A blog about free research software, alternative to commercial paid software.

One way to help people is to share your knowledge with those who could benefit from it. As a researcher , constant effort to solve scientific problems have exposed me to various scientific resources that can be accessed free of charge. Especially these knowledge is useful to labs and institution unable to access expensive software or novice users due to lack of expertise. In this blog, I have provided a comprehensive list of freely available softwares, alternative to commercial software. I shall share with you all that I have learned, as I make the changes or learn something new, I shall document them. Hope this blog will help those finding the way………….

Research software and books

Dec 20, 2010

STRUCTURAL BIOLOGY

 

 

 

APBS


APBS is a research software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media.

Biodesigner

Biodesigner is a molecular modeling and visualization program for personal computers. The program is freely available for downloading. Biodesigner is capable of creating homologous models of proteins, evaluate, and refine the models.

Bioeditor

BioEditor is a standalone Windows program that can be used with Windows NT, Windows ME and Windows 2000 operating systems. BioEditor contains features that enable the user to enter text, graphics, sequence, dynamic structural images and references. Many features link directly to resources on the World Wide Web.

It is designed to be used by structural scientists and researchers reporting and evaluating their data, as well as by educators and students who are seeking to relate structure to function in biological macromolecules. The interface consists of a series of drop-down menus and toolbars and three working areas: folders, comments and palette.

Chimera

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.


HYDROPRO

HYDROPRO computes the hydrodynamic properties of rigid macromolecules (globular proteins, small nucleic acids, etc) from their atomic-level structure, as specified by the atomic coordinates taken from a PDB file supplied by the user, from which the proper hydrodynamic model is built by the program itself. The HYDROPRO calculation comprises was the basic hydrodynamic properties: translational diffusion coefficient, sedimentation coefficient, intrinsic viscosity, and relaxation times, along with the radius of gyration.

Modeller

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. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints 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.

PDB2PQR

PDB2PQR is a Python research software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include:

    * Adding a limited number of missing heavy atoms to biomolecular structures
    * Determining side-chain pKas
    * Placing missing hydrogens
    * Optimizing the protein for favorable hydrogen bonding
    * Assigning charge and radius parameters from a variety of force fields

PEAT

PEAT Protein Engineering Analysis Tool (PEAT) is a collection of software that aids researchers in the field of protein analysis, engineering and design.

Triton

The program TRITON is a graphical tool for computational aided protein engineering. It implements methodology of computational site-directed mutagenesis to design new protein mutants with required properties. It uses the external program Modeller to model structures of new protein mutants based on the wild-type structure by homology modelling method. Subsequently, properties of these protein mutants are modelled. For enzymes, chemical reactions are modelled using semi-empirical quantum mechanical program Mopac. Qualitative prediction of mutant activities can be achieved by evaluating the changes in energies of the system and partial atomic charges of the active site residues during the reaction. Ligand-protein binding properties can be studied by docking methodology using the external program AutoDock. Ligand binding modes and afinities of individual protein mutants are obtained as a result. Binding properties can also be analysed by visualisation of affinity maps or by calculation of electrostatic potential interactions between ligand and individual residues of the binding site. The program TRITON offers graphical tools for preparation of the input files and for visualisation of output data. The program uses projects to organize computational data.

Swiss-PdbViewer

Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

JACKAL

A collection of programs designed for the modeling and analysis of protein structures.

    * scap and Sidechain Rotamer library: prediction of side-chain conformations or residue mutations. The operation can be performed on all or certain residues in one or multiple chains.
    * loopy + loopyMod: prediction of protein loop conformations or segment mutation. loopyMod used by loopBuilder.
    * nest: homology modeling.

Delphi

DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast (the best relaxation parameter is estimated at run time), accurate (calculation of the electrostatic free energy is less dependent on the resolution of the lattice) and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions.

NAMD

NAMD, 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 and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms.

Gromacs

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.t is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.

Jevtrace

Jevtrace is a implementation of the evolutionary tracetree inspired analysis of protein families. Jevtrace includes a multivalent graphical browser for multiple sequence alignment, phylogeny, and structure, as well as underlying object and algorithmic infrastructure. method. The software expands on the evolutionary trace by allowing manipulation of the input data and parameters of analysis, and presents a number of novel.

Poseview

PoseView automatically generates high-quality 2D structure-diagrams of protein-ligand complexes provided as 3D-input. Such input may come directly from crystal structures or be computed for example by a docking program.











2 comments:

Anonymous said...

If any of you feel any problem in using TRITON or would like to know more about it, can write to me in sushil@ncbr.chemi.muni.cz

Dr. Suji George said...

Thanks sushil