

The leucine zipper structure is adopted by one family of the coiled coil proteins. Leucine zippers have a characteristic leucine repeat: Leu–X6–Leu–X6–Leu–X6–Leu (where X may be any...

A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants (1996)

Vieth, Michal, Kolinski, Andrzej, Skolnick, Jeffrey

First published in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23 (1996) published by the American Mathematical Society.

Computer design of idealized β-motifs (1995)

Kolinski, Andrzej, Galazka, Wojciech, Skolnick, Jeffrey

A reduced model of short range interactions in polypeptide chains (1995)

Kolinski, Andrzej, Milik, Mariusz, Rycombel, Jakub, Skolnick, Jeffrey

A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations (1995)

Vieth, Michal, Kolinski, Andrzej, Skolnick, Jeffrey

Spontaneous Translocation of a Polymer across a Curved Membrane (1995)

Baumgärtner, Artur, Skolnick, Jeffrey

Neural network system for the evaluation of side-chain packing in protein structures (1995)

Milik, Mariusz, Kolinski, Andrzej, Skolnick, Jeffrey

An artificial neural network system is used for pattern recognition in protein side-chain-side-chain contact maps. A back-propagation network was trained on a set of patterns which are popular in...

Computer simulation of the folding of coiled coils (1994)

Rey, Antonio, Skolnick, Jeffrey

Flexible algorithm for direct multiple alignment of protein structures and sequences (1994)

Godzik, Adam, Skolnick, Jeffrey

The recently described equivalence between the alignment of two proteins and a conformation of a lattice chain on a two-dimensional square lattice is extended to multiple alignments. The search for...

A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins (1993)

Kolinski, Andrzej, Godzik, Adam, Skolnick, Jeffrey

A lattice dynamics study of a Langmuir monolayer of monounsaturated fatty acids (1993)

Levine, Yehudi K., Kolinski, Andrzej, Skolnick, Jeffrey

Regularities in interaction patterns of globular proteins (1993)

Godzik, Adam, Skolnick, Jeffrey, Kolinski, Andrzej

The description of protein structure in the language of side chain contact maps is shown to offer many advantages over more traditional approaches. Because it focuses on side chain interactions, it...

Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides (1992)

Kolinski, Andrzej, Skolnick, Jeffrey

Effect of double bonds on the dynamics of hydrocarbon chains (1992)

Rey, Antonio, Kolinski, Andrzej, Levine, Yehudi K., Skolnick, Jeffrey

Monte Carlo dynamics study of motions in cis-unsaturated hydrocarbon chains (1991)

Levine, Yehudi K., Skolnick, Jeffrey, Kolinski, Andrzej

Static and dynamic properties of a new lattice model of polypeptide chains (1991)

Kolinski, Andrzej, Milik, Mariusz, Skolnick, Jeffrey

Monte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model (1990)

Milik, Mariusz, Kolinski, Andrzej, Skolnick, Jeffrey

Phenomenological theory of the dynamics of polymer melts. II. Viscoelastic properties (1988)

Skolnick, Jeffrey, Yaris, Robert

Phenomenological theory of the dynamics of polymer melts. I. Analytic treatment of self-diffusion (1988)

Kolinski, Andrzej, Skolnick, Jeffrey, Yaris, Robert

Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. I. The homopolymeric melt (1987)

Kolinski, Andrzej, Skolnick, Jeffrey, Yaris, Robert

Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. II. Probe polymer in a matrix of different degrees of polymerization (1987)

Kolinski, Andrzej, Skolnick, Jeffrey, Yaris, Robert

Does reptation describe the dynamics of entangled, finite length polymer systems? A model simulation (1987)

Kolinski, Andrzej, Skolnick, Jeffrey, Yaris, Robert

The collapse transition of semiflexible polymers. A Monte Carlo simulation of a model system (1986)

Kolinski, Andrzej, Skolnick, Jeffrey, Yaris, Robert

On the short time dynamics of dense polymeric systems and the origin of the glass transition: A model system (1986)

Kolinski, Andrzej, Skolnick, Jeffrey, Yaris, Robert

Monte Carlo dynamics of diamond-lattice multichain systems (1986)

Kolinski, Andrzej, Skolnick, Jeffrey, Yaris, Robert

Effects of topological solitons on autocorrelation functions for chains of coupled torsional oscillators (1983)

Perchak, Dennis, Yaris, Robert, Skolnick, Jeffrey

Mechanism and rates of conformational transitions in heterogeneous polymers (1982)

Helfand, Eugene, Skolnick, Jeffrey

The kinetics of conformational transitions: Effect of variation of bond angle bending and bond stretching force constants (1981)

Helfand, Eugene, Wasserman, Z. R., Weber, Thomas A., Skolnick, Jeffrey, Runnels, John H.

