Topology fingerprint approach to the inverse protein folding problem

Cited by (336)

Items 201–300 of 336

1. Genome-based structural biology
   Dmitrij Frishman, Hans‐Werner Mewes · 1999 · Progress in Biophysics and Molecular Biology
2. Sausage: protein threading with flexible force fields
   Thomas Huber, Anthony J.Russell, Daniel Ayers, Andrew E. Torda · 1999 · Bioinformatics
3. A PRACTICAL METHOD FOR INTERPRETATION OF THREADING SCORES: AN APPLICATION OF NEURAL NETWORK
   Ying Xu, Dong He Xu, Victor N. Olman · 2002
4. Improved recognition of native-like protein structures using a family of designed sequences
   Patrice Koehl, Michael Levitt · 2002 · Proceedings of the National Academy of Sciences
5. Residue–Residue contact substitution probabilities derived from aligned three‐dimensional structures and the identification of common folds
   Michael A. Rodionov, Mark S. Johnson · 1994 · Protein Science
6. [35] Three-dimensional profiles for measuring compatibility of amino acid sequence with three-dimensional structure
   James U. Bowie, Kam Y. J. Zhang, Matthias Wilmanns, David S Eisenberg · 1996 · Methods in enzymology on CD-ROM/Methods in enzymology
7. A Branch-and-Reduce Algorithm for the Contact Map Overlap Problem
   Wei Xie, Nikolaos V. Sahinidis · 2006 · Lecture notes in computer science
8. Problems and solutions in protein engineering — towards rational design
   Tom L. Blundell · 1994 · Trends in biotechnology
9. A branch-and-bound algorithm for optimal protein threading with pairwise (contact potential) amino acid interactions
   Lathrop, Smith · 1994 · Hawaii International Conference on System Sciences (HICSS)
10. Algorithmic research problems in molecular bioinformatics
    Thomas Lengauer · 2002 · Israel Symposium on Theory and Computing Systems (ISTCS)
11. The key role of atom types, reference states, and interaction cutoff radii in the knowledge‐based method: New variational approach
    Anatoly M. Ruvinsky, A. V. Kozintsev · 2005 · Proteins Structure Function and Bioinformatics
12. Exploring the sequence‐structure protein landscape in the glycosyltransferase family
    Ziding Zhang, Sunil Kochhar, Martin Grigorov · 2003 · Protein Science
13. Extracting contact energies from protein structures: A study using a simplified model
    Chao Zhang · 1998 · Proteins Structure Function and Bioinformatics
14. ‘Meta’Approaches to Protein Structure Prediction
    Janusz Marek Bujnicki, Daniel Fischer · 2007 · Nucleic acids and molecular biology
15. Scoring Functions for ab initio Protein Structure Prediction
    Enoch S. Huang, Ram Samudrala, Britt H. Park · 2003 · Humana Press eBooks
16. On the Structure of hisH: Protein Structure Prediction in the Context of Structural and Functional Genomics
    Patrick O’Donoghue, Rommie E. Amaro, Zaida Ann Luthey-Schulten · 2001 · Journal of Structural Biology
17. From local structure to a global framework: recognition of protein folds
    Agnel Praveen Joseph, Alexandre G. de Brevern · 2014 · Journal of The Royal Society Interface
18. Computational Methods for Protein Structure Prediction and Fold Recognition
    Iwona A. Cymerman, Marcin Feder, Marcin PawŁowski, Michal A. Kurowski, Janusz Marek Bujnicki · 2007 · Nucleic acids and molecular biology
19. Three-dimensional threading approach to protein structure recognition
    Haibo Cao, Yungok Ihm, Cai‐Zhuang Wang, James Robert Morris, Mehmet Su, Drena L Dobbs, Kai‐Ming Ho · 2003 · Polymer
20. A polynomial-time algorithm for a class of protein threading problems
    Ying Xu, Edward C. Uberbacher · 1996 · Computer applications in the biosciences
21. BioShell Threader: protein homology detection based on sequence profiles and secondary structure profiles
    Dominik Gront, Mieczysław Błaszczyk, P. Wojciechowski, Andrzej Koliński · 2012 · Nucleic Acids Research
22. Analysis of quaternary structure of a [LDH-like] malate dehydrogenase of Plasmodium falciparum with oligomeric mutants
    Anupam Pradhan, Prasenjit K. Mukherjee, Abhai K. Tripathi, Mitchell A. Avery, Larry Walker, Babu L. Tekwani · 2009 · Molecular and Cellular Biochemistry
23. The dependence of amino acid pair correlations on structural environment
    Adrian P. Cootes, Paul M. G. Curmi, Ross B. Cunningham, Christine F. Donnelly, Andrew E. Torda · 1998 · Proteins Structure Function and Bioinformatics
24. Docking and Scoring in Drug Discovery
    Francesca Spyrakis, Pietro Cozzini, Glen E. Kellogg · 2010 · Wiley eBooks
25. An Anytime Local-to-Global Optimization Algorithm for Protein Threading in O(m 2 ñ 2 ) Space
    Richard H. Lathrop · 1999 · Journal of Computational Biology
26. Recursive dynamic programming for adaptive sequence and structure alignment.
    R Thiele, Ralf Zimmer, Thomas Lengauer · 1995 · PubMed
27. Genetic Threading
    J. Yadgari, Amihood Amir, Ron Unger · 2001 · Constraints
28. ALIGN_MTX—An optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment
    Boris Vishnepolsky, Malak Pirtskhalava · 2009 · Computational Biology and Chemistry
29. A protein‐specifically adapted scoring function for the reranking of docking solutions
    Wolfgang Müller, Heinrich Sticht · 2007 · Proteins Structure Function and Bioinformatics
30. HORI: a web server to compute Higher Order Residue Interactions in protein structures
    Sundaramurthy Pandurangan, Khader Shameer, Raashi Sreenivasan, Sunita Gakkhar, Ramanathan Sowdhamini · 2010 · BMC Bioinformatics
31. Comparative Protein Structure Prediction
    Marc A. Martı́-Renom, Bozidar Jerkovic, Andrej Šali · 2002 · Current Protocols in Protein Science
32. Perceptron learning of pairwise contact energies for proteins incorporating the amino acid environment
    Muyoung Heo, Suhkmann Kim, Eun-Joung Moon, Mookyung Cheon, Kwanghoon Chung, Iksoo Chang · 2005 · Physical Review E
33. Inter-C? atomic potentials derived from the statistics of average interresidue distances in proteins: Application to bovine pancreatic trypsin inhibitor
    Takeshi Kikuchi · 1996 · Journal of Computational Chemistry
34. Protein sequence threading, the alignment problem, and a two-step strategy
    Thomas Huber, Andrew E. Torda · 1999 · Journal of Computational Chemistry
35. Triage protein fold prediction
    Hongxian He, Gregory McAllister, Temple F. Smith · 2002 · Proteins Structure Function and Bioinformatics
