Cited by 339Protein Structure and DynamicsEnzyme Structure and FunctionMachine Learning in Bioinformatics

The DOI matches its Crossref record; 33 of the 34 references it cites were found in a registry or an index.

Topology fingerprint approach to the inverse protein folding problem

Godzik, Adam, Kolinski, Andrzej, Skolnick, Jeffrey·1992·Journal of Molecular Biology

Open this paper in CoChat — free account

Abstract

We describe the most general solution to date of the problem of matching globular protein sequences to the appropriate three-dimensional structures. The screening template, against which sequences are tested, is provided by a protein "structural fingerprint" library based on the contact map and the buried/exposed pattern of residues. Then, a lattice Monte Carlo algorithm validates or dismisses the stability of the proposed fold. Examples of known structural similarities between proteins having weakly or unrelated sequences such as the globins and phycocyanins, the eight-member alpha/beta fold of triose phosphate isomerase and even a close structural equivalence between azurin and immunoglobulins are found.

Integrity signals

Registry

Crossref · 10.1016/0022-2836(92)90693-e

Cites

33 of 33 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

A general method applicable to the search for similarities in the amino acid sequence of two proteins
Needleman, S. B., & Wunsch, C. D. (1970) · Journal of Molecular Biology · doi:10.1016/0022-2836(70)90057-4 · Cited by 11,288
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574
A Method to Identify Protein Sequences That Fold into a Known Three-Dimensional Structure
Bowie, J. U., Lüthy, R., & Eisenberg, D. (1991) · Science · doi:10.1126/science.1853201 · Cited by 2,851
Solvation energy in protein folding and binding
Eisenberg, D. S., & McLachlan, A. D. (1986) · Nature · doi:10.1038/319199a0 · Cited by 1,866
Tertiary templates for proteins
Ponder, J. W., & Richards, F. M. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90358-5 · Cited by 1,480
Profile analysis: detection of distantly related proteins.
Gribskov, M., McLachlan, A. D., & Eisenberg, D. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.13.4355 · Cited by 1,325
Calculation of conformational ensembles from potentials of mena force
Sippl, M. J. (1990) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80269-4 · Cited by 1,068
Selection of representative protein data sets
Hobohm, U., Scharf, M. E., Schneider, R., & Sander, C. (1992) · Protein Science · doi:10.1002/pro.5560010313 · Cited by 816
The refined 2.15 A X‐ray crystal structure of human liver cathepsin B: the structural basis for its specificity.
Müsil, D., Zucić, D., Türk, V., Engh, R. A., Mayr, I., Huber, R., Popovic, T., Türk, V., Towatari, T., & Katunuma, N. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07771.x · Cited by 608
Structure of oxidized poplar plastocyanin at 1·6 Å resolution
Guss, J. M., & Freeman, H. C. (1983) · Journal of Molecular Biology · doi:10.1016/s0022-2836(83)80064-3 · Cited by 507

