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ESyPred3D
ESyPred3D is an automated homology modeling program. Alignments are obtained by combining, weighting and screening the results of several multiple alignment programs. The final three-dimensional structure is built using the modeling package MODELLER. Method To perform homology modeling, the ESyPred3D program first searches for a template (a similar sequence of known structure), before aligning the query and template sequences. EsyPred3D then build the 3D models using the alignment and the template structure, before assessing the final 3D model. The query and the template sequences are aligned using a consensus alignment method. Different multiple sequence alignments are built using different alignment programs on two sets of sequences including the query and the template sequence. The consensus method uses a neural network to find the best aligned residues and analyzing all possible combinations using a dead end elimination algorithm. The final 3D model is built from the target ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Protein Structure Prediction Software
This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ''ab initio'' methods, secondary structure prediction, and transmembrane helix and signal peptide prediction. Software list Below is a list which separates programs according to the method used for structure prediction. Homology modeling Threading/fold recognition ''Ab initio'' structure prediction Secondary structure prediction Detailed list of programs can be found at List of protein secondary structure prediction programs See also *List of protein secondary structure prediction programs *Comparison of nucleic acid simulation software *List of software for molecular mechanics modeling *Molecular design software *Protein design Protein design is the rational design of new protein molecules to design novel activity, behavior, or purpose, and to advance basic understanding of protein funct ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Homology Modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "''template''"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been seen that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure. Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure. It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MODELLER
Modeller, often stylized as MODELLER, is a computer program used for homology modeling to produce models of protein tertiary structures and quaternary structures (rarer). It implements a method inspired by nuclear magnetic resonance spectroscopy of proteins (protein NMR), termed '' satisfaction of spatial restraints'', by which a set of geometrical criteria are used to create a probability density function for the location of each atom in the protein. The method relies on an input sequence alignment between the target amino acid sequence to be modeled and a template protein which structure has been solved. The program also incorporates limited functions for ab initio structure prediction of loop regions of proteins, which are often highly variable even among homologous proteins and thus difficult to predict by homology modeling. Modeller was originally written and is currently maintained by Andrej Sali at the University of California, San Francisco. It runs on the operating syst ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Neural Network
A neural network is a network or circuit of biological neurons, or, in a modern sense, an artificial neural network, composed of artificial neurons or nodes. Thus, a neural network is either a biological neural network, made up of biological neurons, or an artificial neural network, used for solving artificial intelligence (AI) problems. The connections of the biological neuron are modeled in artificial neural networks as weights between nodes. A positive weight reflects an excitatory connection, while negative values mean inhibitory connections. All inputs are modified by a weight and summed. This activity is referred to as a linear combination. Finally, an activation function controls the amplitude of the output. For example, an acceptable range of output is usually between 0 and 1, or it could be −1 and 1. These artificial networks may be used for predictive modeling, adaptive control and applications where they can be trained via a dataset. Self-learning resulting from e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure Prediction
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes). Starting in 1994, the performance of current methods is assessed biannually in the CASP experiment (Critical Assessment of Techniques for Protein Structure Prediction). A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D. Protein structure and terminology Proteins are chains of amino acids joined together by peptide bonds. Many conformations of this chain are possible due to the rotation of the main chain abou ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Homology Modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "''template''"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been seen that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure. Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure. It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