36. A fast, stochastic threading algorithm for proteins.
    Oakley H. Crawford · 1999 · Bioinformatics
37. Modeling Protein Structure from its Sequence
    Marc A. Martı́-Renom, Mallur Srivatsan Madhusudhan, Narayanan Eswar, Ursula Pieper, Min‐Yi Shen, Andrej Šali, András Fiser, Nebojša Mirković, Bino John, Ashley C. Stuart · 2003 · Current Protocols in Bioinformatics
38. The Framework of Computational Protein Design
    Ilan Samish · 2016 · Methods in molecular biology
39. Prediction of the structural similarity between spermidine/putrescine‐binding protein and maltose‐binding protein
    Yo Matsuo, Ken Nishikawa · 1994 · FEBS Letters
40. Recursive approaches to the statistical physics of lattice proteins
    Stolorz · 1994 · Hawaii International Conference on System Sciences (HICSS)
41. Protein structure prediction and design
    Veronica Morea, Raphaël Leplae, Anna Luna Tramontano · 1998 · Biotechnology annual review
42. A Bayesian approach to sequence alignment algorithms for protein structure recognition
    Goldstein, Luthey-Schulten, Wolynes · 1994 · Hawaii International Conference on System Sciences (HICSS)
43. Understanding on the residue contact network using the log‐normal cluster model and the multilevel wheel diagram
    Weitao Sun, Jing J. He · 2010 · Biopolymers
44. Bimal: Bipartite matching alignment for the contact map overlap problem
    Brijnesh Johannes Jain, Klaus Obermayer · 2009 · International Joint Conference on Neural Networks (IJCNN)
45. Efficacy and selectivity in flexible database docking
    Ronald M. A. Knegtel, Markus Wagener · 1999 · Proteins Structure Function and Bioinformatics
46. Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2
    Patrick Aloy, José Manuel Mas, Marc A. Martı́-Renom, Enrique Querol, Francesc Xavier Avilés, Baldomero Oliva · 2000 · Journal of Computer-Aided Molecular Design
47. THE HUMORAL IMMUNE RESPONSE AGAINST BLOOD GROUP ANTIGENS AT THE MOLECULAR LEVEL
    Willem Hendrik Ouwehand, Jacqueline M. Bye, B.D. Gorick, James D. Marks, Erik Timmers, H Griffin, Ricarda Finnern, Nevin C. Hughes-Jones · 1994 · Vox Sanguinis
48. On the existence and implications of an inverse folding code in proteins.
    Shalom R. Rackovsky · 1995 · Proceedings of the National Academy of Sciences
49. How to compute protein residue contacts more accurately?
    Pedro Martins, Vinícius Diniz Mayrink, Sabrina de Azevedo Silveira, Carlos Henrique da Silveira, Leonardo Henrique França de Lima, Raquel C. de Melo-Minardi · 2018 · ACM Symposium on Applied Computing
50. Xylanase homology modeling using the inverse protein folding approach
    Xiannong Chen, David Whitmire, J. Phillip Bowen · 1996 · Protein Science
51. A Contact Energy Function Considering Residue Hydrophobic Environment and Its Application in Protein Fold Recognition
    Mo-Jie Duan, Yan-Hong Zhou · 2005 · Genomics Proteomics & Bioinformatics
52. Sequence-structure specificity of a knowledge based energy function at the secondary structure level
    Dong He Xu, Michael A. Unseren, Ying Xu, Edward C. Uberbacher · 2000 · Bioinformatics
53. Structural Characterization of Vivapain-2 and Vivapain-3, Cysteine Proteases fromPlasmodium vivax: Comparative Protein Modeling and Docking Studies
    Prashant V. Desai, Mitchell A. Avery · 2004 · Journal of Biomolecular Structure and Dynamics
54. Multi-body interactions within the graph of protein structure.
    Peter J. Munson, Raj Kumar Singh · 1997 · PubMed
55. Optimization techniques in molecular structure and function elucidation
    Nikolaos V. Sahinidis · 2009 · Computers & Chemical Engineering
56. The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets
    Evandro Ferrada · 2014 · PLoS Computational Biology
57. Computational Molecular Biology
    Giuseppe Lancia · 2006 · International series in management science/operations research/International series in operations research & management science
58. Understanding contact patterns of protein structures from protein contact map and investigation of unique patterns in the globin‐like folded domains
    Arumugam Amala, Isaac Arnold Emerson · 2018 · Journal of Cellular Biochemistry
59. Fast protein fold recognition and accurate sequence-structure alignment
    Ralf Zimmer, Ralf Thiele · 1996 · Lecture notes in computer science
60. Towards understanding the structure of the capsid of Banana Bunchy Top Virus
    Sundaram Sairam, Ramasamy Selvarajan, Savithri S. Handanahalli, Sangita Venkataraman · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
61. COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices
    Rafael Pereira Lemos, Diego Mariano, Sabrina de Azevedo Silveira, Raquel C. de Melo-Minardi · 2025 · Frontiers in Bioinformatics
62. An Eigendecomposition Method for Protein Structure Alignment
    Satish Chandra Panigrahi, Asish Mukhopadhyay · 2014 · Lecture notes in computer science
63. Protein Structure Prediction: From Recognition of Matches with Known Structures to Recombination of Fragments
    Michał J. Gajda, Marcin Pawlowski, Janusz Marek Bujnicki · 2010 · Springer eBooks
64. A new method for modeling and solving the protein fold recognition problem
    Ying Xu, Dong He Xu, Edward C. Uberbacher · 1998 · University of North Texas Digital Library (University of North Texas)
65. Sensitive methods for determining the relatedness of proteins with limited sequence homology
    Patrick Argos · 1994 · Current Opinion in Biotechnology
66. Remotely related sequences and structures: Analysis and predictive modelling
    William Ramsay Taylor · 1994 · Trends in biotechnology
67. Feasibility in the inverse protein folding protocol
    Motonori Ota, Ken Nishikawa · 1999 · Protein Science
68. Protein fold recognition score functions: Unusual construction strategies
    Daniel Ayers, Thomas Huber, Andrew E. Torda · 1999 · Proteins Structure Function and Bioinformatics
69. Insights into the capsid structure of banana bunchy top virus
    Sangita Venkataraman, Ramasamy Selvarajan, Sundaram S. Subramanian, Savithri S. Handanahalli · 2022 · 3 Biotech
70. Aligning Sequences to Structures
    Liam James McGuffin · 2008 · Humana Press eBooks
71. Information‐theoretic analysis of the reference state in contact potentials used for protein structure prediction
    Armando D. Solis, Shalom R. Rackovsky · 2009 · Proteins Structure Function and Bioinformatics
72. Cornering and catching the common protein fold
    Mark S. Johnson · 1995 · Molecular Medicine Today
73. Protein secondary structure prediction with Bayesian learning method
    Pengliang Wang, Du Zhang · 2003 · IEEE International Conference on Tools with Artificial Intelligence (ICTAI)
74. Counting and classifying possible protein folds
    Adam Godzik · 1997 · Trends in biotechnology
75. Modelling of peptide and protein structures
    S. Fraga, J. M. R. Parker · 1994 · Amino Acids
76. A new method for modeling and solving the protein fold recognition problem (extended abstract)
    Ying Xu, Dong He Xu, Edward C. Uberbacher · 1998 · Research in Computational Molecular Biology
77. Improved algorithms for protein motif recognition
    Bonnie Berger, David Brown Wilson · 1995 · Symposium on Discrete Algorithms
78. Performance of Threading Scoring Functions Designed Using New Optimization Method
    Jadwiga Renata Bienkowska, Robert G. Rogers, Temple F. Smith · 1999 · Journal of Computational Biology
79. CONTSOR—A new knowledge‐based fold recognition potential, based on side chain orientation and contacts between residue terminal groups
    Boris Vishnepolsky, Malak Pirtskhalava · 2011 · Protein Science
80. Homology modeling of the three-dimensional structure of bovine serum albumin
    Lihua Chen, Guohui Liu, Qiang Wang, Wanguo Hou · 2010 · International Conference on Biomedical Engineering and Informatics (BMEI)
81. Comparison of the efficiency of evolutionary change‐based and side chain orientation‐based fold recognition potentials
    Boris Vishnepolsky, Grigol Managadze, Malak Pirtskhalava · 2008 · Proteins Structure Function and Bioinformatics
82. Chapter 4 Computational methods relating protein sequence and structure
    Jaap Heringa, Dmitrij Frishman, Patrick Argos · 1997 · Protein
83. Surface-exposed phenylalanines in the RNP1/RNP2 motif stabilize the cold-shock protein CspB fromBacillus subtilis
    Thomas Hellmut Schindler, Dieter Perl, Peter L. Graumann, Volker Sieber, Mohamed A. Marahiel, Franz Xaver Schmid · 1998 · Proteins Structure Function and Bioinformatics
84. Protein Tertiary Structure Prediction
    Dong He Xu, Ying Xu · 2000 · Current Protocols in Protein Science
85. Superfamily Analysis: Understanding Protein Function from Structure and Sequence
    Patricia Clement Babbitt, Teri E. Klein · 1998 · Wiley eBooks
86. A comparison of computational methods for the maximum contact map overlap of protein pairs.
    Giuseppe Lancia, Natalio Krasnogor, Robert D. Carr, William E. Hart, Edmund Burke, Jonathan D. Hirst, Adam T Zemla · 2003 · OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)
87. The Architecture of Loops in Proteins
    Anna Luna Tramontano · 1996 · Elsevier eBooks
88. From fold to function predictions: an apoptosis regulator protein BID
    Krzysztof Pawłowski, Leszek Rychlewski, John C. Reed, Adam Godzik · 2000 · Computers & Chemistry
89. The comparison of structures and sequences: alignment, searching and the detection of common folds
    Johnson, John P. Overington, Edwards, May, Rodionov · 1994 · Hawaii International Conference on System Sciences (HICSS)
90. Assignment of the disulfide bonds in the sweet protein brazzein
    Masanori Kohmura, Masafumi Ota, Hiroyuki Izawa, Ding Göran Ming Hellekant, Yasuo Ariyoshi · 1996 · Biopolymers
91. Data Based Modeling of Proteins
    Liisa Holm, Burkhard Rost, Chris Sander, Reinhard Schneider, Gert Vriend · 1994 · NATO ASI series. Series B : Physics
92. Bayesian approach to sequence alignment algorithms for protein structure recognition
    Richard A. Goldstein, Zaida Ann Luthey-Schulten, Peter Guy Wolynes · 1995 · UCL Discovery (University College London)
93. Analogy-based protein structure prediction: I. A new database of spatially similar and dissimilar structures of protein domains for testing and optimizing prediction methods
    M. Yu. Lobanov, Natalya S. Bogatyreva, Dmitry N. Ivankov, Alin Finkelshtein · 2009 · Molecular Biology
94. Bioinformatics and Computational Biology in Poland
    Janusz Marek Bujnicki, Jerzy Tiuryn · 2013 · PLoS Computational Biology
95. Parallel Evolution Strategy for Protein Threading
    R. Islam, Alioune Ngom · 2006 · International Conference of the Chilean Computer Science Society (SCCC)
96. Cα-Methyl- l -valine: A Preferential Choice over α-Aminoisobutyric Acid for Designing Right-Handed α-Helical Scaffolds
    Raja Banerjee, Tridip Sheet, Srijan Banerjee, Barbara Biondi, Fernando Formaggio, Claudio Toniolo, Cristina Peggion · 2021 · Biochemistry
97. Determination of optimal effective interactions between amino acids in globular proteins
    Giovanni Settanni, Cristian Micheletti, Jayanth R. Banavar, Amos Maritan · 1999 · arXiv (Cornell University)
98. Extension of the pairwise-contact energy parameters for proteins with the local environments of amino acids
    Muyoung Heo, Mookyung Cheon, Eun-Joung Moon, Suhkmann Kim, Kwanghoon Chung, Hae Jin Kim, Iksoo Chang · 2005 · Physica A Statistical Mechanics and its Applications
99. Threading algorithms
    Jadwiga Renata Bienkowska, Rick Lathrop · 2005 · Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
100. Evaluation of threading specificity and accuracy
     Stephen H. Bryant · 1996 · Proteins Structure Function and Bioinformatics