Relevant bibliographies by topics / Ramachandran plot

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  2. Dissertations / Theses
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Academic literature on the topic 'Ramachandran plot'

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

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Journal articles on the topic "Ramachandran plot"

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Sheik, S. S., P. Sundararajan, A. S. Z. Hussain, and K. Sekar. "Ramachandran plot on the web." Bioinformatics 18, no. 11 (2002): 1548–49. http://dx.doi.org/10.1093/bioinformatics/18.11.1548.

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Carugo, Oliviero, and Kristina Djinović-Carugo. "A proteomic Ramachandran plot (PRplot)." Amino Acids 44, no. 2 (2012): 781–90. http://dx.doi.org/10.1007/s00726-012-1402-z.

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Iwaoka, M., M. Okada, and S. Tomoda. "Quantum Chemical Study of Ramachandran Plot." Seibutsu Butsuri 39, supplement (1999): S115. http://dx.doi.org/10.2142/biophys.39.s115_1.

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K. Gopalakrishnan, G. Sowmiya, S. S. Sheik, and K. Sekar. "Ramachandran Plot on The Web (2.0)." Protein & Peptide Letters 14, no. 7 (2007): 669–71. http://dx.doi.org/10.2174/092986607781483912.

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Gopalakrishnan, K., S. Saravanan, R. Sarani, and K. Sekar. "RPMS: Ramachandran plot for multiple structures." Journal of Applied Crystallography 41, no. 1 (2008): 219–21. http://dx.doi.org/10.1107/s0021889807053708.

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An interactive internet computing server,RPMS(Ramachandran plot for multiple structures) has been developed to visualize the Ramachandran angles of several highly homologous protein structures in a single plot. Options are provided for users to locate the amino acid residues in various regions of the plot. To perform the above, users need to enter the Protein Data Bank (PDB) identification codes. In addition, users can upload the atomic coordinates from the local machine. A Java graphics interface has been deployed and the server has been interfaced with a locally maintained PDB anonymous FTP
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Mannige, Ranjan V. "An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)." PeerJ 5 (May 16, 2017): e3327. http://dx.doi.org/10.7717/peerj.3327.

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The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing th
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Zhou, Alice Qinhua, Corey S. O'Hern, and Lynne Regan. "Revisiting the Ramachandran plot from a new angle." Protein Science 20, no. 7 (2011): 1166–71. http://dx.doi.org/10.1002/pro.644.

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Hollingsworth, Scott A., and P. Andrew Karplus. "A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins." BioMolecular Concepts 1, no. 3-4 (2010): 271–83. http://dx.doi.org/10.1515/bmc.2010.022.

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AbstractThe Ramachandran plot is among the most central concepts in structural biology, seen in publications and textbooks alike. However, with the increasing numbers of known protein structures and greater accuracy of ultra-high resolution protein structures, we are still learning more about the basic principles of protein structure. Here, we use high-fidelity conformational information to explore novel ways, such as geo-style and wrapped Ramachandran plots, to convey some of the basic aspects of the Ramachandran plot and of protein conformation. We point out the pressing need for a standard
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Balasco, Nicole, Luciana Esposito, Alfonso De Simone, and Luigi Vitagliano. "Local Backbone Geometry Plays a Critical Role in Determining Conformational Preferences of Amino Acid Residues in Proteins." Biomolecules 12, no. 9 (2022): 1184. http://dx.doi.org/10.3390/biom12091184.

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The definition of the structural basis of the conformational preferences of the genetically encoded amino acid residues is an important yet unresolved issue of structural biology. In order to gain insights into this intricate topic, we here determined and compared the amino acid propensity scales for different (φ, ψ) regions of the Ramachandran plot and for different secondary structure elements. These propensities were calculated using the Chou–Fasman approach on a database of non-redundant protein chains retrieved from the Protein Data Bank. Similarities between propensity scales were evalua
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Porter, Lauren L., and George D. Rose. "Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints." Proceedings of the National Academy of Sciences 108, no. 1 (2010): 109–13. http://dx.doi.org/10.1073/pnas.1014674107.

