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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, Protein structure prediction#Secondary structure, 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 and 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 *AlphaFold External linksbio.tools finding more tools References {{DEFAULTSORT:Protein structure predictio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Comparison Of Nucleic Acid Simulation Software
This is a list of notable computer programs that are used for nucleic acid Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...s simulations. See also References Computational chemistry software Software comparisons Molecular dynamics software Molecular modelling software {{Computer simulation ... [...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 Protein secondary structure, secondary and Protein tertiary structure, tertiary structure ... {{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 solvation, implicit water models. Mainly designed to simulate the protein folding and DNA-ligand Complex (chemistry), complexes in AMBER Force field (chemistry), force field. Key features * 3D molecular graphics * Automatic Force Field generator for bioelements: H, C, N, O * Building and Molecule editor, editing chemical structures * Library of building blocks * Force field (chemistry), 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 (Quantum Chemistry Program), ORCA, NWChem, Firefly (computer program), Firefly (PC GAMESS), CP2K * Molec ... [...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. Following the structure prediction, I-TASSER has a component for structure-based protein function prediction, 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 National University of Singapore, allowing users to sub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), 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 dynamics (mechanics), dynamic "evolution" of the system. In the most common version, the trajectory, trajectories of atoms and molecules are determined by Numerical integration, numerically solving Newton's laws of motion, Newton's equations of motion for a system of interacting particles, where Force (physics), forces between the particles and their potential energy, potential energies are often calculated using interatomic potentials or molecular mechanics, molecular mechanical Force field (chemistry), 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 analyt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Swiss-model
Swiss-model (stylized as SWISS-MODEL) is a structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. , homology modeling is the most accurate method to generate reliable three-dimensional protein structure models and is routinely used in many practical applications. Homology (or comparative) modelling methods make use of experimental protein structures (templates) to build models for evolutionary related proteins (targets). Today, Swiss-model consists of three tightly integrated components: (1) The Swiss-model pipeline – a suite of software tools and databases for automated protein structure modelling, (2) The Swiss-model Workspace – a web-based graphical user interface workbench, (3) The Swiss-model Repository – a continuously updated database of homology models for a set of model organism proteomes of high biomedical interest. Pipeline Swiss-model pipeline comprises the four main steps that are involved in building a homology model of ... [...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] |
