Jeffrey Skolnick
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Computational biologist
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Computer Science Biology
Jeffrey Skolnick's Degrees
- PhD Biophysics University of California, San Francisco
- Masters Biophysics University of California, San Francisco
- Bachelors Physics University of California, Berkeley
Why Is Jeffrey Skolnick Influential?
(Suggest an Edit or Addition)According to Wikipedia, Jeffrey Skolnick is an American computational biologist. He is currently a Georgia Institute of Technology School of Biology Professor, the Director of the Center for the Study of Systems Biology, the Mary and Maisie Gibson Chair, the Georgia Research Alliance Eminent Scholar in Computational Systems Biology, the Director of the Integrative BioSystems Institute, and was previously the Scientific Advisor at Intellimedix.
Jeffrey Skolnick's Published Works
Published Works
- TM-align: a protein structure alignment algorithm based on the TM-score (2005) (2439)
- Scoring function for automated assessment of protein structure template quality (2004) (1658)
- Electrostatic Persistence Length of a Wormlike Polyelectrolyte (1977) (640)
- Ab initio modeling of small proteins by iterative TASSER simulations (2007) (514)
- SPICKER: A clustering approach to identify near‐native protein folds (2004) (423)
- How well is enzyme function conserved as a function of pairwise sequence identity? (2003) (389)
- Automated structure prediction of weakly homologous proteins on a genomic scale. (2004) (354)
- Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion (2010) (352)
- Topology fingerprint approach to the inverse protein folding problem. (1992) (351)
- The protein structure prediction problem could be solved using the current PDB library. (2005) (324)
- A distance‐dependent atomic knowledge‐based potential for improved protein structure selection (2001) (306)
- A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation (2008) (299)
- Fast procedure for reconstruction of full‐atom protein models from reduced representations (2008) (290)
- Monte carlo simulations of protein folding. I. Lattice model and interaction scheme (1994) (277)
- TOUCHSTONE II: a new approach to ab initio protein structure prediction. (2003) (275)
- MULTIPROSPECTOR: An algorithm for the prediction of protein–protein interactions by multimeric threading (2002) (265)
- MONSSTER: a method for folding globular proteins with a small number of distance restraints. (1997) (259)
- GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. (2011) (237)
- Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. (1998) (223)
- Structural genomics and its importance for gene function analysis (2000) (212)
- TASSER: An automated method for the prediction of protein tertiary structures in CASP6 (2005) (205)
- Reduced models of proteins and their applications (2004) (193)
- Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? (1997) (192)
- On the origin and highly likely completeness of single-domain protein structures. (2006) (184)
- A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins (1993) (173)
- Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome (2006) (172)
- Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. (1991) (169)
- What is the probability of a chance prediction of a protein structure with an rmsd of 6 A? (1998) (167)
- Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm (2004) (167)
- Aerobic uranium (VI) bioprecipitation by metal-resistant bacteria isolated from radionuclide- and metal-contaminated subsurface soils. (2007) (161)
- Local energy landscape flattening: Parallel hyperbolic Monte Carlo sampling of protein folding (2002) (158)
- TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints (2001) (155)
- Ab initio folding of proteins using restraints derived from evolutionary information (1999) (155)
- From genes to protein structure and function: novel applications of computational approaches in the genomic era. (2000) (154)
- Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin (1994) (152)
- Defrosting the frozen approximation: PROSPECTOR— A new approach to threading (2001) (145)
- Development of unified statistical potentials describing protein-protein interactions. (2003) (145)
- The Mosaic Genome of Anaeromyxobacter dehalogenans Strain 2CP-C Suggests an Aerobic Common Ancestor to the Delta-Proteobacteria (2008) (145)
- Efficient prediction of nucleic acid binding function from low-resolution protein structures. (2006) (145)
- Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets (1995) (143)
- Kinetics of conformational transitions in chain molecules (1980) (140)
- In quest of an empirical potential for protein structure prediction. (2006) (139)
- Polyelectrolyte Excluded Volume Paradox (1978) (138)
- Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. (1992) (137)
- Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score (2008) (137)
- Assessment of programs for ligand binding affinity prediction (2008) (133)
- Structural space of protein–protein interfaces is degenerate, close to complete, and highly connected (2010) (131)
- Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. (2003) (131)
- The PDB is a covering set of small protein structures. (2003) (130)
- Prediction of physical protein–protein interactions (2005) (126)
- DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions (2008) (126)
- Insertion of peptide chains into lipid membranes: An off‐lattice Monte Carlo dynamics model (1993) (122)
- Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. (1998) (114)
- APoc: large-scale identification of similar protein pockets (2013) (112)
- Prediction of the folding pathways and structure of the GCN4 leucine zipper. (1994) (109)
- Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides (1992) (107)
- Marker metabolites can be therapeutic targets as well (2008) (107)
- Flexible algorithm for direct multiple alignment of protein structures and sequences (1994) (106)
- Assembly of protein structure from sparse experimental data: An efficient Monte Carlo model (1998) (106)
- Supramolecular self-assembly: molecular dynamics modeling of polyhedral shell formation (1999) (106)
- A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins (2013) (105)
- EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. (2004) (103)
- Lattice representations of globular proteins: How good are they? (1993) (101)
- Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments. (1998) (100)
- On the origin of the cooperativity of protein folding: Implications from model simulations (1996) (99)
- Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. (2004) (98)
- FINDSITE: a combined evolution/structure-based approach to protein function prediction (2009) (98)
- Comprehensive prediction of drug-protein interactions and side effects for the human proteome (2015) (96)
- Accurate reconstruction of all‐atom protein representations from side‐chain‐based low‐resolution models (2000) (95)
- Protein fragment reconstruction using various modeling techniques (2003) (95)
- Computer simulations of globular protein folding and tertiary structure. (1989) (95)
- Generalized comparative modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement (2001) (92)
- Ab initio protein structure prediction using chunk-TASSER. (2007) (92)
- Does reptation describe the dynamics of entangled, finite length polymer systems? A model simulation (1987) (92)
- All-atom ab initio folding of a diverse set of proteins. (2006) (90)
- Structure‐based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase‐1 subfamily (1999) (87)
- Lattice Models of Protein Folding, Dynamics and Thermodynamics (1996) (87)
- Universal similarity measure for comparing protein structures. (2001) (87)
- Correction: Structure Modeling of All Identified G Protein–Coupled Receptors in the Human Genome (2006) (86)
- iAlign: a method for the structural comparison of protein-protein interfaces (2010) (86)
- Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis. (2015) (86)
- The continuity of protein structure space is an intrinsic property of proteins (2009) (83)
- Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques. (1999) (83)
- Local propensities and statistical potentials of backbone dihedral angles in proteins. (2004) (82)
- A method for predicting protein structure from sequence (1993) (82)
- De novo and inverse folding predictions of protein structure and dynamics (1993) (82)
- Regularities in interaction patterns of globular proteins. (1993) (81)
- FINDSITE‐metal: Integrating evolutionary information and machine learning for structure‐based metal‐binding site prediction at the proteome level (2011) (79)
- A Threading-Based Method for the Prediction of DNA-Binding Proteins with Application to the Human Genome (2009) (79)
- The collapse transition of semiflexible polymers. A Monte Carlo simulation of a model system (1986) (78)
- The distribution of ligand-binding pockets around protein-protein interfaces suggests a general mechanism for pocket formation (2012) (76)
- FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling (2009) (76)
- Analysis of TASSER‐based CASP7 protein structure prediction results (2007) (76)
- Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. I. Six-member, Greek key beta-barrel proteins. (1990) (75)
- Application of an artificial neural network to predict specific class I MHC binding peptide sequences (1998) (75)
- TOUCHSTONE: A unified approach to protein structure prediction (2003) (74)
- Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins (1991) (74)
- Genomic‐scale comparison of sequence‐ and structure‐based methods of function prediction: Does structure provide additional insight? (2001) (73)
- Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement (2001) (70)
- Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions (2001) (70)
- M-TASSER: an algorithm for protein quaternary structure prediction. (2008) (70)
- Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures (2000) (69)
- Protein structure prediction by pro-Sp3-TASSER. (2009) (69)
- EFICAz2: enzyme function inference by a combined approach enhanced by machine learning (2009) (67)
- What is the relationship between the global structures of apo and holo proteins? (2007) (66)
- Protein model refinement using an optimized physics-based all-atom force field (2008) (65)
- Can a physics‐based, all‐atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking (2007) (65)
- Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. I. The homopolymeric melt (1987) (64)
- Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations. (1998) (62)
- 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) (62)
- FINDSITEcomb: A Threading/Structure-Based, Proteomic-Scale Virtual Ligand Screening Approach (2013) (62)
- Krylov subspace methods for computing hydrodynamic interactions in brownian dynamics simulations. (2012) (61)
- Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment (2004) (60)
- Molecular Mechanism of the Ring-Flip Process in Polycarbonate (1985) (60)
- Static and dynamic properties of a new lattice model of polypeptide chains (1991) (59)
- Interplay of physics and evolution in the likely origin of protein biochemical function (2013) (59)
- Monte Carlo Simulations of Protein Folding (2003) (58)
- On the short time dynamics of dense polymeric systems and the origin of the glass transition: A model system (1986) (57)
- How do potentials derived from structural databases relate to “true” potentials? (1998) (57)
- DESTINI: A deep-learning approach to contact-driven protein structure prediction (2019) (57)
- What should the Z‐score of native protein structures be? (1998) (57)
- EFICAz2.5: application of a high-precision enzyme function predictor to 396 proteomes (2012) (56)
- Enhanced functional annotation of protein sequences via the use of structural descriptors. (2001) (56)
- Q‐Dock: Low‐resolution flexible ligand docking with pocket‐specific threading restraints (2008) (55)
- Efficient algorithm for the reconstruction of a protein backbone from the α‐carbon coordinates (1992) (55)
- From fold predictions to function predictions: Automation of functional site conservation analysis for functional genome predictions (1999) (55)
- Monte Carlo simulations on an equilibrium globular protein folding model. (1986) (55)
- Structure‐based classification of 45 FK506‐binding proteins (2008) (54)
- Does a backwardly read protein sequence have a unique native state? (1996) (54)
- WeFold: A coopetition for protein structure prediction (2014) (53)
- Phosphoprotein and phosphopeptide interactions with the FHA domain from Arabidopsis kinase-associated protein phosphatase. (2007) (53)
- A method for the improvement of threading‐based protein models (1999) (52)
- Performance of the Pro‐sp3‐TASSER server in CASP8 (2009) (50)
- Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. II. Alpha-helical motifs. (1990) (50)
- Erratum: Scoring function for automated assessment of protein structure template quality (Proteins: Structure, Function and Genetics (2004) 57, (702-710)) (2007) (49)
- TASSER-Lite: an automated tool for protein comparative modeling. (2006) (49)
- Ab initio protein structure prediction on a genomic scale: Application to the Mycoplasma genitalium genome (2002) (48)
- A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state. (2003) (48)
- AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function (2021) (47)
- Computational studies of protein folding (2001) (47)
- A knowledge-based approach for predicting gene-disease associations (2016) (46)
- AF2Complex predicts direct physical interactions in multimeric proteins with deep learning (2022) (46)
- Monte Carlo simulations of the folding of beta-barrel globular proteins. (1988) (45)
- Application of sparse NMR restraints to large-scale protein structure prediction. (2004) (45)
- Spontaneous insertion of polypeptide chains into membranes: a Monte Carlo model. (1992) (44)
- Computer modeling and folding of four‐helix bundles (1993) (44)
- Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects (2018) (44)
- Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteins (1998) (43)
- Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper. (1995) (43)
- Simulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins. (1992) (42)
- Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates (1997) (42)
- TOUCHSTONEX: Protein structure prediction with sparse NMR data (2003) (42)
- Comprehensive Structural and Functional Characterization of the Human Kinome by Protein Structure Modeling and Ligand Virtual Screening (2010) (42)
- Microbial genomes have over 72% structure assignment by the threading algorithm PROSPECTOR_Q (2004) (41)
- Development of a physics-based force field for the scoring and refinement of protein models. (2008) (41)
- Phenomenological theory of the dynamics of polymer melts. I. Analytic treatment of self‐diffusion (1988) (41)
- An Efficient Monte Carlo Model of Protein Chains. Modeling the Short-Range Correlations between Side Group Centers of Mass (1998) (41)
- Sliding of Proteins Non-specifically Bound to DNA: Brownian Dynamics Studies with Coarse-Grained Protein and DNA Models (2014) (40)
- LIGSIFT: an open-source tool for ligand structural alignment and virtual screening (2015) (40)
- Folding simulations and computer redesign of protein A three‐helix bundle motifs (1996) (40)
- Protein model quality assessment prediction by combining fragment comparisons and a consensus Cα contact potential (2008) (40)
- Template‐based protein structure modeling using TASSERVMT (2012) (39)
- A reduced model of short range interactions in polypeptide chains (1995) (38)
- FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs. (2012) (37)
- Further evidence for the likely completeness of the library of solved single domain protein structures. (2012) (37)
- New benchmark metrics for protein‐protein docking methods (2011) (37)
- Monte Carlo simulation of equilibrium globular protein folding: alpha-helical bundles with long loops. (1989) (37)
- Predicting leucine zipper structures from sequence. (1996) (37)
- PoLi: A Virtual Screening Pipeline Based on Template Pocket and Ligand Similarity (2015) (36)
- 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) (36)
- On the importance of hydrodynamic interactions in lipid membrane formation. (2013) (36)
- Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1 (2000) (36)
- Application of statistical potentials to protein structure refinement from low resolution ab initio models (2003) (36)
- Mechanism and rates of conformational transitions in heterogeneous polymers (1982) (36)
- A method for the prediction of surface “U”‐turns and transglobular connections in small proteins (1997) (35)
- Dynamic Monte Carlo study of the folding of a six-stranded Greek key globular protein. (1989) (34)
- Monte carlo studies on equilibrium globular protein folding. III. The four helix bundle (1989) (34)
- A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes. (1995) (33)
- De novo simulations of the folding thermodynamics of the GCN4 leucine zipper. (1999) (33)
- Monte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model (1990) (33)
- Monte carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of β‐barrel proteins (1987) (33)
- Computer design of idealized β‐motifs (1995) (32)
- From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions (2009) (31)
- High precision multi-genome scale reannotation of enzyme function by EFICAz (2006) (31)
- Correlation between knowledge‐based and detailed atomic potentials: Application to the unfolding of the GCN4 leucine zipper (1999) (31)
- Are predicted protein structures of any value for binding site prediction and virtual ligand screening? (2013) (31)
- 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 (2015) (31)
- Averaging interaction energies over homologs improves protein fold recognition in gapless threading (1999) (30)
- Charge Interactions in Cylindrical Polyelectrolytes (1978) (30)
- A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics (2001) (30)
- Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function. (2015) (30)
- Theory of helix-coil transitions of .alpha.-helical, two-chain, coiled coils (1982) (30)
- The kinetics of conformational transitions: Effect of variation of bond angle bending and bond stretching force constants (1981) (30)
- Monte carlo studies on equilibrium globular protein folding. II. β‐barrel globular protein models (1989) (30)
- Comparison of structure‐based and threading‐based approaches to protein functional annotation (2010) (29)
- Phenomenological theory of the dynamics of polymer melts. II. Viscoelastic properties (1988) (29)
- Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling (2013) (29)
- A scoring function for docking ligands to low‐resolution protein structures (2005) (28)
- Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: algorithm and limitations. (2013) (28)
- Metabolomics identifies the intersection of phosphoethanolamine with menaquinone-triggered apoptosis in an in vitro model of leukemia. (2015) (28)
- ENTPRISE: An Algorithm for Predicting Human Disease-Associated Amino Acid Substitutions from Sequence Entropy and Predicted Protein Structures (2016) (28)
- Monte Carlo Study of Local Orientational Order in a Semiflexible Polymer Melt Model (1986) (27)
- Effect of double bonds on the dynamics of hydrocarbon chains (1992) (27)
- Q‐DockLHM: Low‐resolution refinement for ligand comparative modeling (2009) (27)
- Identification of metabolites with anticancer properties by computational metabolomics (2008) (27)
- Sequence evolution and the mechanism of protein folding. (2000) (27)
- FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules (2018) (26)
- Effects of confinement on models of intracellular macromolecular dynamics (2015) (26)
- Dynamics of star branched polymers in a matrix of linear chains—a Monte Carlo study (1994) (26)
- Dynamics of Rigid and Flexible Constraints for Polymers. Effect of the Fixman Potential (1985) (25)
- Experimental validation of FINDSITEcomb virtual ligand screening results for eight proteins yields novel nanomolar and micromolar binders (2014) (25)
- Dynamics of dense polymer systems: computer simulations and analytic theories (2007) (25)
- Chemical space of Escherichia coli dihydrofolate reductase inhibitors: New approaches for discovering novel drugs for old bugs (2018) (25)
- Functional analysis of the Escherichia coli genome for members of the α /β hydrolase family (1998) (25)
- Localized oral histoplasmosis. A regional manifestation of mild chronic disseminated histoplasmosis. (1982) (25)
- Repurposing FDA-approved drugs for anti-aging therapies (2016) (24)
- a-Helix-to-Random-Coil Transition of Two-Chain , Coiled Coils . Theory and Experiments for Thermal Denaturation of a-Tropomyosin at Acidic pH (2001) (24)
- Cross-reactivity virtual profiling of the human kinome by X-react(KIN): a chemical systems biology approach. (2010) (24)
- BioMolQuest: integrated database-based retrieval of protein structural and functional information (2001) (24)
- Ligand binding studies, preliminary structure-activity relationship and detailed mechanistic characterization of 1-phenyl-6,6-dimethyl-1,3,5-triazine-2,4-diamine derivatives as inhibitors of Escherichia coli dihydrofolate reductase. (2015) (24)
- Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules. (2016) (23)
- Order-Disorder Transitions in Tetrahedral Lattice Polymer Systems (1986) (23)
- Neural network system for the evaluation of side-chain packing in protein structures. (1995) (23)
- Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactions (1997) (23)
- Moments and distribution function of polymer chains (1976) (23)
- Dynamic Monte Carlo simulations of globular protein folding. Model studies of in vivo assembly of four helix bundles and four member beta-barrels. (1990) (22)
- Benchmarking of TASSER_2.0: an improved protein structure prediction algorithm with more accurate predicted contact restraints. (2008) (22)
- Method for predicting the state of association of discretized protein models. Application to leucine zippers. (1996) (22)
- Computer simulations of de novo designed helical proteins. (1998) (22)
- Are protein-protein interfaces special regions on a protein's surface? (2015) (21)
- Generalized Fokker-Planck Approach to the Coupling Model and Comparison with Computer Simulations (1992) (21)
- Putting the pathway back into protein folding. (2005) (21)
- The protein folding problem: a biophysical enigma. (2002) (21)
- Alpha-helix-to-random-coil transitions of two-chain, coiled coils: a theoretical model for the "pretransition" in cysteine-190-cross-linked tropomyosin. (1986) (20)
- Improving threading algorithms for remote homology modeling by combining fragment and template comparisons (2010) (20)
- DNA Internal Motion Likely Accelerates Protein Target Search in a Packed Nucleoid. (2017) (20)
- Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants. (2017) (20)
- ENTPRISE-X: Predicting disease-associated frameshift and nonsense mutations (2018) (19)
- A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition. (2003) (19)
- Docking of small ligands to low‐resolution and theoretically predicted receptor structures (2002) (19)
- A lattice dynamics study of a Langmuir monolayer of monounsaturated fatty acids (1993) (19)
- TASSER‐based refinement of NMR structures (2006) (19)
- Young's syndrome: an often unrecognized correctable cause of obstructive azoospermia. (1987) (19)
- Monte Carlo studies of the long-time dynamics of dense polymer systems. The failure of the reptation model (1987) (19)
- Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures (2001) (19)
- Computer Simulations of Simple Models of the Ring-Flip Process in Polycarbonate (1987) (19)
- Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper. (2002) (18)
- The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release (2018) (18)
- Protein Folding: Flexible Lattice Models (2000) (18)
- A novel sequence alignment algorithm based on deep learning of the protein folding code (2020) (18)
- Benchmarking of dimeric threading and structure refinement (2006) (18)
- Damped orientational diffusion model of polymer local main-chain motion. 1. General theory (1982) (18)
- Theory of α-helix-to-random-coil transition of two-chain, coiled coils. Application of the augmented theory to thermal denaturation of ββ tropomyosin (1985) (18)
- On the possible origin of protein homochirality, structure, and biochemical function (2019) (17)
- Reduced protein models and their application to the protein folding problem. (1998) (17)
- Dynamic Monte Carlo Study of the Conformational Properties of Long Flexible Polymers . (1987) (17)
- Faculty Opinions recommendation of LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. (2016) (17)
- Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family. (1998) (17)
- Prediction of protein secondary structure by neural networks: encoding short and long range patterns of amino acid packing. (1992) (17)
- Monte Carlo studies of an idealized model of a lipid-water system (1992) (16)
- Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments (1998) (16)
- Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction. (1997) (16)
- Use of residual dipolar couplings as restraints in ab initio protein structure prediction (2003) (16)
- A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations (1995) (15)
- MEDICASCY: A Machine Learning Approach for Predicting Small Molecule Drug Side Effects, Indications, Efficacy and Mode of Action. (2020) (15)
- Damped orientational diffusion model of polymer local main-chain motion. 3. Inclusion of chain-chain interactions (1983) (15)
- α-Helix-to-random-coil transition of two-chain, coiled coils. Theory and experiments for thermal denaturation of α-tropomyosin at acidic pH (1983) (15)
- Coupling the folding of homologous proteins. (1998) (15)
- From independent modules to molten globules: observations on the nature of protein folding intermediates. (1993) (15)
- A unified approach to the prediction of protein structure and function (2002) (15)
- Correspondence between the Coupling Model Predictions and Computer Simulations: Diffusion of a Probe Polymer in a Matrix Having Different Degrees of Polymerization (1991) (15)
- Antimalarial Peptide and Polyketide Natural Products from the Fijian Marine Cyanobacterium Moorea producens (2020) (14)
- Effect of loop entropy on the helix-coil transition of α-helical, two-chain, coiled coils. 2. Supermatrix formulation of the perfect-matching model (1983) (14)
- Computer simulation of the folding of coiled coils (1994) (14)
- Helix‐coil and beta sheet‐coil transitions in a simplified, yet realistic protein model (2000) (14)
- Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers (2018) (14)
- Further Evidence for the Likely Completeness of the Library of Solved Single Domain Protein Structures (2011) (14)
- Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins. (1998) (13)
- Segment assembly, structure alignment and iterative simulation in protein structure prediction (2013) (13)
- FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening (2021) (13)
- 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. (2015) (13)
- PSiFR: an integrated resource for prediction of protein structure and function (2010) (13)
- Unfolding of globular proteins: monte carlo dynamics of a realistic reduced model. (2003) (12)
- Development and benchmarking of TASSERiter for the iterative improvement of protein structure predictions (2007) (12)
- GS-align for glycan structure alignment and similarity measurement (2015) (12)
- Theory of α-helix-to-random coil transitions of two-chain, coiled coils. Application to a synthetic analog of tropomyosin (1982) (12)
- Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods? (2017) (11)
- Benchmarking of TASSER in the ab initio limit (2007) (11)
- Improved method for prediction of protein backbone U‐turn positions and major secondary structural elements between U‐turns (1997) (11)
- A SYNTHETIC RETROTRANSITION (BACKWARD READING) SEQUENCE OF THE RIGHT-HANDED THREE-HELIX BUNDLE DOMAIN (10-53) OF PROTEIN A SHOWS SIMILARITY IN CONFOMA TION AS PREDICTED BY COMPUTATION (1998) (11)
- TASSER_WT: a protein structure prediction algorithm with accurate predicted contact restraints for difficult protein targets. (2010) (11)
- Sequence-structure specificity--how does an inverse folding approach work? (1997) (11)
- Why not consider a spherical protein? Implications of backbone hydrogen bonding for protein structure and function. (2011) (11)
- Recognition of protein structure on coarse lattices with residue-residue energy functions. (1997) (11)
- Monte Carlo dynamics study of motions in cis‐unsaturated hydrocarbon chains (1991) (11)
- Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach (1998) (11)
- High coordination lattice models of protein structure, dynamics and thermodynamics. (1997) (11)
- Method for low resolution prediction of small protein tertiary structure. (1997) (11)
- On the role of physics and evolution in dictating protein structure and function. (2014) (11)
- Computer simulations of the properties of the α2, α2C, and α2D de novo designed helical proteins (2000) (10)
- Origin of intrinsic 310‐helix versus strand stability in homopolypeptides and its implications for the accuracy of the Amber force field (2007) (10)
- Monte Carlo lattice dynamics and the prediction of protein folds (1997) (10)
- Possible role of helix-coil transitions in the microscopic mechanism of muscle contraction. (1987) (10)
- The role of local versus nonlocal physicochemical restraints in determining protein native structure. (2020) (10)
- On the importance of composite protein multiple ligand interactions in protein pockets (2017) (10)
- Effect of loop entropy on the helix-coil transition of α-helical, two-chain, coiled coils (1983) (10)
- How special is the biochemical function of native proteins? (2016) (9)
- An algorithm for prediction of structural elements in small proteins. (1996) (9)
- Depolarized light scattering from macromolecules: effects of torsional oscillations, conformational transitions, and overall rotations (1981) (9)
- Theory of the Helix-Coil Transition in Doubly Cross-Linked, Two-Chain, Coiled Coils. A Globular Protein Model (1986) (9)
- Catalytic and substrate promiscuity: distinct multiple chemistries catalysed by the phosphatase domain of receptor protein tyrosine phosphatase. (2016) (9)
- Simulations of the folding pathway of triose phosphate isomerase-type a / , 8 barrel proteins (8)
- Learning Protein Folding Energy Functions (2011) (8)
- A Preliminary Examination of End Effects in Polyelectrolyte Theory: The Potential of a Line Segment of Charge (1980) (8)
- Application of the augmented theory of α‐helix‐to‐random‐coil transitions of two‐chain, coiled coils to extant data on synthetic, tropomyosin‐analog peptides (1988) (8)
- Damped orientational diffusion model of polymer local main-chain motion. 2. Application to poly(vinyl acetate) (1982) (8)
- Polymer Electrophoresis across a Model Membrane (1994) (8)
- Differential kinase activity of ACVR1 G328V and R206H mutations with implications to possible TβRI cross-talk in diffuse intrinsic pontine glioma (2020) (8)
- High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function (2021) (8)
- Conformational properties of bolaform electrolytes (1981) (8)
- Kinetics of conformational transitions in polymers containing skeletal double bonds (1981) (7)
- Tasser‐Based Protein Structure Prediction (2010) (7)
- Theory of the helix-coil transition in singly crosslinked, two-chain coiled coils. 2. Role of mismatched states (1986) (7)
- Theory of α-helix-to-random-coil transitions of two-chain, coiled coils. Application to the T1 and T2 fragments of α-tropomyosin (1983) (7)
- Derivation and testing residue-residue mean-force potentials for use in protein structure recognition. (2000) (7)
- The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. (2011) (6)
- Monte Carlo Approaches to the Protein Folding Problem (2007) (6)
- Protein Structure Prediction in the Post Genomic Era (1998) (6)
- Role of topological constraints in the all-or-none transition of a globular protein model: theory of the helix-coil transition in doubly crosslinked, coiled coils. (1985) (6)
- A Threading-Based Method for the Prediction of DNABinding Proteins with Application to the Human GenomeProteins with Application to the Human Genome (2009) (6)
- Application of a high coordination lattice model in protein structure prediction (1998) (6)
- Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks (2022) (6)
- Theory of the Helix-Coil Transition in Singly Cross-Linked, Two-Chain, Coiled Coils (1985) (6)
- Theory of the helix-coil transition in single-chain polypeptides with interhelical contacts. The broken .alpha.-helical hairpin model (1985) (6)
- Damped orientational diffusion model of polymer local main-chain motion. V: Comparaison with three alternative models (1985) (6)
- Protein folds vs. protein folding: Differing questions, different challenges (2022) (6)
- De Novo Predictions of the Quaternary Structure of Leucine Zippers and Other Coiled Coils (1999) (6)
- Comment on "Local knot model of entangled polymer chains" (1993) (6)
- The ethylene group as a peptide bond mimicking unit: A theoretical conformational analysis (1993) (6)
- Computer simulations of protein folding with a small number of distance restraints. (2002) (5)
- TASSER_low‐zsc: An approach to improve structure prediction using low z‐score–ranked templates (2010) (5)
- Numerical estimation of entropy loss on dimerization: improved prediction of the quaternary structure of the GCN4 leucine zipper (2002) (5)
- Effect of Urea on the Intrinsic Viscosity of Randomly Coiled Poly(α-L-glutamate) (1980) (5)
- Predicting direct physical interactions in multimeric proteins with deep learning (2021) (5)
- Stability of the crosslinked tropomyosin dimer: crosslink effect on the cooperativity of the ordering process and on the maximum in the helix probability profile (1982) (5)
- Restricted internal segmental rotational diffusion model with segment-segment interactions. Application to 13C NMR (1984) (5)
- Dynamic Monte Carlo Simulations of Globular Protein Folding, Structure and Dynamics (1990) (5)
- Theory of helix-coil transitions of α-helical, two-chain, coiled coils. Analytic treatment of the homopolymeric, neglect-loop-entropy model (1984) (5)
- Monte Carlo Models of Spontaneous Insertion of Peptides into Lipid Membranes (1996) (5)
- BROWNIAN DYNAMICS SIMULATION OF MACROMOLECULE DIFFUSION IN A PROTOCELL. (2011) (5)
- A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins (1998) (4)
- Scoring function for automated assessment of protein structure template quality (2007) (4)
- Phenomenological model of the stress-strain behavior of glassy polymers (1984) (4)
- PHENOMENOLOGICAL THEORY OF POLYMER MELT DYNAMICS (1989) (4)
- Simulations of the Folding Pathway of TIM-type a/ß Barrel Proteins (1992) (4)
- Computer Simulations of the Properties of the a 2 , a 2 C , and a 2 D De Novo Designed Helical Proteins (1999) (4)
- A theoretical model simulating the anomalous concentration dependence of the equilibrium thermal unfolding curve of noncrosslinked tropomyosin. (1986) (4)
- Rates of conformational transitions in branched chain molecules (1981) (4)
- Novel small molecule binders of human N-glycanase 1, a key player in the endoplasmic reticulum associated degradation pathway. (2016) (4)
- IMPORTANCE OF EXCLUDED VOLUME AND HYDRODYNAMIC INTERACTIONS ON MACROMOLECULAR DIFFUSION IN VIVO. (2013) (4)
- Effects of topological solitons on autocorrelation functions for chains of coupled torsional oscillators (1983) (4)
- Damped orientational diffusion model of polymer local, main chain motion. 4. Effects of probes and side-chains (1985) (4)
- Pocket detection and interaction-weighted ligand-similarity search yields novel high-affinity binders for Myocilin-OLF, a protein implicated in glaucoma. (2017) (4)
- Structure of Proteins : New Approach to Molecular Modeling (2001) (4)
- Computational Identification of Stearic Acid as a Potential PDK1 Inhibitor and In Vitro Validation of Stearic Acid as Colon Cancer Therapeutic in Combination with 5-Fluorouracil (2021) (4)
- Colligative Properties of Helical Polyelectrolytes (1979) (4)
- De novo simulations of the folding of GCN4 and its mutants (1995) (3)
- On the apparent radius of gyration of linear polymers and the experimental determination of the excluded-volume parameter (1988) (3)
- Trans placements, expansion, and asymmetry of starlike polyethylenes bearing similarly charged ends (1981) (3)
- The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release (2018) (3)
- Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants. (1996) (3)
- Correction to Rational Design of Novel Allosteric Dihydrofolate Reductase Inhibitors Showing Antibacterial Effects on Drug-Resistant Escherichia coli Escape Variants. (2018) (3)
- Prediction of severe adverse events, modes of action and drug treatments for COVID-19’s complications (2021) (3)
- Theory of the kinetics of the helix-coil transition in two-chain, coiled coils. I. Infinite chain limit (1984) (3)
- Theory of the kinetics of the helix-coil transition in two-chain, coiled coils. 2. The finite chain (1985) (3)
- [When and how can homologs overcome errors in the energy estimates and make the 3D structure prediction possible]. (1999) (3)
- Time-resolved x-ray crystallography capture of a slow reaction tetrahydrofolate intermediate (2019) (3)
- Faculty Opinions recommendation of Towards increasing the clinical relevance of in silico methods to predict pathogenic missense variants. (2016) (2)
- Dynamics of Dense Polymer Systems Dynamic Monte Carlo Simulation Results and Analytic Theory (1989) (2)
- De Novo Prediction of Protein Tertiary Structure (1994) (2)
- A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants (1996) (2)
- The role of computational biology in the genomics revolution (1999) (2)
- Career accomplishments of Harold A. Scheraga. (2012) (2)
- Novel Computational Approaches to Drug Discovery (2010) (2)
- LeMeDISCO is a computational method for large-scale prediction & molecular interpretation of disease comorbidity (2021) (2)
- Chapter 11 – Application of Reduced Models to Protein Structure Prediction (1999) (2)
- Reply to Zimmerman et al.: The space of single domain protein structures is continuous and highly connected (2009) (2)
- Monte Carlo dynamics of diamond‐lattice multichain systems (1986) (2)
- Theory of helix-coil transitions of a-helical (1982) (2)
- a-Helix-to-Random-Coil Transitions of Two-Chain , Coiled Coils : A Theoretical Model for the “ Pretransition ” in Cysteine-190-Cross-Linked Tropomyosint (2001) (2)
- Fit of a nonreptative model of polymer melt dynamics to experimental melt diffusion constant measurements (1989) (2)
- Overcoming the Crudeness of Energy Estimates in Protein 3 D Structure Prediction by Homologs : The When and the How (2000) (2)
- Protein Structure Prediction (2007) (2)
- Dynamic Monte Carlo Simulation of a melt of ring polymers (1989) (2)
- A General Framework to Learn Tertiary Structure for Protein Sequence Characterization (2021) (2)
- Biography of Harold A. Scheraga (2012) (2)
- Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein-Protein Interactions. (2022) (2)
- MOATAI-VIR - an AI algorithm that predicts severe adverse events and molecular features for COVID-19's complications (2021) (1)
- Tribute to Harold A. Scheraga. (2020) (1)
- Monte Carlo studies on equilibrium globular protein folding. I. Homopolymeric lattice models of beta-barrel proteins. (1987) (1)
- Integrating the whole from the sum of the parts: vignettes in computational biology. (2017) (1)
- Computer simulations of the properties of the alpha2, alpha2C, and alpha2D de novo designed helical proteins. (2000) (1)
- Memories of Harold Scheraga. (2021) (1)
- An Object-Oriented Environment for Artifical Evolution of Protein Sequences: The Example of Rational Design of Transmembrane Sequences (1995) (1)
- Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria (2022) (1)
- Time-resolved x-ray crystallography capture of a slow reaction tetrahydrofolate intermediate. (2019) (1)
- On the emergence of homochirality and life itself (2021) (1)
- Spatial heterogeneity of glioblastoma cells reveals sensitivity to NAD+ depletion at tumor edge (2020) (1)
- A general framework to learn tertiary structure for protein sequence annotation (2021) (1)
- Emerging Topics in Life Sciences: 1 (3) (2017) (0)
- E. coli DHFR ternary complex with NADP and dihydrofolate (2019) (0)
- Differential kinase activity of ACVR1 G328V and R206H mutations with implications to possible TβRI cross-talk in diffuse intrinsic pontine glioma (2020) (0)
- Faculty Opinions recommendation of Catalytic versatility and backups in enzyme active sites: the case of serum paraoxonase 1. (2016) (0)
- Faculty Opinions recommendation of Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59. (2016) (0)
- Towards Simulation of Virtual Cells: The Kinesin-Microtubule Molecular Motor (2015) (0)
- Conformational Properties of Bolaform (2002) (0)
- New Approaches to Protein Functional Inference and Ligand Screening: Application to the Human Kinome (2011) (0)
- E. coli DHFR substrate complex with Dihydrofolate (2019) (0)
- E. coli DHFR product complex with (6S)-5,6,7,8-TETRAHYDROFOLATE (2019) (0)
- Cover Picture: Computational Molecular Biophysics: 40 Years of Achievements (Isr. J. Chem. 8-9/2014) (2014) (0)
- Segment assembly, structure alignment and iterative simulation in protein structure prediction (2013) (0)
- Faculty Opinions recommendation of NLRP3 inflammasome activation drives tau pathology. (2019) (0)
- On the Structural Space of Protein-Protein Interfaces (2012) (0)
- Faculty of 1000 evaluation for Origins of coevolution between residues distant in protein 3D structures. (2018) (0)
- How DNA medicines could transform treatment of glioblastoma multiforme. (2020) (0)
- P Computational Studies of Protein Folding B I O E N G I N E E R I N G a N D B I O P H Y S I C S Feasibility of Structural Refinement (2001) (0)
- Protein Folding and Dynamics─An Overview on the Occasion of Harold Scheraga's 100th Birthday. (2023) (0)
- Keynote I (2010) (0)
- DESTINI: A deep-learning approach to contact-driven protein structure prediction (2019) (0)
- Helix-Coil Transition in Two-Chain , Coiled Coils . 1 . Infinite-Chain Limit (0)
- Repurposed FDA-approved drugs targeting genes influencing aging can extend lifespan and healthspan in rotifers (2018) (0)
- Repurposed antibiotic and antiviral drugs inhibit the immune evasive endoribonuclease of SARS-CoV-2 and restrict coronavirus infection in vitro (2022) (0)
- E. coli DHFR complex modeled with two ligand states (2019) (0)
- The crystal structure and slow time-resolved oxidative decay of an E. coli DHFR complex with tetrahydrofolate with implications to drug design (2019) (0)
- OF GLOBULAR PROTEIN FOLDING AND TERTIARY STRUCTURE (1989) (0)
- An Order-Disorder Theory of Stress Strain Behaviour of Glassy Polymers (1982) (0)
- Monte Carlo simulation of designed helical proteins. (2000) (0)
- Prediction of protein structure and function on a genomic scale (2000) (0)
- Faculty Opinions recommendation of Identifying facial phenotypes of genetic disorders using deep learning. (2019) (0)
- Chronic pain, fatigue, GI dysmotility and the mitochondrial chaperone TRAP1 (2015) (0)
- Commentary Fromindependent modules tomolten globules: Observations onthe nature ofprotein folding intermediates (1993) (0)
- Guest Editorial: Computational Molecular Biophysics: 40 Years of Achievements (2014) (0)
- Dynamic Monte Carlo Globular Protein Folding and Structure (1990) (0)
- Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects (2018) (0)
- Spontaneous insertion ofpolypeptide chains intomembranes: A MonteCarlomodel (1992) (0)
- In Silico Study Of Nonspecific DNA-protein Encounter Complexes (2009) (0)
- Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold. (2021) (0)
- PHEVIR: an artificial intelligence algorithm that predicts the molecular role of pathogens in complex human diseases (2022) (0)
- Monte Carlo Studies on Equilibrium Globular Protein Folding . I . Homopolymeric Lattice Models of P-Barrel Proteins (2003) (0)
- A lattice dynamics study of a Langmuir monolayer fatty acids (1993) (0)
- Faculty of 1000 evaluation for A new class of synthetic retinoid antibiotics effective against bacterial persisters. (2018) (0)
- Protein Structure Prediction - Session Introduction (1999) (0)
- YOU MAY BE INTERESTED IN Perspective : Towards single shot time-resolved microscopy using short wavelength table-top light sources Structural Dynamics (2019) (0)
- TMIC-12. TUMOR EDGE-DESTINED CELLS IN GBM CELLS IN A CELL-INTRINSIC MECHANISM (2019) (0)
- Polymer Melt Model (2001) (0)
- Repurposing FDA-approved drugs for anti-aging therapies (2016) (0)
- 3P270 Krylov subspace methods for computing correlated Brownian noise vectors in Brownian dynamics simulations with hydrodynamic interactions(24. Mathematical biology,Poster) (2013) (0)
- 183 On the origin and completeness of ligand binding pockets with applications to drug discovery (2015) (0)
- Personalized and Precision Medicine (PPM) as a model of healthcare services of the next-step generation to secure the national stability and the biosafety (2019) (0)
- Structural and Functional Implications of Modeling Non Synonymous Mutations in Patients with SCN1A-related Seizure Disorders (S29.007) (2014) (0)
- PROTEIN STRUCTURE PREDICTION II (2009) (0)
- N-Glycan Structure Modeling and in Silico Glycosylation: Template-Based Structure Prediction of Carbohydrate Structures of Glycoconjugates (2013) (0)
- The Role of Hydrodynamic Interactions in Self-Organization of Biological Molecules (2012) (0)
- Faculty Opinions recommendation of Rapid molecular evolution of pain insensitivity in multiple African rodents. (2019) (0)
- Monte Carlo Studies of an Idealized Model of a Lipid-Water Systemt (2001) (0)
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