2001
Betancourt, MR, Skolnick J. 2001. Universal similarity measure for comparing protein structures. Biopolymers. 59(5):305-9. PDF
Di Gennaro, JA, Siew N, Hoffman BT, ZHANG L, Skolnick J, Neilson LI, Fetrow JS. 2001. Enhanced functional annotation of protein sequences via the use of structural descriptors. Journal of structural biology. 134(2-3):232-45. PDF
Bukhman, YV, Skolnick J. 2001. BioMolQuest: integrated database-based retrieval of protein structural and functional information. Bioinformatics (Oxford, England). 17(5):468-78. PDF
Fetrow, JS, Siew N, Di Gennaro JA, Martinez-Yamout M, Dyson HJ, Skolnick J. 2001. Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight? Protein Science. 10(5):1005-14. PDF
Skolnick, J, Kihara D. 2001. Defrosting the frozen approximation: PROSPECTOR–a new approach to threading. Proteins. 42(3):319-31. PDF
Kihara, D, Lu H, Kolinski A, Skolnick J. 2001. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proceedings of the National Academy of Sciences of the United States of America. 98(18):10125-30. PDF
Lu, H, Skolnick J. 2001. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins. 44(3):223-32. PDF
Kolinski, A, Betancourt MR, Kihara D, Rotkiewicz P, Skolnick J. 2001. Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins. 44(2):133-49. PDF
Skolnick, J, Kolinski A, Kihara D, Betancourt MR, Rotkiewicz P, Boniecki M. 2001. Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement.. Proteins. Suppl 5:149-56. PDF
Zhang, Y, Skolnick J. 2001. Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures. The Journal of Chemical Physics. 115(11):5027. PDF
Betancourt, MR, Skolnick J. 2001. Finding the needle in a haystack: educing native folds from ambiguousab initio protein structure predictions. Journal of Computational Chemistry. 22(3):339-353. PDF
Skolnick, J, Kolinski A. 2001. Computational studies of protein folding. Computing in Science & Engineering. 3:22-31. PDF
Gront, D, Kolinski A, Skolnick J. 2001. A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics. Journal of Computational Physics. 115:1569-1574. PDF
2000
Feig, M, Rotkiewicz P, Kolinski A, Skolnick J, Brooks CL. 2000. Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models. Proteins. 41(1):86-97. PDF
Ortiz, AR, Skolnick J. 2000. Sequence evolution and the mechanism of protein folding. Biophysical journal. 79(4):1787-99. PDF
Skolnick, J, Fetrow JS, Kolinski A. 2000. Structural genomics and its importance for gene function analysis. Nature biotechnology. 18(3):283-7. PDF
Sikorski, A, Kolinski A, Skolnick J. 2000. Computer simulations of the properties of the alpha2, alpha2C, and alpha2D de novo designed helical proteins. Proteins. 38(1):17-28. PDF
Skolnick, J, Kolinski A, Ortiz A. 2000. Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins. 38(1):3-16. PDF
Skolnick, J, Fetrow JS. 2000. From genes to protein structure and function: novel applications of computational approaches in the genomic era. Trends in biotechnology. 18(1):34-9. PDF
Gront, D, Kolinski A, Skolnick J. 2000. Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures. The Journal of Chemical Physics. 113(12):5065. PDF
Kolinski, A, Rotkiewicz P, Ilkowski B, Skolnick J. 2000. Protein Folding: Flexible Lattice Models. Progress of Theoretical Physics Supplement. 138:292-300. PDF
Ilkowski, B, Skolnick J, Kolinski A. 2000. Helix-coil and beta sheet-coil transitions in a simplified, yet realistic protein model. Macromolecular Theory and Simulations. 9(8):523-533. PDF
Simmerling, C, Lee MR, Ortiz A.R, Kolinski A, Skolnick J, Kollman PA. 2000. Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1. Journal of the American Chemical Society. 122(35):8392-8402. PDF
Kolinski, A, Rotkiewicz P, Skolnick J. 2000. Structure of proteins: New approach to molecular modeling. Polish J. Chem. 75:587-599. PDF
1999
Fetrow, JS, Siew N, Skolnick J. 1999. Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily. The FASEB journal: official publication of the Federation of American Societies for Experimental Biology. 13(13):1866-74. PDF
Reva, BA, Skolnick J, Finkelstein AV. 1999. Averaging interaction energies over homologs improves protein fold recognition in gapless threading.. Proteins. 35(3):353-9. PDF
Zhang, B, Rychlewski L, Pawłowski K, Fetrow JS, Skolnick J, Godzik A. 1999. From fold predictions to function predictions: automation of functional site conservation analysis for functional genome predictions. Protein science : a publication of the Protein Society. 8(5):1104-15. PDF
Mohanty, D, Kolinski A, Skolnick J. 1999. De novo simulations of the folding thermodynamics of the GCN4 leucine zipper. Biophysical journal. 77(1):54-69. PDF
Kolinski, A, Rotkiewicz P, Ilkowski B, Skolnick J. 1999. A method for the improvement of threading-based protein models. Proteins. 37(4):592-610. PDF
Kolinski, A, Ilkowski B, Skolnick J. 1999. Dynamics and thermodynamics of beta-hairpin assembly: insights from various simulation techniques. Biophysical journal. 77(6):2942-52. PDF
Ortiz, AR, Kolinski A, Rotkiewicz P, Ilkowski B, Skolnick J. 1999. Ab initio folding of proteins using restraints derived from evolutionary information. Proteins. Suppl 3:177-85. PDF
RAPAPORT, D, JOHNSON J, Skolnick J. 1999. Supramolecular self-assembly: molecular dynamics modeling of polyhedral shell formation. Computer Physics Communications. 121-122:231-235. PDF
Skolnick, J, Kolinski A, Ortiz A.R. 1999. Application of reduced models to protein structure prediction. Computational Molecular Biology, Theoretical Computational Chemistry. 8:397-440. PDF
Kolinski, A, Godzik A, Skolnick J. 1999. Contact Maps. Encyclopedia of Molecular Biology. :567-571. PDF
Mohanty, D, Dominy BN, Kolinski A, Brooks CL, Skolnick J. 1999. Correlation between knowledge‐based and detailed atomic potentials: Application to the unfolding of the GCN4 leucine zipper. Proteins: Structure, Function, and Genetics. 35(4):447-452. PDF
Skolnick, J, Kolinski A, Mohanty D. 1999. De novo predictions of the quaternary structure of leucine zippers and other coiled coils. International Journal of Quantum Chemistry. 75(3):165-176. PDF
Reva, BA, Finkelstein AV, Skolnick J. 1999. Derivation and testing residue-residue mean force potentials for use in protein structure recognition. Protein Structure Prediction Methods and Protocols. :155-174. PDF
Finkelstein, AV, Rykunov DS, Yu M, Lobanov A, Badretdinov Y, Reva BA, Skolnick J, Mirny LA, Shakhnovich EI. 1999. Overcoming the crudeness of energy estimates in protein 3D structure prediction by homologs: The when and the how. Biophysica. 44:980-991. PDF
Skolnick, J, Fetrow JS, Ortiz AR, Kolinski A. 1999. The role of computational biology in the genomics revolution. National Research Council’s Chemical Sciences Roundtable Workshop on the Impact of Advances in Computing and Communications Technologies on Chemical Sciences and Technology. PDF
1998
Fetrow, JS, Skolnick J. 1998. Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. Journal of molecular biology. 281(5):949-68. PDF
Kolinski, A, Skolnick J. 1998. Assembly of protein structure from sparse experimental data: an efficient Monte Carlo model. Proteins. 32(4):475-94. PDF
Fetrow, JS, Godzik A, Skolnick J. 1998. 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. Journal of molecular biology. 282(4):703-11. PDF
Skolnick, J, Kolinski A, Ortiz AR. 1998. Reduced protein models and their application to the protein folding problem. Journal of biomolecular structure & dynamics. 16(2):381-96. PDF
Keasar, C, Tobi D, Elber R, Skolnick J. 1998. Coupling the folding of homologous proteins. Proceedings of the National Academy of Sciences of the United States of America. 95(11):5880-3. PDF
Ortiz, AR, Kolinski A, Skolnick J. 1998. Fold assembly of small proteins using monte carlo simulations driven by restraints derived from multiple sequence alignments. Journal of molecular biology. 277(2):419-48. PDF
Sikorski, A, Kolinski A, Skolnick J. 1998. Computer simulations of de novo designed helical proteins. Biophysical journal. 75(1):92-105. PDF
ZHANG, L, Skolnick J. 1998. How do potentials derived from structural databases relate to “true” potentials? Protein science : a publication of the Protein Society. 7(1):112-22. PDF
Ortiz, AR, Kolinski A, Skolnick J. 1998. Nativelike topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations. Proceedings of the National Academy of Sciences of the United States of America. 95(3):1020-5. PDF
Ortiz, AR, Kolinski A, Skolnick J. 1998. Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. Proteins. 30(3):287-94. PDF
Milik, M, Sauer D, Brunmark AP, Yuan L, Vitiello A, Jackson MR, Peterson PA, Skolnick J, Glass CA. 1998. Application of an artificial neural network to predict specific class I MHC binding peptide sequences. Nature biotechnology. 16(8):753-6. PDF
ZHANG, L, Godzik A, Skolnick J, Fetrow JS. 1998. Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family. Folding & design. 3(6):535-48. PDF
Kolinski, A, Galazka W, Skolnick J. 1998. Monte Carlo studies of the thermodynamics and kinetics of reduced protein models: Application to small helical, β, and α/β proteins. The Journal of Chemical Physics. 108(6):2608. PDF
Reva, BA, Finkelstein AV, Skolnick J. 1998. What is the probability of a chance prediction of a protein structure with an rmsd of 6 A? Folding & design. 3(2):141-7. PDF
Witte, K, Skolnick J, Wong C-H. 1998. A Synthetic Retrotransition (Backward Reading) Sequence of the Right-Handed Three-Helix Bundle Domain (10-53) of Protein A Shows Similarity in Confomation as Predicted by Computation. Journal of the American Chemical Society. 120(50):13042-13045. PDF
Kolinski, A, Jaroszewski L, Rotkiewicz P, Skolnick J. 1998. An Efficient Monte Carlo Model of Protein Chains. Modeling the Short-Range Correlations between Side Group Centers of Mass. The Journal of Physical Chemistry B. 102(23):4628-4637. PDF
Zhang, L, Skolnick J. 1998. What should the Z-score of native protein structures be? Protein Science. 7(5):1201-1207. PDF
REVA, BORISA, Rykunov DS, FINKELSTEIN ALEXEIV, Skolnick J. 1998. Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach. Journal of Computational Biology. 5(3):531-538. PDF
Kolinski, A, Rotkiewicz P, Skolnick J. 1998. Application of a high coordination lattice model in protein structure prediction. Proceedings of the Workshop on Monte Carlo Approach to Biopolymers and Protein Folding. Singapore: World Scientific, 377-388. PDF
Ortiz, A.R, Kolinski A, Skolnick J. 1998. Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins. Proceedings of the Pacific Symposium on Biocomputing (PSB-98). Altman, R., A.K. Dunker, L. Hunter and T.E. Klein, eds. Singapore: World Scientific Pub. 1998: 377-388. PDF
Skolnick, J, Kolinski A. 1998. Monte Carlo approaches to the protein folding problem. In: Ferguson, D., J.I. Siepmann, D.G. Truhlar, eds. Monte Carlo Methods in Chemical Physics. Advances in Chemical Physics Series. John Wiley & Sons, 203-242. PDF
Skolnick, J, Kolinski A. 1998. Protein Modeling. Encyclopedia of Computational Chemistry. :2200-2211.
Reva, BA, Finkelstein AV, Skolnick J. 1998. A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. Proceedings of the Second Annual International Conference on Computational Molecular Biology (RECOMB98) and J Comput Biol Special Issue, 214-220. PDF
1997
Reva, BA, Finkelstein AV, Sanner M, Olson AJ, Skolnick J. 1997. Recognition of protein structure on coarse lattices with residue-residue energy functions. Protein engineering. 10(10):1123-30. PDF
Skolnick, J, Jaroszewski L, Kolinski A, Godzik A. 1997. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein science : a publication of the Protein Society. 6(3):676-88. PDF
Skolnick, J, Kolinski A, Ortiz AR. 1997. MONSSTER: a method for folding globular proteins with a small number of distance restraints. Journal of molecular biology. 265(2):217-41. PDF
Kolinski, A, Skolnick J, Godzik A, Hu WP. 1997. A method for the prediction of surface “U”-turns and transglobular connections in small proteins. Proteins. 27(2):290-308. PDF
Hu, WP, Kolinski A, Skolnick J. 1997. Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turns. Proteins. 29(4):443-60. PDF
Hu, WP, Godzik A, Skolnick J. 1997. Sequence-structure specificity–how does an inverse folding approach work? Protein engineering. 10(4):317-31. PDF
Kolinski, A, Skolnick J. 1997. Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactions. The Journal of Chemical Physics. 107(3):953. PDF
Koliński, A, Skolnick J. 1997. High coordination lattice models of protein structure, dynamics and thermodynamics. Acta biochimica Polonica. 44(3):389-422. PDF
Keasar, C, Elber R, Skolnick J. 1997. Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction. Folding & design. 2(4):247-59. PDF
Milik, M, Kolinski A, Skolnick J. 1997. Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates. Journal of Computational Chemistry. 18(1):80-85. PDF
Ortiz, A.R, Hu WP, Kolinski A, Skolnick J. 1997. Method for low resolution prediction of small protein tertiary structure. Pacific Symposium on Biocomputing 1997. :316-327. PDF
Skolnick, J, Milik M. 1997. Modeling of Membrane Proteins and Peptides. In: Membrane Proteins Assembly, Part IV. Modeling and Simulation, von Heijne, G., ed. Austin: R.G. Landes Company: 201-220. PDF
Skolnick, J, Kolinski A. 1997. Monte Carlo Lattice Dynamics and the Prediction of Protein Folds. Computer Simulations of Biomolecular Systems. In: Theoretical and Experimental Studies. van Gunsteren, W. F., P.K. Weiner and A. J. Wilkinson, eds. Leiden, The Netherlands: ESCOM Science, 1997: 395-429. PDF
Skolnick, J. 1997. A Monte Carlo model of fd and Pf1 coat proteins in membranes. Chemtracts. 10:242-245. PDF
1996
Kolinski, A, Galazka W, Skolnick J. 1996. On the origin of the cooperativity of protein folding: implications from model simulations.. Proteins. 26(3):271-87. PDF
Olszewski, KA, Kolinski A, Skolnick J. 1996. Folding simulations and computer redesign of protein A three-helix bundle motifs. Proteins. 25(3):286-99. PDF
Vieth, M, Kolinski A, Skolnick J. 1996. Method for predicting the state of association of discretized protein models. Application to leucine zippers. Biochemistry. 35(3):955-67. PDF
Olszewski, KA, Kolinski A, Skolnick J. 1996. Does a backwardly read protein sequence have a unique native state? Protein engineering. 9(1):5-14. PDF
DeBolt, SE, Skolnick J. 1996. Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions. Protein engineering. 9(8):637-55. PDF
Hirst, JD, Vieth M, Skolnick J, Brooks CL. 1996. Predicting leucine zipper structures from sequence. Protein engineering. 9(8):657-62. PDF
Kolinski, A, Skolnick J, Godzik A. 1996. An algorithm for prediction of structural elements in small proteins. Proceedings of the Pacific Symposium on Biocomputing (PSB-96), Hunter, L., T. Klein, Eds. World Scientific, Singapore: 446-460. PDF
Vieth, M, Kolinski A, Brooks CL, Skolnick J. 1996. A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants. DIMACS. 23:233-236. PDF
Kolinski, A, Skolnick J. 1996. Lattice Models of Protein Folding. Dynamics and Thermodynamics. Austin: R.G. Landes Company: 202.
Skolnick, J, Milik M. 1996. Monte Carlo Models of Spontaneous Insertion of Peptides into Lipid Membranes. In: Membrane Structures & Dynamics. Merz, K., B. Roux, Eds. Boston: Birkhauser: 535-554. PDF