Kinetics of conformational transitions in chain molecules (1980)

Skolnick, Jeffrey, Helfand, Eugene

Investigations on a rodlike polyelectrolyte model. (1978)

Skolnick, Jeffrey.

Thesis (Ph. D.)--Yale University.

Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations

Ortiz, Angel R., Kolinski, Andrzej, Skolnick, Jeffrey

By incorporating predicted secondary and tertiary restraints derived from multiple sequence alignments into ab initio folding simulations, it has been possible to assemble native-like tertiary...

TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints

Kihara, Daisuke, Lu, Hui, Kolinski, Andrzej, Skolnick, Jeffrey

The successful prediction of protein structure from amino acid sequence requires two features: an efficient conformational search algorithm and an energy function with a global minimum in the native...

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

Kihara, Daisuke, Zhang, Yang, Lu, Hui, Kolinski, Andrzej, Skolnick, Jeffrey

An ab initio protein structure prediction procedure, TOUCHSTONE, was applied to all 85 small proteins of the Mycoplasma genitalium genome. TOUCHSTONE is based on a Monte Carlo refinement of a lattice...

Multimeric Threading-Based Prediction of Protein–Protein Interactions on a Genomic Scale: Application to the Saccharomyces cerevisiae Proteome

Lu, Long, Arakaki, Adrian K., Lu, Hui, Skolnick, Jeffrey

MULTIPROSPECTOR, a multimeric threading algorithm for the prediction of protein–protein interactions, is applied to the genome of Saccharomyces cerevisiae. Each possible pairwise interaction among...

Automated structure prediction of weakly homologous proteins on a genomic scale

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

We have developed tasser, a hierarchical approach to protein structure prediction that consists of template identification by threading, followed by tertiary structure assembly via the rearrangement...

Tian, Weidong, Arakaki, Adrian K., Skolnick, Jeffrey

EFICAz (Enzyme Function Inference by Combined Approach) is an automatic engine for large-scale enzyme function inference that combines predictions from four different methods developed and optimized...

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

Putting the pathway back into protein folding

For single-domain proteins, we examine the completeness of the structures in the current Protein Data Bank (PDB) library for use in full-length model construction of unknown sequences. To address...

Skolnick, Jeffrey

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

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

We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is...

Viñals, Jorge, Kolinski, Andrzej, Skolnick, Jeffrey

A lattice-based model of a protein and the Monte Carlo simulation method are used to calculate the entropy loss of dimerization of the GCN4 leucine zipper. In the representation used, a protein is a...

A Minimal Physically Realistic Protein-Like Lattice Model: Designing an Energy Landscape that Ensures All-Or-None Folding to a Unique Native State

Pokarowski, Piotr, Kolinski, Andrzej, Skolnick, Jeffrey

A simple protein model restricted to the face-centered cubic lattice has been studied. The model interaction scheme includes attractive interactions between hydrophobic (H) residues, repulsive...

Development of Unified Statistical Potentials Describing Protein-Protein Interactions

Lu, Hui, Lu, Long, Skolnick, Jeffrey

A residue-based and a heavy atom-based statistical pair potential are developed for use in assessing the strength of protein-protein interactions. To ensure the quality of the potentials, a...

TOUCHSTONE II: A New Approach to Ab Initio Protein Structure Prediction

Zhang, Yang, Kolinski, Andrzej, Skolnick, Jeffrey

We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting Cα atoms, with attached Cβ atoms and...

Unfolding of Globular Proteins: Monte Carlo Dynamics of a Realistic Reduced Model

Kolinski, Andrzej, Klein, Piotr, Romiszowski, Piotr, Skolnick, Jeffrey

Reduced lattice models of proteins and Monte Carlo dynamics were used to simulate the initial stages of the unfolding of several proteins of various structural types, and the results were compared to...

Application of Sparse NMR Restraints to Large-Scale Protein Structure Prediction

Li, Wei, Zhang, Yang, Skolnick, Jeffrey

The protein structure prediction algorithm TOUCHSTONEX that uses sparse distance restraints derived from NMR nuclear Overhauser enhancement (NOE) data to predict protein structures at low-to-medium...

Tertiary Structure Predictions on a Comprehensive Benchmark of Medium to Large Size Proteins

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

We evaluate tertiary structure predictions on medium to large size proteins by TASSER, a new algorithm that assembles protein structures through rearranging the rigid fragments from threading...

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

G protein–coupled receptors (GPCRs), encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction...

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

Zhang, Yang, Hubner, Isaac A., Arakaki, Adrian K., Shakhnovich, Eugene, Skolnick, Jeffrey

The size and origin of the protein fold universe is of fundamental and practical importance. Analyzing randomly generated, compact sticky homopolypeptide conformations constructed in generic...

Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations

Ortiz, Angel R., Kolinski, Andrzej, Skolnick, Jeffrey

By incorporating predicted secondary and tertiary restraints derived from multiple sequence alignments into ab initio folding simulations, it has been possible to assemble native-like tertiary...

TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints

Kihara, Daisuke, Lu, Hui, Kolinski, Andrzej, Skolnick, Jeffrey

The successful prediction of protein structure from amino acid sequence requires two features: an efficient conformational search algorithm and an energy function with a global minimum in the native...

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

Kihara, Daisuke, Zhang, Yang, Lu, Hui, Kolinski, Andrzej, Skolnick, Jeffrey

An ab initio protein structure prediction procedure, TOUCHSTONE, was applied to all 85 small proteins of the Mycoplasma genitalium genome. TOUCHSTONE is based on a Monte Carlo refinement of a lattice...

Multimeric Threading-Based Prediction of Protein–Protein Interactions on a Genomic Scale: Application to the Saccharomyces cerevisiae Proteome

Lu, Long, Arakaki, Adrian K., Lu, Hui, Skolnick, Jeffrey

MULTIPROSPECTOR, a multimeric threading algorithm for the prediction of protein–protein interactions, is applied to the genome of Saccharomyces cerevisiae. Each possible pairwise interaction among...

Automated structure prediction of weakly homologous proteins on a genomic scale

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

We have developed tasser, a hierarchical approach to protein structure prediction that consists of template identification by threading, followed by tertiary structure assembly via the rearrangement...

Tian, Weidong, Arakaki, Adrian K., Skolnick, Jeffrey

EFICAz (Enzyme Function Inference by Combined Approach) is an automatic engine for large-scale enzyme function inference that combines predictions from four different methods developed and optimized...

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

Putting the pathway back into protein folding

For single-domain proteins, we examine the completeness of the structures in the current Protein Data Bank (PDB) library for use in full-length model construction of unknown sequences. To address...

Skolnick, Jeffrey

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

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

We have developed TM-align, a new algorithm to identify the best structural alignment between protein pairs that combines the TM-score rotation matrix and Dynamic Programming (DP). The algorithm is...

Viñals, Jorge, Kolinski, Andrzej, Skolnick, Jeffrey

A lattice-based model of a protein and the Monte Carlo simulation method are used to calculate the entropy loss of dimerization of the GCN4 leucine zipper. In the representation used, a protein is a...

A Minimal Physically Realistic Protein-Like Lattice Model: Designing an Energy Landscape that Ensures All-Or-None Folding to a Unique Native State

Pokarowski, Piotr, Kolinski, Andrzej, Skolnick, Jeffrey

A simple protein model restricted to the face-centered cubic lattice has been studied. The model interaction scheme includes attractive interactions between hydrophobic (H) residues, repulsive...

Development of Unified Statistical Potentials Describing Protein-Protein Interactions

Lu, Hui, Lu, Long, Skolnick, Jeffrey

A residue-based and a heavy atom-based statistical pair potential are developed for use in assessing the strength of protein-protein interactions. To ensure the quality of the potentials, a...

TOUCHSTONE II: A New Approach to Ab Initio Protein Structure Prediction

Zhang, Yang, Kolinski, Andrzej, Skolnick, Jeffrey

We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting Cα atoms, with attached Cβ atoms and...

Unfolding of Globular Proteins: Monte Carlo Dynamics of a Realistic Reduced Model

Kolinski, Andrzej, Klein, Piotr, Romiszowski, Piotr, Skolnick, Jeffrey

Reduced lattice models of proteins and Monte Carlo dynamics were used to simulate the initial stages of the unfolding of several proteins of various structural types, and the results were compared to...

Application of Sparse NMR Restraints to Large-Scale Protein Structure Prediction

Li, Wei, Zhang, Yang, Skolnick, Jeffrey

The protein structure prediction algorithm TOUCHSTONEX that uses sparse distance restraints derived from NMR nuclear Overhauser enhancement (NOE) data to predict protein structures at low-to-medium...

Tertiary Structure Predictions on a Comprehensive Benchmark of Medium to Large Size Proteins

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

We evaluate tertiary structure predictions on medium to large size proteins by TASSER, a new algorithm that assembles protein structures through rearranging the rigid fragments from threading...

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

G protein–coupled receptors (GPCRs), encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction...

Zhang, Yang, Hubner, Isaac A., Arakaki, Adrian K., Shakhnovich, Eugene, Skolnick, Jeffrey

The size and origin of the protein fold universe is of fundamental and practical importance. Analyzing randomly generated, compact sticky homopolypeptide conformations constructed in generic...

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

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

Arakaki, Adrian K, Tian, Weidong, Skolnick, Jeffrey

Ab initio modeling of small proteins by iterative TASSER simulations

Wu, Sitao, Skolnick, Jeffrey, Zhang, Yang

TASSER-Lite: An Automated Tool for Protein Comparative Modeling

Pandit, Shashi Bhushan, Zhang, Yang, Skolnick, Jeffrey

This study involves the development of a rapid comparative modeling tool for homologous sequences by extension of the TASSER methodology, developed for tertiary structure prediction. This comparative...

The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria

Thomas, Sara H., Wagner, Ryan D., Arakaki, Adrian K., Skolnick, Jeffrey, Kirby, John R., Shimkets, Lawrence J., ...

Anaeromyxobacter dehalogenans strain 2CP-C is a versaphilic delta-Proteobacterium distributed throughout many diverse soil and sediment environments. 16S rRNA gene phylogenetic analysis groups A....

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

Fetrow, Jacquelyn S., Siew, Naomi, Di Gennaro, Jeannine A., Martinez-Yamout, Maria, Dyson, H. Jane, Skolnick, Jeffrey

A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method...

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

Brylinski, Michal, Skolnick, Jeffrey

The detection of ligand-binding sites is often the starting point for protein function identification and drug discovery. Because of inaccuracies in predicted protein structures, extant binding...

Identification of metabolites with anticancer properties by computational metabolomics

Arakaki, Adrian K, Mezencev, Roman, Bowen, Nathan J, Huang, Ying, McDonald, John F, Skolnick, Jeffrey

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

Ab Initio Protein Structure Prediction Using Chunk-TASSER

The structures of DNA–protein complexes have illuminated the diversity of DNA–protein binding mechanisms shown by different protein families. This lack of generality could pose a great challenge...

Zhou, Hongyi, Skolnick, Jeffrey

We have developed an ab initio protein structure prediction method called chunk-TASSER that uses ab initio folded supersecondary structure chunks of a given target as well as threading templates for...

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

Jagielska, Anna, Wroblewska, Liliana, Skolnick, Jeffrey

One of the greatest challenges in protein structure prediction is the refinement of low-resolution predicted models to high-resolution structures that are close to the native state. Although...

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

Pandit, Shashi Bhushan, Skolnick, Jeffrey

M-TASSER: An Algorithm for Protein Quaternary Structure Prediction

Chen, Huiling, Skolnick, Jeffrey

In a cell, it has been estimated that each protein on average interacts with roughly 10 others, resulting in tens of thousands of proteins known or suspected to have interaction partners; of these,...

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

Development of a Physics-Based Force Field for the Scoring and Refinement of Protein Models

DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of...

Wroblewska, Liliana, Jagielska, Anna, Skolnick, Jeffrey

The minimal requirements of a physics-based potential that can refine protein structures are the existence of a correlation between the energy with native similarity and the scoring of the native...

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

Arakaki, Adrian K, Huang, Ying, Skolnick, Jeffrey

FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling

Brylinski, Michal, Skolnick, Jeffrey

Ligand virtual screening is a widely used tool to assist in new pharmaceutical discovery. In practice, virtual screening approaches have a number of limitations, and the development of new...

Benchmarking of TASSER_2.0: An Improved Protein Structure Prediction Algorithm with More Accurate Predicted Contact Restraints

Lee, Seung Yup, Skolnick, Jeffrey

To improve tertiary structure predictions of more difficult targets, the next generation of TASSER, TASSER_2.0, has been developed. TASSER_2.0 incorporates more accurate side-chain contact restraint...

A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome