Search Software

  • AMBER. Assisted Model Building with Energy Refinement.

  • The Collaborative Computational Project Number 4 (CCP4) program suite is a collection of disparate programs, which communicate via standard data files, rather than all operations being integrated into one huge program, covering most of the computations required for macromolecular crystallography.

  • CHARMm (Chemistry at HARvard Molecular Mechanics) is the academic version of the CHARMM simulation program available through Harvard. CHARMm uses empirical energy functions to describe the forces on atoms in molecules.
  • "CMfinder is a RNA motif prediction tool. It is an expectation maximization algorithm using covariance models for motif description, carefully crafted heuristics for effective motif search, and a novel Bayesian framework for structure prediction combining folding energy and sequence covariation.

  • CNS

    Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination.

  • CREST (Clipping Reveals Structure) is a new algorithm for detecting genomic structural variations at base-pair resolution using next-generation sequencing data. Publication: http://www.ncbi.nlm.nih.gov/pubmed/21666668

     

  • d*TREK is a flexible, customizable, device-independent software suite and toolkit which processes single crystal X-ray diffraction images from two-dimensional position sensitive detectors such as imaging plate area detectors and charged-coupled device (CCD) detectors.

  • Desmond is a software package developed at D. E. Shaw research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters.
  • Discovery Studio® provides the most advanced software solutions for life science researchers available today.

  • The DSSP program was designed by Wolfgang Kabsch and Chris Sander to standardize secondary structure assignment. DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).

  • FEBio is a nonlinear finite element solver that is specifically designed for biomechanical applications. It offers modeling scenarios, constitutive models and boundary conditions that are relevant to many research areas in biomechanics.

  • GraphClust can be used for structural clustering of RNA sequences. Especially it can be used for clustering of very large dataset with thousands of RNAs.

    http://www.bioinf.uni-freiburg.de/Software/GraphClust/

  • GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

  • The structure determination of protein-protein complexes is a rather tedious and lengthy process, both by NMR and X-ray crystallography. Several methods based on docking to study protein complexes have been well developed over the past few years.

  • HKL-2000 program package is based on the extended versions of Denzo, Xdisplayf and Scalepack. It consists of several subprograms coordinated by the graphical command center.

  • "Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).

  • "LocaRNA is a package of tools for producing fast and high-quality pairwise and multiple alignment of RNA sequences. It uses a complex RNA energy model for simultaneous folding and sequence/structure alignment of the RNAs.

  • MODELLER is used for homology or comparative modeling of protein three-dimensional structures. 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.

  • MOE
    The Molecular Operating Environment (MOE) is the next generation of chemical computing software. MOE is an integrated Applications Environment and Methodology Development Platform. MOE integrates visualization, simulation and application development in one package.
  • MolMol - MOLecule analysis and MOLecule display

  • MolScript is a program for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually, but not exclusively, protein structures.

  • NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.  Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms.

  • NMRPipe is a system of spectral analysis tools by Frank Delaglio of NIH.

  • NMRView is a program by Bruce A. Johnson of Merck Research Laboratories for the visualization and analysis of NMR datasets. The following summarizes some of the features of NMRView. Multiple views on one or more NMR spectra. Unlimited number of spectral windows.

  • The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data.

  • From the ProFit homepage ProFit is designed to be the ultimate protein least squares fitting program. It has many features including flexible specification of fitting zones and atoms, calculation of RMS over different zones or atoms, RMS-by-residue calculation, on-line help facility, etc.

  • "RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST+ suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler."

  •  

    "RNAshapes offers three powerful RNA analysis tools in one single software package:

  • "RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. It can be used in genome wide screens to detect functional RNA structures, as found in noncoding RNAs and cis-acting regulatory elements of mRNAs."

  • Schrödinger provides a complete suite of software solutions with the latest advances in pharmaceutical research and computational chemistry.
  • From the SOLVE/RESOLVE home page:

    SOLVE/RESOLVE is a program that can carry out all the steps of macromolecular structure determination from scaling data to calculation of an electron density map, automatically.

  • trf

    "TRF (Tandem Repeats Finder) is a program to locate and display tandem repeats in DNA sequences."

    Homepage:

    http://www.mybiosoftware.com/sequence-analysis/4083

  • From the X-PLOR Manual: