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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 fun ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Protein Secondary Structure Prediction Programs
List of notable protein secondary structure prediction programs See also * List of protein structure prediction software * 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 ... {{DEFAULTSORT:Protein Structure Prediction Structural bioinformatics software Protein structure Protein methods ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Abalone (molecular Mechanics)
Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model) or in implicit water models. Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field. Key features * 3D molecular graphics Automatic Force Field generator for bioelements: H, C, N, O* Building and editing chemical structures * Library of building blocks * Force fields: Assisted Model Building with Energy Refinement (AMBER) 94, 96, 99SB, 03; Optimized Potentials for Liquid Simulations (OPLS) * Geometry optimizing * Molecular dynamics with multiple time step integrator * Hybrid Monte Carlo * Replica exchange * Interface with quantum chemistry - ORCA, NWChem, Firefly (PC GAMESS), CP2K CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
I-TASSER
I-TASSER (Iterative Threading ASSEmbly Refinement) is a bioinformatics method for predicting three-dimensional structure model of protein molecules from amino acid sequences. It detects structure templates from the Protein Data Bank by a technique called fold recognition (or threading). The full-length structure models are constructed by reassembling structural fragments from threading templates using replica exchange Monte Carlo simulations. I-TASSER is one of the most successful protein structure prediction methods in the community-wide CASP experiments. I-TASSER has been extended for structure-based protein function predictions, which provides annotations on ligand binding site, gene ontology and enzyme commission by structurally matching structural models of the target protein to the known proteins in protein function databases. It has an on-line server built in thYang Zhang Labat the University of Michigan, Ann Arbor, allowing users to submit sequences and obtain structure an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RaptorX / Software For Protein Modeling And Analysis
RaptorX is a software and web server for protein structure and function prediction that is free for non-commercial use. RaptorX is among the most popular methods for protein structure prediction. Like other remote homology recognition/protein threading techniques, RaptorX is able to regularly generate reliable protein models when the widely used PSI-BLAST cannot. However, RaptorX is also significantly different from those profile-based methods (e.g., HHPred and Phyre2) in that RaptorX excels at modeling of protein sequences without a large number of sequence homologs by exploiting structure information. RaptorX Server has been designed to ensure a user-friendly interface for users inexpert in protein structure prediction methods. Description The RaptorX project was started in 2008 and RaptorX Server was released to the public in 2011. Standard usage After pasting a protein sequence into the RaptorX submission form, a user will typically wait a couple of hours (depending on ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Supercomputing Facility For Bioinformatics And Computational Biology
Supercomputing Facility for Bioinformatics and Computational Biology, also known as SCFBio IIT Delhi, is a center for Bioinformatics & Computational Biology in Indian Institute of Technology, Delhi. This facility was established in 2002 under the aegis of the Department of Chemistry, IIT Delhi. It is recognized as a center of excellence in Bioinformatics by the Department of Biotechnology ( DBT), Government of India. History The Supercomputing Facility for Bioinformatics and Computational Biology, (SCFBio), IIT Delhi, was established in July 2002 with funding from Department of Biotechnology under the guidance of Prof. B. Jayaram. It aims at developing novel scientific methods and new software for genome analysis, protein structure prediction, and in silico drug design. The facility was inaugurated by the Honorable Minister of Science and Technology and Human Resource Development Shri Murli Manohar Joshi, IITD adopted SCFBio as a Central Facility of National importance in March ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
