Relevant bibliographies by topics / Computational protein design

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Computational protein design'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 July 2025

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Journal articles on the topic "Computational protein design"

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Kraemer-Pecore, Christina M., Andrew M. Wollacott, and John R. Desjarlais. "Computational protein design." Current Opinion in Chemical Biology 5, no. 6 (2001): 690–95. http://dx.doi.org/10.1016/s1367-5931(01)00267-8.

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Street, Arthur G., and Stephen L. Mayo. "Computational protein design." Structure 7, no. 5 (1999): R105—R109. http://dx.doi.org/10.1016/s0969-2126(99)80062-8.

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MacDonald, James T., and Paul S. Freemont. "Computational protein design with backbone plasticity." Biochemical Society Transactions 44, no. 5 (2016): 1523–29. http://dx.doi.org/10.1042/bst20160155.

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The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as ‘scaffolds’ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but prom
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Schreiber, Gideon, and Sarel J. Fleishman. "Computational design of protein–protein interactions." Current Opinion in Structural Biology 23, no. 6 (2013): 903–10. http://dx.doi.org/10.1016/j.sbi.2013.08.003.

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Kortemme, Tanja, and David Baker. "Computational design of protein–protein interactions." Current Opinion in Chemical Biology 8, no. 1 (2004): 91–97. http://dx.doi.org/10.1016/j.cbpa.2003.12.008.

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Kundert, Kale, and Tanja Kortemme. "Computational design of structured loops for new protein functions." Biological Chemistry 400, no. 3 (2019): 275–88. http://dx.doi.org/10.1515/hsz-2018-0348.

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Abstract The ability to engineer the precise geometries, fine-tuned energetics and subtle dynamics that are characteristic of functional proteins is a major unsolved challenge in the field of computational protein design. In natural proteins, functional sites exhibiting these properties often feature structured loops. However, unlike the elements of secondary structures that comprise idealized protein folds, structured loops have been difficult to design computationally. Addressing this shortcoming in a general way is a necessary first step towards the routine design of protein function. In th
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J. Bienstock, Rachelle. "Computational Drug Design Targeting Protein-Protein Interactions." Current Drug Metabolism 18, no. 9 (2012): 1240–54. http://dx.doi.org/10.2174/138920012799362891.

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J. Bienstock, Rachelle. "Computational Drug Design Targeting Protein-Protein Interactions." Current Pharmaceutical Design 18, no. 9 (2012): 1240–54. http://dx.doi.org/10.2174/138161212799436449.

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Frappier, Vincent, and Amy E. Keating. "Data-driven computational protein design." Current Opinion in Structural Biology 69 (August 2021): 63–69. http://dx.doi.org/10.1016/j.sbi.2021.03.009.

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Samish, Ilan, Christopher M. MacDermaid, Jose Manuel Perez-Aguilar, and Jeffery G. Saven. "Theoretical and Computational Protein Design." Annual Review of Physical Chemistry 62, no. 1 (2011): 129–49. http://dx.doi.org/10.1146/annurev-physchem-032210-103509.

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Dissertations / Theses on the topic "Computational protein design"

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Traore, Seydou. "Computational approaches toward protein design." Thesis, Toulouse, INSA, 2014. http://www.theses.fr/2014ISAT0033/document.

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Le Design computationnel de protéines, en anglais « Computational Protein Design » (CPD), est un champ derecherche récent qui vise à fournir des outils de prédiction pour compléter l'ingénierie des protéines. En effet,outre la compréhension théorique des propriétés physico-chimiques fondamentales et fonctionnelles desprotéines, l’ingénierie des protéines a d’importantes applications dans un large éventail de domaines, y comprisdans la biomédecine, la biotechnologie, la nanobiotechnologie et la conception de composés respectueux del’environnement. Le CPD cherche ainsi à accélérer le design de p
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Wood, Christopher Robin Wells. "Computational design of parameterisable protein folds." Thesis, University of Bristol, 2016. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.715832.

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Hong, Eun-Jong 1975. "Exact rotamer optimization for computational protein design." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/44421.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2008.<br>Includes bibliographical references (leaves 235-244).<br>The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP-hard optimization problem. Dead-end elimination (DEE) methods combined with systematic A* search (DEE/A*) have proven useful, but may not be strong enough as we attempt to solve protein design problem
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Biddle, Jason Charles. "Methods and applications in computational protein design." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/61792.

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Thesis (S.M.)--Massachusetts Institute of Technology, Computation for Design and Optimization Program, 2010.<br>This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.<br>Cataloged from student-submitted PDF version of thesis.<br>Includes bibliographical references (p. 107-111).<br>In this thesis, we summarize our work on applications and methods for computational protein design. First, we apply computational protein design to address the problem of degradation in stored proteins. Specifically, we target
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Fuller, Jonathan Christopher. "Computational approaches for drug design at the protein-protein interface." Thesis, University of Leeds, 2010. http://etheses.whiterose.ac.uk/1699/.

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The ability to design drugs that disrupt formation of protein-protein interfaces is of particular interest to the pharmaceutical industry due to its promise for opening an entire new range of drug targets, many of which have already been well characterised in terms of their disease causing effect on the human body. Furthermore these interactions can be involved in many processes unique and essential to bacteria and viruses. We show that pockets on protein-protein interface are smaller but more numerous than those of marketed drugs using a pocket fnding algorithm (Q-SiteFinder). We investigate
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Davey, James A. "Multistate Computational Protein Design: Theories, Methods, and Applications." Thesis, Université d'Ottawa / University of Ottawa, 2016. http://hdl.handle.net/10393/35541.

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Traditional computational protein design (CPD) calculations model sequence perturbations and evaluate their stabilities using a single fixed protein backbone template in an approach referred to as single‐state design (SSD). However, certain design objectives require the explicit consideration of multiple conformational states. Cases where a multistate framework may be advantageous over the single‐state approach include the computer aided discovery of new enzyme substrates, the prediction of protein stabilities, and the design of protein dynamics. These design objectives can be tackled using mu
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MARCHETTI, FILIPPO. "COMPUTATIONAL STUDIES OF PROTEIN-PROTEIN AND PROTEIN-ANTIBODY INTERACTIONS: IMPLICATION FOR MOLECULAR DESIGN." Doctoral thesis, Università degli Studi di Milano, 2021. http://hdl.handle.net/2434/825462.

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High performance computing has opened the possibility to investigate complex systems by simulating their dynamics and study of equilibrium and non-equilibrium settings in realistic settings. Molecular Dynamics (MD) simulations have emerged as one of the privileged methods to disentangle the intricacies of biochemical systems but, despite the validity of Moore’s Law, the timescale of the events that can be simulated has an upper limit of the millisecond with tailor-made computers which is not enough to study some biologically relevant phenomena. Starting from these considerations, in this thes
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Grigoryan, Gevorg Ph D. Massachusetts Institute of Technology. "Computational approaches for the design and prediction of protein-protein interactions." Thesis, Massachusetts Institute of Technology, 2007. http://hdl.handle.net/1721.1/38997.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2007.<br>Includes bibliographical references (leaves 167-187).<br>There is a large class of applications in computational structural biology for which atomic-level representation is crucial for understanding the underlying biological phenomena, yet explicit atomic-level modeling is computationally prohibitive. Computational protein design, homology modeling, protein interaction prediction, docking and structure recognition are among these applications. Models that are commonly applied to these problems combine atomic-lev
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Park, Daniel J. (Daniel John) 1979. "Computational tools for including specificity in protein design." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/87286.

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Sisu, Cristina Smaranda Domnica. "Computational studies on protein similarity, specificity and design." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609407.

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Books on the topic "Computational protein design"

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Samish, Ilan, ed. Computational Protein Design. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-6637-0.

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Torsten, Schwede, and Peitsch Manuel C, eds. Computational structural biology: Methods and applications. World Scientific, 2008.

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Moreira, Irina S., Miguel Machuqueiro, and Joana Mourão, eds. Computational Design of Membrane Proteins. Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1468-6.

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Stoddard, Barry L., ed. Computational Design of Ligand Binding Proteins. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3569-7.

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Mather A. R. Sadiq Al-Baghdadi. CFD models for analysis and design of PEM fuel cells CFD models for analysis & design of PEM fuel cells. Nova Science Publishers, 2008.

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Maher A. R. Sadiq Al-Baghdadi. CFD modeling and analysis of different novel designs of air-breathing PEM fuel cells. Nova Science Publishers, 2009.

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Maher A. R. Sadiq Al-Baghdadi. CFD modeling and analysis of different novel designs of air-breathing PEM fuel cells. Nova Science Publishers, 2010.

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Harren, Jhoti, and Leach Andrew R, eds. Structure-based drug discovery. Springer, 2007.

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Takao, Kumazawa, Kruger Lawrence, and Mizumura Kazue, eds. The polymodal receptor: A gateway to pathological pain. Elsevier, 1996.

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Samish, Ilan. Computational Protein Design. Springer New York, 2016.

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Book chapters on the topic "Computational protein design"

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Saven, Jeffery G. "Computational Protein Design." In Protein Engineering Handbook. Wiley-VCH Verlag GmbH & Co. KGaA, 2011. http://dx.doi.org/10.1002/9783527634026.ch12.

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Shifman, Julia, and Anamika Singh. "Computational Protein Design." In Encyclopedia of Biophysics. Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-642-35943-9_10084-1.

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Zhou, Yichao, Bruce R. Donald, and Jianyang Zeng. "Parallel Computational Protein Design." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6637-0_13.

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Kuhlman, Brian, Tim Jacobs, and Tom Linskey. "Computational Design of Protein Linkers." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3569-7_20.

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Kiss, Gert, Scott A. Johnson, Geoffrey Nosrati, et al. "Computational Design of New Protein Catalysts." In Modeling of Molecular Properties. Wiley-VCH Verlag GmbH & Co. KGaA, 2011. http://dx.doi.org/10.1002/9783527636402.ch16.

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Samish, Ilan. "The Framework of Computational Protein Design." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-6637-0_1.

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O’Mara, Megan L., and Evelyne Deplazes. "Polypeptide and Protein Modeling for Drug Design." In Encyclopedia of Computational Neuroscience. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4614-6675-8_732.

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O’Mara, Megan L., and Evelyne Deplazes. "Polypeptide and Protein Modeling for Drug Design." In Encyclopedia of Computational Neuroscience. Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4614-7320-6_732-1.

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Johnson, Lucas B., Thaddaus R. Huber, and Christopher D. Snow. "Methods for Library-Scale Computational Protein Design." In Methods in Molecular Biology. Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1486-9_7.

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Carbonell, Pablo, and Jean-Yves Trosset. "Computational Protein Design Methods for Synthetic Biology." In Methods in Molecular Biology. Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1878-2_1.

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Conference papers on the topic "Computational protein design"

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Mungu�a-L�pez, Aurora del C., Panzheng Zhou, Ugochukwu M. Ikegwu, Reid C. Van Lehn, and Victor M. Zavala. "A Fast Computational Framework for the Design of Solvent-Based Plastic Recycling Processes." In Foundations of Computer-Aided Process Design. PSE Press, 2024. http://dx.doi.org/10.69997/sct.175924.

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Multilayer plastic films are widely used in packaging applications because of their unique properties. These materials combine several layers of different polymers to protect food and pharmaceuticals from external factors such as oxygen, water, temperature, and light. Unfortunately, this design complexity also hinders the use of traditional recycling methods, such as mechanical recycling. Solvent-based separation processes are a promising alternative to recover high-quality pure polymers from multilayer film waste. One such process is the Solvent-Targeted Recovery and Precipitation (STRAPTM) p
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Adey, Robert A., Andres Peratta, and John M. W. Baynham. "Application of Computational Modeling to Predict the Effectiveness of CP on a PCCP Transmission Pipeline." In CORROSION 2011. NACE International, 2011. https://doi.org/10.5006/c2011-11002.

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Abstract Prestressed Concrete Cylinder Pipe (PCCP) is a rigid pipe designed to take optimum advantage of the tensile strength of steel and of the compressive strength and corrosion inhibiting properties of concrete and is frequently used for water transmission. PCCP consists of a steel cylinder embedded in a concrete core, which is helically wrapped with high-strength, hard-drawn wire after curing. The wire is embedded in thick cement slurry and coated with a dense cement mortar. While the cement mortar and additional coatings usually protect the prestressing wires from corrosion, in certain c
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Cignatta, J. V. "Computer Aided Engineering for Design of Ventilation Systems at Industrial Painting Projects." In CORROSION 1997. NACE International, 1997. https://doi.org/10.5006/c1997-97538.

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Abstract Computers have now become indispensable in evaluating alternative ventilation system designs employed to protect workers from lead dust at industrial painting projects. As the capabilities of personal computers increased in speed and dynamic memory, off-the-shelf computational fluid dynamic simulation programs could be run. Thus, a desktop computer now can be used to evaluate the complex airflow patterns and lead dust concentrations resulting in a containment when lead paint is dry abrasively blasted off steel bridges, tanks, and other industrial structures. This paper reviews the bas
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Larose, Guy, Maryam Al Labbad, Sharon Schajnoha, and Junting Chen. "A Comparative Study of the Use of Experimental and Computational Techniques to Assess Turbulence Above the FATO to Support the Design and Operations of Vertiports in the Built Environment." In Vertical Flight Society 81st Annual Forum and Technology Display. The Vertical Flight Society, 2025. https://doi.org/10.4050/f-0081-2025-186.

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Turbulence conditions at hospital heliports in the built environment are routinely assessed at the design stage through experimental, physical testing in boundary layer wind tunnels. Wind tunnel testing is the gold standard to evaluate wind conditions on and around buildings where human safety is of the upmost concern. Numerical techniques, such as computation fluid dynamics (CFD) are continuously improving and may offer a viable alternative to wind tunnel testing in some cases. Within the CFD toolbox, there are several techniques to simulate a flow field in an urban or suburban context. These
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Upadhyay, Vinod, Julio Mendez, Siva Palani, Alan Rose, and Keith Legg. "Corrosion Susceptibility Prediction and Lifetime Extension of Nuclear Dry Storage Canister Using Weather Data." In CONFERENCE 2023. AMPP, 2023. https://doi.org/10.5006/c2023-19441.

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Abstract The U.S. Energy Information Administration estimates that the annual use of nuclear energy for electricity generation in the US is almost 20 % as of 2021. However, the used nuclear fuel rods require a safe storage strategy because they are still radioactive. For the first few years they are stored underwater and then transferred to interim dry cask storage systems (DCSS), consisting of welded stainless-steel cylinders designed to safely store the fuel for a few decades. In the absence of any permanent safe storage strategy these DCSS are expected to be used much longer. With time the
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Arikawa, Keisuke. "A Computational Framework for Predicting the Motions of a Protein System From a Robot Kinematics Viewpoint." In ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/detc2013-12527.

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There is an analogy between the kinematic structures of proteins and robotic mechanisms. On the basis of this analogy, we have so far developed some methods for predicting the internal motions of proteins from their three-dimensional structural data in protein data bank (PDB). However, these methods are basically applicable to a single protein molecule. In this study, we extended these methods to apply them to systems that consist of multiple molecules including proteins (protein systems), and developed a computational framework for predicting the motions of the molecules. The model used in th
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Tortosa, Pablo. "Active Sites by Computational Protein Design." In FROM PHYSICS TO BIOLOGY: The Interface between Experiment and Computation - BIFI 2006 II International Congress. AIP, 2006. http://dx.doi.org/10.1063/1.2345625.

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LI, XIANG, and JIE LIANG. "COMPUTATIONAL DESIGN OF COMBINATORIAL PEPTIDE LIBRARY FOR MODULATING PROTEIN-PROTEIN INTERACTIONS." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2004. http://dx.doi.org/10.1142/9789812702456_0004.

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SMADBECK, JAMES, GEORGE A. KHOURY, MEGHAN B. PETERSON, and CHRISTODOULOS A. FLOUDAS. "ADVANCES IN DE NOVO PROTEIN DESIGN FOR MONOMERIC, MULTIMERIC, AND CONFORMATIONAL SWITCH PROTEINS." In International Symposium on Mathematical and Computational Biology. WORLD SCIENTIFIC, 2013. http://dx.doi.org/10.1142/9789814520829_0010.

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Shahbazi, Zahra, Horea T. Ilies¸, and Kazem Kazerounian. "On Hydrogen Bonds and Mobility of Protein Molecules." In ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2009. http://dx.doi.org/10.1115/detc2009-87470.

