Progress in Modeling of Protein Structures and Interactions.

Cited by (295)

Items 101–200 of 295

1. A 13C{31P} REDOR NMR Investigation of the Role of Glutamic Acid Residues in Statherin- Hydroxyapatite Recognition
   Moise Ndao, Jason T. Ash, Nicholas F. Breen, Gil Goobes, Patrick S. Stayton, Gary P. Drobny · 2009 · Langmuir
2. Saturating representation of loop conformational fragments in structure databanks.
   Narcís Fernández‐Fuentes, András Fiser · 2006 · BMC Structural Biology
3. A network model to correlate conformational change and the impedance spectrum of single proteins
   Eleonora Alfinito, C. Pennetta, Lino Reggiani · 2008 · Nanotechnology
4. Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations
   Hongzhi Li, Donghong Min, Yusong Liu, Wei Yuan Yang · 2007 · The Journal of Chemical Physics
5. Similar chemistry, but different bond preferences in inter versus intra‐protein interactions
   Mati Cohen, Dana Reichmann, Hani Neuvirth, Gideon Schreiber · 2008 · Proteins Structure Function and Bioinformatics
6. Fundamental molecular biology
   Akif Uzman · 2007 · Biochemistry and Molecular Biology Education
7. Rosetta and the Design of Ligand Binding Sites
   Rocco Moretti, Brian J. Bender, Brittany Allison, Jens Meiler · 2016 · Methods in molecular biology
8. Designing coarse grained-and atom based-potentials for protein-protein docking
   Dror Tobi · 2010 · BMC Structural Biology
9. Microsecond Subdomain Folding in Dihydrofolate Reductase
   Munehito Arai, Masahiro Iwakura, C. Robert Matthews, Osman Bilsel · 2011 · Journal of Molecular Biology
10. Reduced Cβ statistical potentials can outperform all‐atom potentials in decoy identification
    James E. Fitzgerald, Abhishek Jha, Andrés Colubri, Tobin R. Sosnick, Karl F. Freed · 2007 · Protein Science
11. Rigorous performance evaluation in protein structure modelling and implications for computational biology
    John Moult · 2006 · Philosophical Transactions of the Royal Society B Biological Sciences
12. T-Cell Epitope-Based Vaccines: A Promising Strategy for Prevention of Infectious Diseases
    Xin Song, Yongfeng Li, Hongxia Wu, Hua‐Ji Qiu, Yuan Sun · 2024 · Vaccines
13. A pair‐to‐pair amino acids substitution matrix and its applications for protein structure prediction
    Eran Eyal, Milana Frenkel‐Morgenstern, V. M. Sobolev, Shmuel Pietrokovski · 2007 · Proteins Structure Function and Bioinformatics
14. Role of Topology, Nonadditivity, and Water-Mediated Interactions in Predicting the Structures of α/β Proteins
    Chenghang Chuck Zong, Garegin A. Papoian, Johan Ulander, Peter Guy Wolynes · 2006 · Journal of the American Chemical Society
15. Structural Dynamics of the Magnesium-Bound Conformation of CorA in a Lipid Bilayer
    Olivier Dalmas, Luis G. Cuello, Vishwanath Jogini, D. Marien Cortés, Benoı̂t Roux, Eduardo Perozo · 2010 · Structure
16. Self-Association of Arrestin Family Members
    Qiuyan Chen, Ya Zhuo, Mi‐Yeon Kim, Susan M. Hanson, Derek J. Francis, Sergey A. Vishnivetskiy, Christian Altenbach, Candice S. Klug, Wayne L. Hubbell, Vsevolod V. Gurevich · 2013 · Handbook of experimental pharmacology
17. Chaperones Rescue Luciferase Folding by Separating Its Domains
    Zackary N. Scholl, Weitao Yang, Piotr E. Marszałek · 2014 · Journal of Biological Chemistry
18. Computational design of protein-small molecule interfaces
    Brittany Allison, Steven A. Combs, Samuel DeLuca, Gordon Lemmon, Laura S. Mizoue, Jens Meiler · 2013 · Journal of Structural Biology
19. The Basic Concepts of Molecular Modeling
    Akansha Saxena, Diana Y. Wong, Karthikeyan Diraviyam, David Sept · 2009 · Methods in enzymology on CD-ROM/Methods in enzymology
20. FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator
    Rajkumar Bondugula, M. S. Lee, Anders Wallqvist · 2008 · Nucleic Acids Research
21. Funnel Hunting in a Rough Terrain: Learning and Discriminating Native Energy Funnels
    Nir London, Ora Schueler‐Furman · 2008 · Structure
22. The Dominance of Symmetry in the Evolution of Homo-oligomeric Proteins
    Georg E. Schulz · 2009 · Journal of Molecular Biology
23. Scoring predictive models using a reduced representation of proteins: model and energy definition
    Federico Fogolari, Lidia Pieri, Agostino Dovier A, Luca Bortolussi, GILBERTO GIUGLIARELLI, Alessandra Corazza, Gennaro Esposito, Paolo Viglino · 2007 · BMC Structural Biology
24. Structure-guided Antigen Engineering Yields Pneumolysin Mutants Suitable for Vaccination against Pneumococcal Disease
    Eliud O. Oloo, Jeremy A. Yethon, Martina M. Ochs, Bruce W. Carpick, Raymond P. Oomen · 2011 · Journal of Biological Chemistry
25. Redesigning the Blue Copper Azurin into a Redox-Active Mononuclear Nonheme Iron Protein: Preparation and Study of Fe(II)-M121E Azurin
    Jing Liu, Katlyn K. Meier, Shiliang Tian, Jun‐Long Zhang, Hongchao Guo, Charles E. Schulz, Howard H. Robinson, Mark J. Nilges, Eckard Münck, Yi Lu · 2014 · Journal of the American Chemical Society
26. Bioinformatics Resources for Cancer Research with an Emphasis on Gene Function and Structure Prediction Tools
    Daisuke Kihara, Yifeng David Yang, Troy Hawkins · 2006 · Cancer Informatics
27. Introduction to protein folding for physicists
    Pablo Echenique · 2007 · Contemporary Physics
28. Conformational stability as a design target to control protein aggregation
    Joseph A. Costanzo, Christopher J. O'Brien, Kathryn E. Tiller, Erin Tamargo, Anne Skaja Robinson, Christopher J. Roberts, Erik Fernández · 2014 · Protein Engineering Design and Selection
29. Calculation of the Free Energy and Cooperativity of Protein Folding
    Alex Kentsis, Tatyana S. Gindin, Mihaly Mezei, Roman Osman · 2007 · PLoS ONE
30. Towards the computational design of protein post-translational regulation
    Marta Strumillo, Pedro Beltrão · 2015 · Bioorganic & Medicinal Chemistry
31. The size of the intermolecular energy funnel in protein–protein interactions
    Jagtar Singh Hunjan, Andrey Tovchigrechko, Ying Duo Gao, Ilya A. Vakser · 2008 · Proteins Structure Function and Bioinformatics
32. Specificity and affinity quantification of protein–protein interactions
    Zhiqiang Yan, Liyong Guo, Liang Hu, Jin Wang · 2013 · Bioinformatics
33. Structure–Activity Relationships for Carcinogenic Potential
    Raghuraman Venkatapathy, Nina Ching Y. Wang, Todd M. Martin, Paul F. Harten, Douglas Young · 2009 · General, Applied and Systems Toxicology
34. Lethal mutants and truncated selection together solve a paradox of the origin of life
    Saakian, David B., Biebricher, Christof K., Hu, Chin-Kun · 2011 · PLoS ONE
35. Simulated tempering yields insight into the low‐resolution Rosetta scoring functions
    Gregory R. Bowman, Vijay S. Pande · 2008 · Proteins Structure Function and Bioinformatics
36. Membrane protein native state discrimination by implicit membrane models
    Olga Yuzlenko, Themis Lazaridis · 2012 · Journal of Computational Chemistry
37. Targeting Metastable Coiled-Coil Domains by Computational Design
    Patrick Barth, Allyn J. Schoeffler, Tom Alber · 2008 · Journal of the American Chemical Society
38. An efficient conformational sampling method for homology modeling
    Rong-Sheng Han, Alejandra Leo‐Macías, Daniel R. Zerbino, Ugo Bastolla, Bruno Contreras‐Moreira, Ángel R. Ortíz · 2007 · Proteins Structure Function and Bioinformatics
39. Accurate prediction for atomic‐level protein design and its application in diversifying the near‐optimal sequence space
    Menachem Fromer, Chen Yanover · 2008 · Proteins Structure Function and Bioinformatics
40. Optimal Mutation Sites for PRE Data Collection and Membrane Protein Structure Prediction
    Huiling Chen, Fei Ji, Victor N. Olman, Charles K. Mobley, Yizhou Liu, Yunpeng Zhou, John Hackett Bushweller, James H. Prestegard, Ying Xu · 2011 · Structure
41. Tryptophan Rotamers as Evidenced by X-Ray, Fluorescence Lifetimes, and Molecular Dynamics Modeling
    Samuel L. C. Moors, Mario Hellings, Marc De Maeyer, Yves Engelborghs, Arnout Jozef Ceulemans · 2006 · Biophysical Journal
42. Octarellin VI: Using Rosetta to Design a Putative Artificial (β/α)8 Protein
    Maximiliano Figueroa, N. V. Oliveira, Annabelle Lejeune, Kristian W. Kaufmann, Brent M. Dorr, André Matagne, JOSEPH A. MARTIAL, Jens Meiler, Cécile Van de Weerdt · 2013 · PLoS ONE
43. Genetic Algorithm inAb Initio Protein Structure Prediction Using Low Resolution Model: A Review
    Md Tamjidul Hoque, Madhu Chetty, Abdul Sattar · 2009 · Studies in computational intelligence
44. Conformer generation under restraints
    Paul I. W. de Bakker, Nicholas Furnham, Tom L. Blundell, Mark A. DePristo · 2006 · Current Opinion in Structural Biology
45. In-depth computational analysis of calcium-dependent protein kinase 3 of Toxoplasma gondii provides promising targets for vaccination
    Hamidreza Majidiani, Shahrzad Soltani, Ali Dalir Ghaffari, Mohamad Sabaghan, Ali Taghipour, Masoud Foroutan · 2020 · Clinical and Experimental Vaccine Research
46. Exploring the Intermediate States of ADP−ATP Exchange: A Simulation Study on Eg5
    Wei Zhang · 2010 · The Journal of Physical Chemistry B
47. Computational design of membrane proteins using RosettaMembrane
    Amanda M. Duran, Jens Meiler · 2017 · Protein Science
48. Pareto optimization in computational protein design with multiple objectives
    Maria Suarez Diez, Pablo Tortosa, Javier Carrera, Alfonso Jaramillo · 2008 · Journal of Computational Chemistry
49. Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools.
    Daisuke Kihara, Yifeng David Yang, Troy Hawkins · 2007 · PubMed Central
50. A computational framework to empower probabilistic protein design
    Menachem Fromer, Chen Yanover · 2008 · Bioinformatics
51. Large‐scale characteristics of the energy landscape in protein–protein interactions
    Nicholas O’Toole, Ilya A. Vakser · 2007 · Proteins Structure Function and Bioinformatics
52. Protein loop closure using orientational restraints from NMR data
    Chittaranjan Tripathy, Jianyang Zeng, Pei Zhou, Bruce Randall Donald · 2011 · Proteins Structure Function and Bioinformatics
53. Less is often more: Applied inverse problems using hp-forward models
    Danny Smyl, Dong Liu · 2019 · Journal of Computational Physics
54. Molecular characterization of a disease associated conformational epitope on GAD65 recognised by a human monoclonal antibody b96.11
    Gustavo Fenalti, Christiane S. Hampe, Karen O’Connor, Jasvinder Paul Banga, Ian R. Mackay, Merrill J. Rowley, Ossama A. L. El-Kabbani · 2006 · Molecular Immunology
55. The effect of using a polarizable solvent model upon the folding equilibrium of different β-peptides
    Zhixiong Lin, Nathan Schmid, Wilfred F. Van Gunsteren A · 2011 · Molecular Physics
56. Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?