Show all 34 references

Sorted by citations

Profile hidden Markov models
Eddy, S. R. (1998) · Bioinformatics · doi:10.1093/bioinformatics/14.9.755 · Cited by 5,515
Comparative Protein Structure Modeling of Genes and Genomes
Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.291 · Cited by 3,169
Modeller: Generation and Refinement of Homology-Based Protein Structure Models
Fiser, A., & Šali, A. (2003) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(03)74020-8 · Cited by 1,708
Enhanced genome annotation using structural profiles in the program 3D-PSSM 1 1Edited by J. Thornton
Kelley, L. A., MacCallum, R. M., & Sternberg, M. J. E. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3741 · Cited by 1,464
Hidden Markov models
Eddy, S. R. (1996) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(96)80056-x · Cited by 1,445
Evaluation of comparative protein modeling by M ODELLER
Šali, A., Potterton, L., Feng, Y., van Vlijmen, H., & Karplus, M. (1995) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340230306 · Cited by 1,088
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
Muegge, I., & Martin, Y. C. (1999) · Journal of Medicinal Chemistry · doi:10.1021/jm980536j · Cited by 1,008
Can correct protein models be identified?
Wallner, B., & Elofsson, A. (2003) · Protein Science · doi:10.1110/ps.0236803 · Cited by 714
Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells
Phan, Q. T., Myers, C. L., Fu, Y., Sheppard, D. C., Yeaman, M. R., Welch, W. H., Ibrahim, A. S., Edwards, J. E., & Filler, S. G. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050064 · Cited by 641
Knowledge-based potentials for proteins
Sippl, M. J. (1995) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(95)80081-6 · Cited by 605
Threading a database of protein cores
Madej, T., Gibrat, J.-F., & Bryant, S. H. (1995) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340230309 · Cited by 444
Energy Functions that Discriminate X-ray and Near-native Folds from Well-constructed Decoys
Park, B. H., & Levitt, M. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0256 · Cited by 409
An empirical energy function for threading protein sequence through the folding motif
Bryant, S. H., & Lawrence, C. E. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340160110 · Cited by 397
MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information
Wu, S., & Zhang, Y. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.21945 · Cited by 381
Statistical potentials for fold assessment
Melo, F., Sánchez, R., & Šali, A. (2002) · Protein Science · doi:10.1002/pro.110430 · Cited by 349
Protein modeling and structure prediction with a reduced representation.
Koliński, A. (2004) · Acta Biochimica Polonica · doi:10.18388/abp.2004_3575 · Cited by 337
Advances in comparative protein-structure modelling
Sánchez, R., & Šali, A. (1997) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(97)80027-9 · Cited by 331
Protein fold recognition using sequence‐derived predictions
Fischer, D., & Eisenberg, D. S. (1996) · Protein Science · doi:10.1002/pro.5560050516 · Cited by 302
Functional and Structural Diversity in the Als Protein Family of Candida albicans
Sheppard, D. C., Yeaman, M. R., Welch, W. H., Phan, Q. T., Fu, Y., Ibrahim, A. S., Filler, S. G., Zhang, M., Waring, A. J., & Edwards, J. E. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m401929200 · Cited by 300
Monte carlo simulations of protein folding. I. Lattice model and interaction scheme
Koliński, A., & Skolnick, J. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340180405 · Cited by 294
Self-citation
Derivation of rules for comparative protein modeling from a database of protein structure alignments
Šali, A., & Overington, J. P. (1994) · Protein Science · doi:10.1002/pro.5560030923 · Cited by 299
A distance‐dependent atomic knowledge‐based potential for improved protein structure selection
Lu, H. J., & Skolnick, J. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.1087 · Cited by 292
Self-citation
RAPTOR: OPTIMAL PROTEIN THREADING BY LINEAR PROGRAMMING
Xu, J., Li, M., Kim, D., & Xu, Y. (2003) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720003000186 · Cited by 294
Use of pair potentials across protein interfaces in screening predicted docked complexes
Moont, G., Gabb, H. A., & Sternberg, M. J. E. (1999) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19990515)35:3 · Cited by 256
MULTIPROSPECTOR: An algorithm for the prediction of protein–protein interactions by multimeric threading
Lu, L. J., Lu, H. J., & Skolnick, J. (2002) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.10222 · Cited by 242
Self-citation
The structural alignment between two proteins: Is there a unique answer?
Godzik, A. (1996) · Protein Science · doi:10.1002/pro.5560050711 · Cited by 236
Self-citation
Comparative Protein Structure Modeling: Introduction and Practical Examples with Modeller
Sánchez, R., & Šali, A. (2003) · Humana Press eBooks · doi:10.1385/1-59259-368-2:97 · Cited by 238
Knowledge-Based Protein Modeling
Johnson, M. S., Srinivasan, N., Sowdhamini, R., & Blundell, T. L. (1994) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409239409086797 · Cited by 236
Three-dimensional protein structure prediction: Methods and computational strategies
Dorn, M., Silva, M. B. E., Buriol, L. S., & Lamb, L. C. (2014) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2014.10.001 · Cited by 221
Prediction of contact maps with neural networks and correlated mutations
Fariselli, P., Olmea, O., Valencia, A., & Casadio, R. (2001) · Protein Engineering Design and Selection · doi:10.1093/protein/14.11.835 · Cited by 206
Application of multiple sequence alignment profiles to improve protein secondary structure prediction
Cuff, J. A., & Barton, G. J. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20000815)40:3 · Cited by 773
Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?
Skolnick, J., Godzik, A., Jaroszewski, L., & Koliński, A. (1997) · Protein Science · doi:10.1002/pro.5560060317 · Cited by 201
Self-citation
All are not equal: A benchmark of different homology modeling programs
Wallner, B., & Elofsson, A. (2005) · Protein Science · doi:10.1110/ps.041253405 · Cited by 201
Novel knowledge-based mean force potential at atomic level
Melo, F., & Feytmans, E. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0868 · Cited by 196
A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins
Koliński, A., Godzik, A., & Skolnick, J. (1993) · The Journal of Chemical Physics · doi:10.1063/1.464706 · Cited by 193
Self-citation
Reduced models of proteins and their applications
Koliński, A., & Skolnick, J. (2003) · Polymer · doi:10.1016/j.polymer.2003.10.064 · Cited by 190
Self-citation
A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization
Liwo, A., Pincus, M. R., Wawak, R. J., Rackovsky, S. R., dziej, S. O., & Scheraga, H. A. (1997) · Journal of Computational Chemistry · doi:10.1002/(sici)1096-987x(199705)18:7 · Cited by 186
Molecular Modeling of Proteins and Mathematical Prediction of Protein Structure
Neumaier, A. (1997) · SIAM Review · doi:10.1137/s0036144594278060 · Cited by 173
Algorithmic aspects of protein structure similarity
Goldman, D., Istrail, S., & Papadimitriou, C. H. (2003) · Annual Symposium on Foundations of Computer Science · doi:10.1109/sffcs.1999.814624 · Cited by 170
Delaunay Tessellation of Proteins: Four Body Nearest-Neighbor Propensities of Amino Acid Residues
Singh, R. K., Tropsha, A., & Vaisman, I. I. (1996) · Journal of Computational Biology · doi:10.1089/cmb.1996.3.213 · Cited by 172
A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence
Rice, D. W., & Eisenberg, D. S. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.0924 · Cited by 162
Clique-detection models in computational biochemistry and genomics
Butenko, S. I., & Wilhelm, W. E. (2005) · European Journal of Operational Research · doi:10.1016/j.ejor.2005.05.026 · Cited by 162
Factors affecting the ability of energy functions to discriminate correct from incorrect folds
Park, B. H., Huang, E. S., & Levitt, M. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0809 · Cited by 160
Modelling mutations and homologous proteins
Šali, A. (1995) · Current Opinion in Biotechnology · doi:10.1016/0958-1669(95)80074-3 · Cited by 160
1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap
Caprara, A., Carr, R. D., Istrail, S., Lancia, G., & Walenz, B. P. (2004) · Journal of Computational Biology · doi:10.1089/106652704773416876 · Cited by 157
Generating and testing protein folds
Wodak, S. J., & Rooman, M. J. (1993) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(05)80160-5 · Cited by 152
Protein Structure Prediction: Recognition of Primary, Secondary, and Tertiary Structural Features from Amino Acid Sequence
Eisenhaber, F., Persson, B., & Argos, P. (1995) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409239509085139 · Cited by 155
Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners
Pollastri, G., & Baldi, P. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s62 · Cited by 151
Statistics of sequence-structure threading
Bryant, S. H., & Altschul, S. F. (1995) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(95)80082-4 · Cited by 149
Global Optimum Protein Threading with Gapped Alignment and Empirical Pair Score Functions
Lathrop, R. H., & Smith, T. F. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0053 · Cited by 150
Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets
Godzik, A., Skolnick, J., & Koliński, A. (1995) · Protein Science · doi:10.1002/pro.5560041016 · Cited by 146
Self-citation
Monte carlo simulations of protein folding. II. Application to protein A, ROP, and crambin
Koliński, A., & Skolnick, J. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340180406 · Cited by 143
Self-citation
Learning effective amino acid interactions through iterative stochastic techniques
Micheletti, C., Seno, F., Banavar, J. R., & Maritan, A. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20010215)42:3 · Cited by 55
Self-citation
Protein threading using context-specific alignment potential
Ma, J., Wang, S., Zhao, F., & Xu, J. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt210 · Cited by 141
Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination.
Godzik, A., & Skolnick, J. (1992) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.89.24.12098 · Cited by 137
Self-citation
The structural coverage of the human proteome before and after AlphaFold
Porta-Pardo, E., Ruiz-Serra, V., Valentini, S., & Valencia, A. (2022) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009818 · Cited by 131
Comparative Protein Structure Modelling
Fiser, A. (2008) · Springer eBooks · doi:10.1007/978-1-4020-9058-5_3 · Cited by 133
Practical lessons from protein structure prediction
Ginalski, K. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki327 · Cited by 124
Statistical theory for protein combinatorial libraries. packing interactions, backbone flexibility, and the sequence variability of a main-chain structure11Edited by J. Thornton
Kono, H., & Saven, J. G. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4422 · Cited by 124
Linear programming optimization and a double statistical filter for protein threading protocols
Meller, J., & Elber, R. (2001) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.1145 · Cited by 123
Improving the quality of twilight‐zone alignments
Jaroszewski, L., Godzik, A., & Rychlewski, L. (2000) · Protein Science · doi:10.1110/ps.9.8.1487 · Cited by 119
Self-citation
Combination of threading potentials and sequence profiles improves fold recognition 1 1Edited by B. Honig
Panchenko, A. R., Marchler‐Bauer, A., & Bryant, S. H. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3541 · Cited by 115
101 optimal PDB structure alignments
Lancia, G., Carr, R. D., Walenz, B. P., & Istrail, S. (2001) · doi:10.1145/369133.369199 · Cited by 113
Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force
Babajide, A., Hofacker, I. L., Sippl, M. J., & Stadler, P. F. (1997) · Folding and Design · doi:10.1016/s1359-0278(97)00037-0 · Cited by 110
Fold and function predictions for Mycoplasma genitalium proteins
Rychlewski, L., Zhang, B., & Godzik, A. (1998) · Folding and Design · doi:10.1016/s1359-0278(98)00034-0 · Cited by 104
Self-citation
Protein fold recognition
Jones, D. T., & Thornton, J. M. (1993) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf02337560 · Cited by 103
Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins
da Silveira, C. H., Pires, D. E. V., de Melo-Minardi, R. C., Ribeiro, C. O., Veloso, C. J. M., Lopes, J. C. D., Meira, W., Neshich, G., Ramos, C. H. I., Habesch, R., et al. (2008) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22187 · Cited by 101
Progress in fold recognition
Flöckner, H., Braxenthaler, M., Lackner, P., Jaritz, M., Ortner, M., & Sippl, M. J. (1995) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340230311 · Cited by 101
Statistical significance of hierarchical multi‐body potentials based on Delaunay tessellation and their application in sequence‐structure alignment
Munson, P. J., & Singh, R. K. (1997) · Protein Science · doi:10.1002/pro.5560060711 · Cited by 97
In search for more accurate alignments in the twilight zone
Jaroszewski, L., Li, W., & Godzik, A. (2002) · Protein Science · doi:10.1110/ps.4820102 · Cited by 97
Self-citation
Ranking potential binding peptides to MHC molecules by a computational threading approach
Altuvia, Y., Schueler‐Furman, O., & Margalit, H. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0293 · Cited by 96
Detecting distant homology with Meta-BASIC
Ginalski, K., von Grotthuss, M., Grishin, N. V., & Rychlewski, L. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh370 · Cited by 94
Polar and nonpolar atomic environments in the protein core: Implications for folding and binding
Koehl, P., & Delarue, M. H. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340200307 · Cited by 91
Fold prediction by a hierarchy of sequence, threading, and modeling methods
Jaroszwski, Ł., Rychlewski, L., Zhang, B., & Godzik, A. (1998) · Protein Science · doi:10.1002/pro.5560070620 · Cited by 94
Self-citation
De novo and inverse folding predictions of protein structure and dynamics
Godzik, A., Kolinski, A., & Skolnick, J. (1993) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf02337559 · Cited by 91
Self-citation
SSALN: An alignment algorithm using structure‐dependent substitution matrices and gap penalties learned from structurally aligned protein pairs
Qiu, J., & Elber, R. (2005) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.20854 · Cited by 90
Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments
Ortíz, Á. R., Koliński, A., & Skolnick, J. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1595 · Cited by 90
Self-citation
Modular determinants of antimicrobial activity in platelet factor-4 family kinocidins.
Yeaman, M., Yount, N., Waring, A., Gank, K. D., Kupferwasser, D., Wiese, R., Bayer, A., & Welch, W. (2007) · Biochimica et Biophysica Acta · doi:10.1016/j.bbamem.2006.11.010 · Cited by 86