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Modeling protein molecules as kinematic chains provides the foundation for developing powerful approaches to the design, manipulation and fabrication of peptide based molecules and devices. Nevertheless, these models possess a high number of degrees of freedom (DOF) with considerable computational implications. On the other hand, real protein molecules appear to exhibits a much lower mobility during the folding process than what is suggested by existing kinematic models. The key contributor to the lower mobility of real proteins is the formation of Hydrogen bonds during the folding process. In
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Reports on the topic "Computational protein design"

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Sapiro, Guillermo. New Forcefields and Algorithms for Computational Protein Design. Defense Technical Information Center, 2003. http://dx.doi.org/10.21236/ada428012.

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Avdjieva, Irena, Ivan Terziyski, Gergana Zahmanova, Anelia Nisheva, and Dimitar Vassilev. Fusion Protein Design with Computational Homologybased Structure Prediction. "Prof. Marin Drinov" Publishing House of Bulgarian Academy of Sciences, 2021. http://dx.doi.org/10.7546/crabs.2021.07.07.

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Mahajan, Abhishaike, and Eryney Marrogi. AI-Designed Enzymes. Asimov Press, 2025. https://doi.org/10.62211/97ry-32pk.

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Yedidia, I., H. Senderowitz, and A. O. Charkowski. Small molecule cocktails designed to impair virulence targets in soft rot Erwinias. United States-Israel Binational Agricultural Research and Development Fund, 2020. http://dx.doi.org/10.32747/2020.8134165.bard.

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Chemical signaling between beneficial or pathogenic bacteria and plants is a central factor in determining the outcome of plant-microbe interactions. Pectobacterium and Dickeya (soft rot Erwinias) are the major cause of soft rot, stem rot, and blackleg formed on potato and ornamentals, currently with no effective control. Our major aim was to establish and study specific bacterial genes/proteins as targets for anti-virulence compounds, by combining drug design tools and bioinformatics with experimental work. The approach allowed us to identify and test compounds (small molecules) that specific
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Gershoni, Jonathan M., David E. Swayne, Tal Pupko, et al. Discovery and reconstitution of cross-reactive vaccine targets for H5 and H9 avian influenza. United States Department of Agriculture, 2015. http://dx.doi.org/10.32747/2015.7699854.bard.

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Research objectives: Identification of highly conserved B-cell epitopes common to either H5 or H9 subtypes of AI Reconstruction of conserved epitopes from (1) as recombinantimmunogens, and testing their suitability to be used as universal vaccine components by measuring their binding to Influenza vaccinated sera of birds Vaccination of chickens with reconstituted epitopes and evaluation of successful vaccination, clinical protection and viral replication Development of a platform to investigate the dynamics of immune response towards infection or an epitope based vaccine Estimate our ability t
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Fernando, P. U. Ashvin Iresh, Gilbert Kosgei, Matthew Glasscott, Garrett George, Erik Alberts, and Lee Moores. Boronic acid functionalized ferrocene derivatives towards fluoride sensing. Engineer Research and Development Center (U.S.), 2022. http://dx.doi.org/10.21079/11681/44762.

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In this technical report (TR), a robust, readily synthesized molecule with a ferrocene core appended with one or two boronic acid moieties was designed, synthesized, and used toward F- (free fluoride) detection. Through Lewis acid-base interactions, the boronic acid derivatives are capable of binding with F- in an aqueous solution via ligand exchange reaction and is specific to fluoride ion. Fluoride binding to ferrocene causes significant changes in fluorescence or electrochemical responses that can be monitored with field-portable instrumentation at concentrations below the WHO recommended l
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Or, Etti, David Galbraith, and Anne Fennell. Exploring mechanisms involved in grape bud dormancy: Large-scale analysis of expression reprogramming following controlled dormancy induction and dormancy release. United States Department of Agriculture, 2002. http://dx.doi.org/10.32747/2002.7587232.bard.

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The timing of dormancy induction and release is very important to the economic production of table grape. Advances in manipulation of dormancy induction and dormancy release are dependent on the establishment of a comprehensive understanding of biological mechanisms involved in bud dormancy. To gain insight into these mechanisms we initiated the research that had two main objectives: A. Analyzing the expression profiles of large subsets of genes, following controlled dormancy induction and dormancy release, and assessing the role of known metabolic pathways, known regulatory genes and novel se
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