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*  Protein primary structure
... tertiary structure). Protein sequence can be used to predict local features, such as segments of secondary structure, or trans- ... Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure ... However, the complexity of protein folding currently prohibits predicting the tertiary structure of a protein from its sequence ... Knowing the structure of a similar homologous sequence (for example a member of the same protein family) allows highly accurate ...
*  Structural alignment software
Sippl, M.; Wiederstein, M. (2012). "Detection of spatial correlations in protein structures and molecular complexes". Structure ... Secondary Structure Elements Alignment; Seq -- Sequence-based alignment Pair -- Pairwise Alignment (2 structures *only*); Multi ... Brown, P.; Pullan W.; Yang Y.; Zhou Y. (Oct 2015). "Fast and accurate non-sequential protein structure alignment using a new ... Minami, S.; Sawada K.; Chikenji G. (Jan 2013). "MICAN : a protein structure alignment algorithm that can handle Multiple-chains ...
*  Protein secondary structure
The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with ... Protein secondary structure is the three dimensional form of local segments of proteins. The two most common secondary ... Distant relationships between proteins whose primary structures are unalignable can sometimes be found by secondary structure. ... Kihara D (Aug 2005). "The effect of long-range interactions on the secondary structure formation of proteins". Protein Science ...
*  List of protein secondary structure prediction programs
... List of protein structure prediction software Protein structure ...
*  Homology-derived Secondary Structure of Proteins
Protein Data Bank (PDB) STING Schneider, R., de Daruvar, A., & Sander, C. (1997). "The HSSP database of protein structure- ... HSSP is also a database of homology-based implied protein structures. ... This database has the information of the alignment of all available homologs of proteins from the PDB database As a result of ... HSSP is a database that combines structural and sequence information about proteins. ...
*  Protein tertiary structure
The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the ... A number of tertiary structures may fold into a quaternary structure. The science of the tertiary structure of proteins has ... The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or ... Protein tertiary structure is the three dimensional shape of a protein. ...
*  Protein structure prediction
The protein structure can be considered as a sequence of secondary structure elements, such as α helices and β sheets, which ... Protein design Protein function prediction Protein structure prediction software De novo protein structure prediction Molecular ... Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence-that ... Secondary structure prediction is a set of techniques in bioinformatics that aim to predict the local secondary structures of ...
*  List of protein structure prediction software
Detailed list of programs can be found at List of protein secondary structure prediction programs List of protein secondary ... This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction, ... The Rosetta software suite for computational modeling and analysis of protein structures. From local structure to a global ... including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and ...
*  Jpred
psipred Protein structure prediction software "JPred4: A Protein Secondary Structure Prediction Server". Retrieved 16 July 2015 ... "Application of multiple sequence alignment profiles to improve protein secondary structure prediction". Proteins. 40: 502-11. ... In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The ... Jpred v.4 is the latest version of the popular JPred Protein Secondary Structure Prediction Server which provides predictions ...
*  Beta sheet
Anatomy & Taxonomy of Protein Structures -survey NetSurfP - Secondary Structure and Surface Accessibility predictor. ... Tertiary Protein Structure and Folds: section 4.3.2.1. From Principles of Protein Structure, Comparative Protein Modelling, and ... Hutchinson EG, Thornton JM (1990). "HERA--a program to draw schematic diagrams of protein secondary structures". Proteins. 8 (3 ... Cooper J (31 May 1996). "Super Secondary Structure - Part II". Principles of Protein Structure Using the Internet. Retrieved 25 ...
*  Pyridoxine 5'-phosphate oxidase
This structure is due, in part, to the disulfide bonds present in the secondary protein structure of this enzyme. Multiple ... Both alpha-helices and beta-sheets are present in the protein motif, which is best described as a split-barrel structure. ... Vitamin B6 is a coenzyme in the metabolism of carbohydrates, fats and proteins. This means that the enzymes which break these ... Musayev FN, Di Salvo ML, Ko TP, Schirch V, Safo MK (2003). "Structure and properties of recombinant human pyridoxine 5'- ...
*  LiveBench
... is a continuously running benchmark project for assessing the quality of protein structure prediction and secondary ... LiveBench focuses mainly on homology modeling and protein threading but also includes secondary structure prediction, comparing ... continuous assessment of automated protein structure prediction. Protein Sci 14(1):240-5. PMID 15608124 LiveBench main site. ... continuous benchmarking of protein structure prediction servers. Protein Sci 10(2):352-61. PMID 11266621 Rychlewski L, Fischer ...
*  Ram Samudrala
Hung L-H, Samudrala R. PROTINFO: Secondary and tertiary protein structure prediction. Nucleic Acids Research 31: 3296-3299, ... Ab initio prediction of protein structure using a combined hierarchical approach. Proteins: Structure, Function, and Genetics ... A database of incorrect protein conformations to improve protein structure prediction. Protein Science 9: 1399-1401, 2000. Liu ... Handling context-sensitivity in protein structures using graph theory: bona fide prediction. Proteins: Structure, Function, and ...
*  EVA (benchmark)
Methods for predicting both secondary structure and tertiary structure - including homology modeling, protein threading, and ... 2001). EVA: large-scale analysis of secondary structure prediction. Proteins Suppl 5:192-9. PMID 11835497 Eyrich VA, Marti- ... running benchmark project for assessing the quality and value of protein structure prediction and secondary structure ... were compared to results from each week's newly solved protein structures deposited in the Protein Data Bank. The project aims ...
*  STRIDE
In protein structure, STRIDE (Structural identification) is an algorithm for the assignment of protein secondary structure ... Frishman D, Argos P. (1995). Knowledge-based protein secondary structure assignment. Proteins 23(4):566-79. doi:10.1002/prot. ... 2005). Protein secondary structure assignment revisited: a detailed analysis of different assignment methods. BMC Struct Biol 5 ... from empirical examinations of solved structures with visually assigned secondary structure elements extracted from the Protein ...
*  Probabilistic Approach for Protein NMR Assignment Validation
Protein secondary structure Protein Chemical Shift Prediction Chemical shift index Wang, B; Wang, Y.; Wishart, D.S. (2010). "A ... That is, with PANAV there is no need to know the structure of the protein in advance of correcting any chemical shift ... This makes PANAV particularly useful for NMR studies involving novel or newly assigned proteins, where the structure has yet to ... It also makes it very hard to structurally interpret chemical shifts (i.e. identify secondary structures or perform chemical ...
*  Chou-Fasman method
Kyngas J, Valjakka J (1998). "Unreliability of the Chou-Fasman parameters in predicting protein secondary structure". Protein ... Chou PY, Fasman GD (1978). "Prediction of the secondary structure of proteins from their amino acid sequence". Adv Enzymol ... Kabsch W, Sander C (1983). "How good are predictions of protein secondary structure?". FEBS Lett. 155 (2): 179-82. doi:10.1016/ ... The Chou-Fasman method is an empirical technique for the prediction of secondary structures in proteins, originally developed ...
*  FAM83A
Sen TZ, Jernigan RL, Garnier J, Kloczkowski A (June 2005). "GOR V server for protein secondary structure prediction". ... This may still provide valuable information, though, on a possible partial structure for this protein. FAM83A is expressed in ... Protein FAM83A (family member with sequence similarity 83) also known as tumor antigen BJ-TSA-9 is a protein that in humans is ... This protein is predicted to contain one domain of unknown function 1669 (DUF1669), which places this protein into the PLDc_ ...
*  Circular dichroism
... use of this normalized CD is important in studies of protein structure. Methods for estimating secondary structure in polymers ... It may be of interest to note that the protein CD spectra used in secondary structure estimation are related to the π to π* ... That is, for instance, a protein molecule with a helical secondary structure can have a CD that changes with changes in the ... Most notably, UV CD is used to investigate the secondary structure of proteins. UV/Vis CD is used to investigate charge- ...
*  Machine learning in bioinformatics
... and the quartenary structure. Protein secondary structure prediction is a main focus of this subfield as the further protein ... are determined based on the secondary structure. Solving the true structure of a protein is an incredibly expensive and time- ... "Sixty-five years of the long march in protein secondary structure prediction: the final stretch?". Briefings in Bioinformatics ... Wang, Sheng; Peng, Jian; Ma, Jianzhu; Xu, Jinbo (December 1, 2015). "Protein secondary structure prediction using deep ...
*  Turing Institute
"Protein Secondary Structure Prediction using logic-based machine learning". Protein Engineering. 5 (7): 647-657. doi:10.1093/ ... Applications included the discovery of rules for protein folding (with Ross King) and drug design as well as systems such as ... Tatjana Zrimec used the system to investigate how playing robots could develop structured knowledge about their world while ... Structured Induction in Expert Systems. Turing Institute Press. ASIN 0201178133. Muggleton, Stephen (1990). Inductive ...
*  Antiparallel (biochemistry)
Many proteins may adopt a beta sheet as part of their secondary structure. In beta sheets, sections of a single polypeptide may ... "Secondary structure of Proteins". www.chembio.uoguelph.ca. Retrieved 2017-04-01. ... G-quadruplexes, also known as G4 DNA are secondary structures found in nucleic acids that are rich in guanine. These structures ... Beta sheets can also be either a parallel or anti-parallel secondary structure. However, an anti-parallel beta sheet is ...
*  Bidirectional recurrent neural networks
"Exploiting the past and the future in protein secondary structure prediction." Bioinformatics 15.11 (1999): 937-946. Pollastri ... "Porter: a new, accurate server for protein secondary structure prediction." Bioinformatics 21.8 (2005): 1719-1720. [1] ... Translation Handwritten Recognition Protein Structure Prediction Artificial neural network Recurrent neural networks Long short ... The general structure of RNN and BRNN can be depicted in the right diagram. By using two time directions, input information ...
*  Ross D. King
A machine learning approach to the problem of predicting a protein's secondary structure from its primary structure (PROMIS) ( ... "Machine learning approach for the prediction of protein secondary structure". Journal of Molecular Biology. 216 (2): 441-457. ... "Identification and application of the concepts important for accurate and reliable protein secondary structure prediction". ... "Music to my DNA structure". Times Higher Education 2001-05-25. "The Shamen - S2 Translation (S2 Protein)" on YouTube Buckley, ...
*  Chris Sander (scientist)
Rost, B.; Sander, C. (1993). "Prediction of Protein Secondary Structure at Better than 70% Accuracy". Journal of Molecular ... Kabsch, W.; Sander, C. (1983). "Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and ... database and the DSSP algorithm for assigning secondary structure to the amino acids of a protein, given the atomic-resolution ... "A database of protein structure families with common folding motifs". Protein Science. 1 (12): 1691-1698. doi:10.1002/pro. ...
*  Hairpin (disambiguation)
... a secondary structure motif of proteins Hairpins (film), a 1920 film directed by Fred Niblo Hairpin, in music, the nickname for ...
*  DSSP (hydrogen bond estimation algorithm)
"Continuum secondary structure captures protein flexibility". Structure. 10 (2): 175-184. doi:10.1016/S0969-2126(02)00700-1. ... The DSSP algorithm is the standard method for assigning secondary structure to the amino acids of a protein, given the atomic- ... STRIDE (protein) an alternative algorithm Chris Sander (Scientist) Kabsch W, Sander C (1983). "Dictionary of protein secondary ... where it is the name of the Pascal program that implements the algorithm Define Secondary Structure of Proteins. DSSP begins by ...