    Jean-François Taly, Antoine Marin, Jean-François Gibrat · 2008 · BMC Bioinformatics
57. The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation
    Nupur Bansal, Zheng Zheng, Lin Frank Song, Jun Pei, Kenneth M. Merz · 2018 · Journal of the American Chemical Society
58. Recognizing protein–protein interfaces with empirical potentials and reduced amino acid alphabets
    Guillaume Launay, Raúl Méndez, Shoshana J. Wodak, Thomas Simonson · 2007 · BMC Bioinformatics
59. Mapping of Protein–Protein Interaction Sites by the ‘Absence of Interference’ Approach
    Arunkumar Dhayalan, Tomasz Piotr Jurkowski, Heike Laser, Richard Reinhardt, Da Jia, Xiaodong Cheng, Albert Jeltsch · 2007 · Journal of Molecular Biology
60. DFS-generated pathways in GA crossover for protein structure prediction
    Md Tamjidul Hoque, Madhu Chetty, Andrew Lewis, Abdul Sattar, Vicky M. Avery · 2010 · Neurocomputing
61. Efficient model chemistries for peptides. I. General framework and a study of the heterolevel approximation in RHF and MP2 with Pople split‐valence basis sets
    Pablo Echenique, José Luis Alonso · 2008 · Journal of Computational Chemistry
62. Folding by Numbers: Primary Sequence Statistics and Their Use in Studying Protein Folding
    Brent Wathen, Zongchao Jia · 2009 · International Journal of Molecular Sciences
63. Recent progress and future challenges in structure-based protein-protein interaction prediction
    Rongqing Yuan, Jing Zhang, Jian Zhou, Qian Cong · 2025 · Molecular Therapy
64. Dividing the Periodic Box into Subdivisions with Their Surroundings to Accelerate Molecular Dynamics Simulation with High Accuracy
    Cui Liu, Jian Fei Zhao, Zhong‐Zhi Yang, Dong‐Xia Zhao · 2020 · Journal of Chemical Theory and Computation
65. Sequence specificity between interacting and non-interacting homologs identifies interface residues – a homodimer and monomer use case
    Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, K. Anton Feenstra · 2015 · BMC Bioinformatics
66. Assessing the energy landscape of CAPRI targets by FunHunt
    Nir London, Ora Schueler‐Furman · 2007 · Proteins Structure Function and Bioinformatics
67. FunHunt: model selection based on energy landscape characteristics
    Nir London, Ora Schueler‐Furman · 2008 · Biochemical Society Transactions
68. Current performance gains from utilizing the GPU or the ASIC MDGRAPE‐3 within an enhanced Poisson Boltzmann approach
    Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Siegfried Höfinger · 2009 · Journal of Computational Chemistry
69. Docking protein domains in contact space
    Stefano Lise, Alice Walker-Taylor, David T. Jones · 2006 · BMC Bioinformatics
70. Ground state and glass transition of the RNA secondary structure
    Sheng Tony Hui, Lei‐Han Tang · 2006 · The European Physical Journal B
71. SHARPEN—Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network
    Ilya V. Loksha, James R. Maiolo, Cheng W. Hong, Albert Ng, Christopher Davis Snow · 2009 · Journal of Computational Chemistry
72. Rational protein design: developing next‐generation biological therapeutics and nanobiotechnological tools
    Corey J. Wilson · 2014 · Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology
73. Protofold II: Enhanced Model and Implementation for Kinetostatic Protein Folding1
    Pouya Tavousi, Morad Behandish, Horea Ilieş, Kazem Kazerounian · 2015 · Journal of Nanotechnology in Engineering and Medicine
74. Exploring conformational changes coupled to ionization states using a hybrid Rosetta‐MCCE protocol
    Yifan Song · 2011 · Proteins Structure Function and Bioinformatics
75. Scoring function accuracy for membrane protein structure prediction
    Cen Gao, Harry A. Stern · 2007 · Proteins Structure Function and Bioinformatics
76. Recent applications of bio-engineering principles to modulate the functionality of proteins in food systems
    Ankita Kataria, Rajan Sharma, Savita Sharma, Baljit Singh, Gurkirat Kaur, Caleb Maina Yakubu · 2021 · Trends in Food Science & Technology
77. Protein–protein alternative binding modes do not overlap
    Petras J. Kundrotas, Ilya A. Vakser · 2013 · Protein Science
78. Protein Loop Structure Prediction Using Conformational Space Annealing
    Seungryong Heo, Juyong Lee, Keehyoung Joo, Hang‐Cheol Shin, Jooyoung Lee · 2017 · Journal of Chemical Information and Modeling
79. Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase
    Zackary N. Scholl, Weitao Yang, Piotr E. Marszałek · 2017 · Biophysical Journal
80. Integration of Cryo-EM with Atomic and Protein–Protein Interaction Data
    Friedrich G. Förster, Elizabeth Villa · 2010 · Methods in enzymology on CD-ROM/Methods in enzymology
81. A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation
    Letizia Chiodo, Thérèse E. Malliavin, Luca Maragliano, Grazia Cottone, Giovanni Ciccotti · 2015 · PLoS ONE
82. Agent-based protein structure prediction
    Luca Bortolussi, Agostino Dovier A, Federico Fogolari · 2007 · Multiagent and Grid Systems
83. Metals Coordinate Protein–Protein Interactions
    Kağan Kerman, Heinz‐Bernhard Kraatz · 2008 · Angewandte Chemie International Edition
84. Probing Distal Regions of the A2B Adenosine Receptor by Quantitative Structure−Activity Relationship Modeling of Known and Novel Agonists
    Andrei A. Ivanov, Ben Wang, Athena M. Klutz, Vincent Lingzhi Chen, Zhan‐Guo Gao, Kenneth A. Jacobson · 2008 · Journal of Medicinal Chemistry
85. A relaxation model of ideal folding in a homogenous viscous medium
    К. В. Шайтан · 2015 · BIOPHYSICS
86. GFP-Based Biosensors
    E. Donna, Yao-Ming Huang, J. Derek, Christian D. Schenkelberg, Keith Fraser, Stephen J. Macari, Christopher Bystroff · 2013 · InTech eBooks
87. A Historical Perspective and Overview of Protein Structure Prediction
    John Wooley, Yuzhen Ye · 2007 · Springer eBooks
88. Computational Study of a Heterostructural Model of Type I Collagen and Implementation of an Amino Acid Potential Method Applicable to Large Proteins
    Jay Quinson Eifler, Paul Rulis, Rex Tai, W. Y. Ching · 2014 · Polymers
89. Molecular Modeling in Enzyme Design, Toward In Silico Guided Directed Evolution
    Emanuele Monza, Sandra Acebes, Maria Fátima Lucas, Vı́ctor Guallar · 2017 · Springer eBooks
90. Quantum Mechanical Investigation of Three-Dimensional Activity Cliffs Using the Molecules-in-Molecules Fragmentation-Based Method
    Bishnu Thapa, Jon A. Erickson, Krishnan Raghavachari · 2020 · Journal of Chemical Information and Modeling
91. Targeting Ras-binding domain of ELMO1 by computational nanobody design
    Chunlai Tam, Mutsuko Kukimoto‐Niino, Yukako Miyata-Yabuki, Kengo Tsuda, Chiemi Mishima-Tsumagari, Kentaro Ihara, Mio Inoue, Mayumi Yonemochi, Kazuharu Hanada, Takehisa Matsumoto et al. · 2023 · Communications Biology
92. Identification of DNA-binding protein target sequences by physical effective energy functions, free energy analysis of lambda repressor-DNA complexes
    Elisabetta Moroni, Michele Caselle, Federico Fogolari · 2007 · BMC Structural Biology
93. Protein Thermostabilization Requires a Fine-tuned Placement of Surface-charged Residues
    D.J. You, Satoshi Fukuchi, Kazutaka Nishikawa, Yuichi Koga, Kazufumi Takano, Shigenori Kanaya · 2007 · The Journal of Biochemistry
94. How the excluded volume architecture influences ion-mediated forces between proteins
    Vincent Dahirel, Marie Jardat, J.-F. Dufrêche, Pierre Turq · 2007 · Physical Review E
95. Atomistic Peptide Folding Simulations Reveal Interplay of Entropy and Long-Range Interactions in Folding Cooperativity
    Jianlin Chen, Xiaorong Liu, Jianhan Chen · 2018 · Scientific Reports
96. High-Resolution Protein Structure Determination by NMR
    Hiroyuki Takashima · 2006 · Annual reports on NMR spectroscopy
97. A stochastic method for the reconstruction of protein structures from one-dimensional structural profiles
    Katrin Wolff, Michele Vendruscolo, Markus Porto · 2008 · Gene
98. A comprehensive application of FiveFold for conformation ensemble-based protein structure prediction
    Sarfaraz K. Niazi, Jiaan Yang · 2025 · Scientific Reports
99. Automated protein design: Landmarks and operational principles
    Anil Kumar, Ranjit Sudhakar Ranbhor, Kirti P. Patel, Vibin Ramakrishnan, Susheel Durani · 2016 · Progress in Biophysics and Molecular Biology
100. Efficient identification of near‐native conformations in ab initio protein structure prediction using structural profiles
     Katrin Wolff, Michele Vendruscolo, Markus Porto · 2009 · Proteins Structure Function and Bioinformatics