A BAR Domain in the N Terminus of the Arf GAP ASAP1 Affects Membrane Structure and Trafficking of Epidermal Growth Factor Receptor
Nie, Z., Hirsch, D. S., Luo, R., Jian, X., Stauffer, S., Cremesti, A. E., Andrade, J., Lebowitz, J., Marino, M., Ahvazi, B., et al. (2006) · Current Biology · doi:10.1016/j.cub.2005.11.069 · Cited by 88
Role of explicitly cooperative interactions in protein folding funnels: A simulation study
Eastwood, M. P., & Wolynes, P. G. (2001) · The Journal of Chemical Physics · doi:10.1063/1.1315994 · Cited by 83
An Efficient Computational Method for Globally Optimal Threading1
Xu, Y., Xu, D. H., & Uberbacher, E. C. (1998) · Journal of Computational Biology · doi:10.1089/cmb.1998.5.597 · Cited by 82
Three-dimensional profiles from residue-pair preferences: identification of sequences with beta/alpha-barrel fold.
Wilmanns, M., & Eisenberg, D. S. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.4.1379 · Cited by 80
A method for predicting protein structure from sequence
Skolnick, J., Koliński, A., Brooks, C. L., Godzik, A., & Rey, A. (1993) · Current Biology · doi:10.1016/0960-9822(93)90348-r · Cited by 80
Self-citation
The Trap-like Relaxin-binding Site of the Leucine-rich G-protein-coupled Receptor 7
Büllesbach, E. E., & Schwabe, C. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m500030200 · Cited by 78
Statistical theory of combinatorial libraries of folding proteins: energetic discrimination of a target structure
Zou, J., & Saven, J. G. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3426 · Cited by 78
Structural alignment of large—size proteins via lagrangian relaxation
Caprara, A., & Lancia, G. (2002) · doi:10.1145/565196.565209 · Cited by 77
A simplified amino acid potential for use in structure predictions of proteins
Wallqvist, A., & Ullner, M. (1994) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340180308 · Cited by 78
Homology Modeling with Low Sequence Identity
Tramontano, A. L. (1998) · Methods · doi:10.1006/meth.1998.0585 · Cited by 76
Self Generating Metaheuristics in Bioinformatics: The Proteins Structure Comparison Case
Krasnogor, N. (2004) · Genetic Programming and Evolvable Machines · doi:10.1023/b:genp.0000023687.41210.d7 · Cited by 76
Discriminating compact nonnative structures from the native structure of globular proteins.
Wang, Y., Zhang, H., Li, W., & Scott, R. A. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.3.709 · Cited by 75
Crystal Structure of the Human Cell Cycle Protein CksHs1: Single Domain Fold with Similarity to Kinase N-lobe Domain
Arvai, A. S., Bourne, Y., Hickey, M. J., & Tainer, J. A. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0341 · Cited by 72
Self‐consistently optimized statistical mechanical energy functions for sequence structure alignment
Koretke, K. K., Luthey-Schulten, Z. A., & Wolynes, P. G. (1996) · Protein Science · doi:10.1002/pro.5560050607 · Cited by 71
ARAP2 effects on the actin cytoskeleton are dependent on Arf6-specific GTPase-activating-protein activity and binding to RhoA-GTP
Yoon, H., Miura, K., Cuthbert, E. J., Davis, K., Ahvazi, B., Casanova, J. E., & Randazzo, P. A. (2006) · Journal of Cell Science · doi:10.1242/jcs.03237 · Cited by 70
Predictions of protein segments with the same aminoacid sequence and different secondary structure: A benchmark for predictive methods
Jacoboni, I., Martelli, P. L., Fariselli, P., Compiani, M., & Casadio, R. (2000) · Proteins Structure Function and Bioinformatics · doi:10.1002/1097-0134(20001201)41:4 · Cited by 44
The foldon universe: a survey of structural similarity and self-recognition of independently folding units 1 1Edited by F. E. Cohen
Panchenko, A. R., Luthey-Schulten, Z. A., Cole, R., & Wolynes, P. G. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1205 · Cited by 72
Platelet Microbicidal Protein 1: Structural Themes of a Multifunctional Antimicrobial Peptide
Yount, N. Y., Gank, K. D., Xiong, Y. Q., Bayer, A. S., Pender, T., Welch, W. H., & Yeaman, M. R. (2004) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.48.11.4395-4404.2004 · Cited by 68
Structural insights into the Plasmodium falciparum histone deacetylase 1 (PfHDAC-1): A novel target for the development of antimalarial therapy
Mukherjee, P. K., Pradhan, A., Shah, F., Tekwani, B. L., & Avery, M. A. (2008) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2008.03.005 · Cited by 66
The structure of full-length LysR-type transcriptional regulators. Modeling of the full-length OxyR transcription factor dimer
Zaim, J. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg234 · Cited by 63
Sequence specificity, statistical potentials, and three‐dimensional structure prediction with self‐correcting distance geometry calculations of β‐sheet formation in proteins
Zhu, H., & Braun, W. A. (1999) · Protein Science · doi:10.1110/ps.8.2.326 · Cited by 62
Protein structure: what is it possible to predict now?
Finkelstein, A. V. (1997) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(97)80008-5 · Cited by 62

Authors: Godzik, A., Kolinski, A., & Skolnick, J.
Affiliations: Scripps Research Institute (US)
Corresponding author: Skolnick, Jeffrey
ORCID: Godzik, Adam
Skolnick, Jeffrey
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 1992-09
Volume: 227
Issue: 1
Pages: 227-238
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1016/0022-2836(92)90693-e
OpenAlex: W2040594319
Cited by: 339
References: 34
Citations by year: 2025: 3 · 2022: 2 · 2021: 1 · 2020: 3 · 2018: 3 · 2017: 2 · 2016: 5 · 2015: 3 · 2014: 6 · 2013: 4 · 2012: 2
FWCI: 7.82
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Funders: National Institute of General Medical Sciences (GM 37408, R01GM037408)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Keywords: inverse protein folding, protein structure prediction, structural fingerprints, contact maps, lattice Monte Carlo simulation, globin, phycocyanin, triosephosphate isomerase, azurin, immunoglobulins, structural equivalence
MeSH terms: Algorithms, Azurin, Bacterial Outer Membrane Proteins, Bacterial Proteins, Globins, Immunoglobulin lambda-Chains, Models, Molecular, Phycocyanin, Plant Proteins, Plastocyanin, Protein Conformation, Structure-Activity Relationship, Thermodynamics, Databases, Factual, Sequence Alignment

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Topology fingerprint approach to the inverse protein folding problem

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks