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CCBB

Director: Southerland, William, Ph.D.

Summary:

CCBB is a state-of-the-art center equipped with the necessary computer hardware, software and personnel for the support of computational biology and bioinformatics research at Howard University.

People:

Resources:

Software

  • AMBER ( Software )

  • ArgusLab ( Software )

    "ArgusLab is a molecular modeling, graphics, and drug design program for Windows operating systems."

  • AutoDock ( Software )

    "AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure."

  • CHARMM ( Software )

    "CHARMM (Chemistry at HARvard Macromolecular Mechanics):
    Is a versatile and widely used molecular simulation program with broad application to many-particle systems.

    Has been developed with a primary focus on the study of molecules of biological interest, including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments

    Provides a large suite of computational tools that encompass numerous conformational and path sampling methods, free energy estimates, molecular minimization, dynamics, and analysis techniques, and model-building capabilities

    Is useful for a much broader class of many-particle systems

    Can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models

    Has been ported to numerous platforms in both serial and parallel architectures"

  • Clustal X1.8.1 ( Software )

    "Clustal X is a windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results."

  • EMBOSS ( Software )

    "EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages."

  • FASTA ( Software )

    "The FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families."

  • Gaussian ( Software )

    For quantum chemistry. With Linda 7.1

  • GeneHunter ( Software )

    "GeneHunter is a powerful software solution for optimization problems which utilizes a state-of-the-art genetic algorithm methodology. GeneHunter includes an Excel Add-In which allows the user to run an optimization problem from Microsoft Excel, as well as a Dynamic Link Library of genetic algorithm functions that may be called from programming languages such as Microsoft® Visual Basic or C."

  • Glimmer ( Software )

    "Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. The IMM approach, described in our Nucleic Acids Research paper on Glimmer 1.0 and in our subsequent paper on Glimmer 2.0 , uses a combination of Markov models from 1st through 8th-order, weighting each model according to its predictive power. Glimmer uses 3-periodic nonhomogenous Markov models in its IMMs.

    Glimmer was the primary microbial gene finder used at The Institute for Genomic Research (TIGR), where it was first developed, and has been used to annotate the complete genomes of over 100 bacterial species from TIGR and other labs. Glimmer3 predictions are available for all NCBI RefSeq bacterial genomes at their ftp site."

  • Hmmer ( Software )

    "HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs)."

  • MODELLER ( Software )

    "MODELLER is used for homology or comparative modeling of protein three-dimensional structures (1,2). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (3,4), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. "

  • MOE ( Software )

    "-Structure-Based Design
    -Pharmacophore Discovery
    -Protein & Antibody Modeling
    -Molecular Modeling & Simulations
    -Cheminformatics & (HTS) QSAR
    -Medicinal Chemistry Applications"

  • mpiBLAST ( Software )

    "mpiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST. By efficiently utilizing distributed computational resources through database fragmentation, query segmentation, intelligent scheduling, and parallel I/O, mpiBLAST improves NCBI BLAST performance by several orders of magnitude while scaling to hundreds of processors. mpiBLAST is also portable across many different platforms and operating systems. Lastly, a renewed focus and consolidation of the many codebases has positioned mpiBLAST to continue to be of high utility to the bioinformatics community."

  • MrBayes ( Software )

    "MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models."

  • PHYLIP ( Software )

    "PHYLIP is a free package of programs for inferring phylogenies."

  • PyMol ( Software )

    "PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures."

  • Qmol ( Software )

    "Qmol is a program for viewing molecular structures and animating molecular trajectories."

  • QUANTA ( Software )

    Macromolecular visualization and modeling.

  • RasTop ( Software )

    "RasTop is a molecular visualization software adapted from the program RasMol, which was initially developed by Roger Sayle. RasTop is particularly adapted for educational purposes and for the rapid analysis of macromolecules at the bench. RasTop wraps a user-friendly graphical interface around the "RasMol molecular engine". There is no need to type on the command line; each command in the menu generates its own script. Through an extended menu and a command panel, users can manipulate numerous molecules rapidly and learn about them. Work sessions are saved in script format and are fully regenerated with a simple mouse click.

    RasTop is available on Windows and Linux platforms."

  • S.A.G.E. ( Software )

    "S.A.G.E. (Statistical Analysis for Genetic Epidemiology)
    is free software package containing programs for use in the genetic analysis of family, pedigree and individual data."

  • STATA ( Software )

    "Stata is a complete, integrated statistical package that provides everything you need for data analysis, data management, and graphics. Stata is not sold in modules, which means you get everything you need in one package. And, you can choose a perpetual license, with nothing more to buy ever. Annual licenses are also available."

  • SYBYL ( Software )

  • T-Coffee ( Software )

    "T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).

    T-Coffee can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information (3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA secondary structures (R-Coffee)."

  • UCSF Chimera ( Software )

    "UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated."

  • VMD ( Software )

    "VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. "


Last updated: 2012-10-24T13:23:06.044-05:00

Copyright © 2016 by the President and Fellows of Harvard College
The eagle-i Consortium is supported by NIH Grant #5U24RR029825-02 / Copyright 2016