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A protein backbone has two degrees of conformational freedom per residue, described by its φ,ψ-angles. Accordingly, the energy landscape of a blocked peptide unit can be mapped in two dimensions, as shown by Ramachandran, Sasisekharan, and Ramakrishnan almost half a century ago. With atoms approximated as hard spheres, the eponymous Ramachandran plot demonstrated that steric clashes alone eliminate ¾ of φ,ψ-space, a result that has guided all subsequent work. Here, we show that adding hydrogen-bonding constraints to these steric criteria eliminates another substantial region of φ,ψ-space for a
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Dissertations / Theses on the topic "Ramachandran plot"

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Chakraborty, Promita. "A Computational Framework for Interacting with Physical Molecular Models of the Polypeptide Chain." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/47932.

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Although nonflexible, scaled molecular models like Pauling-Corey's and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees-of-freedom in the peptide backbone. The coarse-grained backbone model cons
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Chen, Yen-Ru, and 陳彥儒. "A Protein Structure Prediction Method Based on Ramachandran Plot." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/sa3566.

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碩士<br>國立東華大學<br>資訊工程學系<br>95<br>In general, the structure of a protein will be changed if its primary sequence is changed. However, not every change in sequence results in a change in structure. Properties of protein structure cannot be detected precisely by sequence alignment methods. Therefore, to establish evolutionary relationship between proteins that share no or nearly no common primary structures is helpful to the annotation and characterization of biological processes. In this thesis, we propose a protein secondary structure prediction method based on Ramachandran region. By training
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Kalvoda, Tadeáš. "Studium konformačního chování krátkých peptidových fragmentů metodami kvantové chemie." Master's thesis, 2020. http://www.nusl.cz/ntk/nusl-436427.

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To what extent conformational preference of short peptide sequences within proteins determine their three-dimensional structure? Large-scale quantum chemical calculations coupled with modern solvation methods represent unique set of tools to elucidate key determinants of the biomolecular structure ab initio. Full conformational sampling was performed on model systems representing short peptide fragments. The computed data reveal some of the underlying physico-chemical principles determining the spatial structure of proteins, and provide very important data for finding and tuning the optimal al
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Chen, Wei-Chen, and 陳維成. "Bonding, Substituent and Hydrogen Bonding Effects on Structure and Cyclization Reaction: Using Density Functional Theory to Study the Myers-Satio Reaction, the Adamantan-2-one Cycloaddition Reaction and the Potential Energy Surface of Ramachandran plot." Thesis, 1999. http://ndltd.ncl.edu.tw/handle/92172298082254317600.

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碩士<br>國立清華大學<br>化學系<br>87<br>This thesis includes three parts: the potential energy surface corresponding to the Ramachandran plot, the 1,3-dipolar cycloaddition reactions of acetonitrile oxide with 5-substituted adamantan-2-one and its derivatives, and the structure effects on the Myers-Satio reaction. In the study of Ramachandran plot, the backbone energy of glycine was estimated using a model molecule with the B3LYP/D95++** method. The beta and beta'-sheets distribute at the ranges of energy lower than 2 kcal/mol. The alpha-helix and collagen structures are at higher energy regio
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Book chapters on the topic "Ramachandran plot"

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Gooch, Jan W. "Ramachandran Plot." In Encyclopedic Dictionary of Polymers. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-4419-6247-8_14641.

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LASKOWSKI, ROMAN A., NICHOLAS FURNHAM, and JANET M. THORNTON. "THE RAMACHANDRAN PLOT AND PROTEIN STRUCTURE VALIDATION." In Biomolecular Forms and Functions. WORLD SCIENTIFIC / INDIAN INST OF SCIENCE, INDIA, 2013. http://dx.doi.org/10.1142/9789814449144_0005.

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Vyshnavi, Hima, Aswin Mohan, Shahanas Naisam, Suvanish Kumar, and Nidhin Sreekumar. "Homology Modeling and Evaluation of Sars-Cov-2 Spike Protein Mutant." In Research Anthology on Bioinformatics, Genomics, and Computational Biology. IGI Global, 2023. http://dx.doi.org/10.4018/979-8-3693-3026-5.ch039.

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Severe acute respiratory syndrome coronavirus 2 (SARS‐Cov-2), a global pandemic, affected the world, increasing every day. A mutated variant D614G, showing more virulence and transmission, was studied for forecasting the emergence of more virulent and pathogenic viral strains. This study focuses on structure modeling and validation. Characterization of proteins homologous to wild spike protein was done, and homology models of the mutated variant were modeled using these proteins. Validation of models was done using Ramachandran plot and ERRAT plot. Molecular dynamics simulation was used to val
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Adebiyi, Marion Olubunmi, and Ibidun Christiana Obagbuwa. "Homology Modeling and Binding Site Analysis of SARS-CoV-2 (COVID-19) Main Protease 3D Structure." In Research Anthology on Bioinformatics, Genomics, and Computational Biology. IGI Global, 2023. http://dx.doi.org/10.4018/979-8-3693-3026-5.ch038.

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The severe acute respiratory syndrome coronavirus 2 (SAR-Cov-2) caused the coronavirus (COVID-19) pandemic. The global concern is the discovery of a new target drug for the total cure. Recently, some research showed that a few COVID-19 enzymes may have been contemplated to be potential drug targets, but not much is known about its structural biology. This research investigates the 3-D structure of protease SAR-CoV-2. The tertiary structure was determined by homology modeling. The Swiss-Model workspace and the basic local alignment search tool (BLAST) were employed for modeling, and the resulte
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Adebiyi, Marion Olubunmi, and Ibidun Christiana Obagbuwa. "Homology Modeling and Binding Site Analysis of SARS-CoV-2 (COVID-19) Main Protease 3D Structure." In Advanced Bioinspiration Methods for Healthcare Standards, Policies, and Reform. IGI Global, 2022. http://dx.doi.org/10.4018/978-1-6684-5656-9.ch004.

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The severe acute respiratory syndrome coronavirus 2 (SAR-Cov-2) caused the coronavirus (COVID-19) pandemic. The global concern is the discovery of a new target drug for the total cure. Recently, some research showed that a few COVID-19 enzymes may have been contemplated to be potential drug targets, but not much is known about its structural biology. This research investigates the 3-D structure of protease SAR-CoV-2. The tertiary structure was determined by homology modeling. The Swiss-Model workspace and the basic local alignment search tool (BLAST) were employed for modeling, and the resulte
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Sujatha, Kabilan, and Ayyasamy Mahalakshmi. "Can Lactobacilli be Used as Probiotics? – An Insight." In Exploring Lactobacilli - Biology, Roles and Potential Applications in Food Industry and Human Health. IntechOpen, 2025. https://doi.org/10.5772/intechopen.115610.

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Lactic acid bacteria (LAB) are widely used in the food and health industries due to their Generally Recognized as Safe (GRAS) status and Qualified Presumption of Safety (QPS) designation. However, recent research has revealed that some Lactobacillus species harbor antimicrobial-resistance genes, which may contribute to the rise of antimicrobial resistance (AMR). Genome analysis of LAB, available through resources like the National Centre for Biotechnology Information (NCBI) database, which lists over 13,711 genomes within the Lactobacillaceae family, provides valuable insights into strain sele
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Sony, G., Md Mehdiya Muskaan, and Y. Sabitha. "In-Silico Identification of Structural Changes and Molecular Interactions of Mutations in Multiple Drug Resistant (MDR) Bacteria." In Convergence of Technology & Biology - Transforming Life Sciences. Shanlax Publications, 2025. https://doi.org/10.34293/ctbtls.2025.ch022.

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Introduction: Multiple Drug Resistance (MDR) in bacteria is a significant global health challenge, reducing the effectiveness of antibiotics and necessitating the discovery of alternative therapeutic strategies. Understanding the molecular basis of resistance at a structural and functional level is crucial for developing novel drug targets. Computational approaches provide efficient methods for analysing bacterial resistance proteins, identifying mutational impacts. Methodology: This study utilizes an in-silico approach to analyse structural and functional changes in multiple drug-resistant (M
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Bhargavi, M., Sri Gayathri Bhargavi, and Esha Sripada. "Computational Approach for HDAC1 Predicting Protein-Ligand Interactions for Cancer through Homology Modelling, Virtual Screening and Molecular Docking." In Convergence of Technology & Biology - Transforming Life Sciences. Shanlax Publications, 2025. https://doi.org/10.34293/ctbtls.2025.ch002.

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Histone Deacetylase 1 (HDAC1) is vital for controlling gene expression, chromatin remodelling, and biological functions like distinction and cellular proliferation by acetylation of histone tail residues. Its abnormal expression is of high significance in inflammatory diseases, cancers and allergic diseases. Thus, considering the structure and function of HDAC1 is very crucial because it may be used as a therapeutic target for cancer, neurologicalillnesses, and other disorders. In this study, the structure of HDAC1 was predicted using homology modelling. First, based on the known crystal struc
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Dash, Anirban, and Mirza Fareedulla Baig. "Revolutionizing Health – Care: In-Silico Vaccine Designing." In Convergence of Technology & Biology - Transforming Life Sciences. Shanlax Publications, 2025. https://doi.org/10.34293/ctbtls.2025.ch021.

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In - Silico Vaccine Designing represents a paradigm shift in vaccine research, using computational tools to accelerate and refine the development process. By integrating bioinformatics, immunoinformatics, and structural biology, this approach enables researchers to identify and predict antigenic regions with high precision, reducing the time and cost associated with traditional vaccine development. Tuberculosis (TB) is a global health threat, making it necessary to develop innovative vaccine strategies. This study focuses on the insilico design of a multi-epitope vaccine targeting the integral
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Nambigari, Navaneetha, Pushpanjali Pendyala, and Glory Prathiba. "DRUG DESIGN BY HOMOLOGY MODELING TO INHIBIT BREAST CANCER TARGETING PIGF PROTEIN." In Futuristic Trends in Chemical Material Sciences & Nano Technology Volume 3 Book 15. Iterative International Publishers, Selfypage Developers Pvt Ltd, 2024. http://dx.doi.org/10.58532/v3becs15p7ch1.

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The imbalance between apoptosis and cell proliferation or over-expression of a particular protein and deviation in biological pathways leads to cancer. Several types of cancers exist in which breast cancer is known since ancient times. 5-10% of breast cancers are due to inherited genetic disposition. Obesity, lack of exercise, alcoholism and exposure to ionizing radiations are a few risk factors for the development of breast cancer. In recent research, January 2022, in the United States, around 3.8 million women were identified with breast cancer history. PIGF (Placental growth factor), an ang
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Conference papers on the topic "Ramachandran plot"

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Purushe, Shweta, Sanjay Krishna Anbalagan, and Georges Grinstein. "Development of an Interactive Ramachandran Plot in Weave." In 2011 15th International Conference Information Visualisation (IV). IEEE, 2011. http://dx.doi.org/10.1109/iv.2011.109.

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Maack, Robin Georg Claus, Christina Gillmann, and Hans Hagen. "Uncertainty-Aware Ramachandran Plots." In 2019 IEEE Pacific Visualization Symposium (PacificVis). IEEE, 2019. http://dx.doi.org/10.1109/pacificvis.2019.00034.

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Alexander-Uribe, Jonny, Julián D. Arias-Londoño, and Alexandre Perera-Lluna. "Protein Disorder Prediction using Jumping Motifs from Torsion Angles Dynamics in Ramachandran Plots." In 9th International Conference on Bioinformatics Models, Methods and Algorithms. SCITEPRESS - Science and Technology Publications, 2018. http://dx.doi.org/10.5220/0006647900380048.

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Uribe, Jonny A., Julián D. Arias-Londoño, and Alexandre Perera-Lluna. "Protein Disorder Prediction using Information Theory Measures on the Distribution of the Dihedral Torsion Angles from Ramachandran Plots." In 8th International Conference on Bioinformatics Models, Methods and Algorithms. SCITEPRESS - Science and Technology Publications, 2017. http://dx.doi.org/10.5220/0006140500430051.

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