Life Sciences

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"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules that are in the public domain, and are used in a variety of simulation programs; and a package of molecular simulation programs.

 

http://amber.scripps.edu/

  

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Charmm is a versatile and widely used molecular simulation program with broad application to many-particle systems. Charmm has been developed with a primary focus on the study of molecules of biological interest, such as peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments. Charmm 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. Charm can also be useful for a much broader class of many-particle systems and 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.

 

http://www.charmm.org/

  

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The CRYSTAL program was jointly developed by the Theoretical Chemistry Group at the University of Torino and the Computational Materials Science group in CLRC. The program computes the electronic structure of periodic materials within Hartree Fock, density functional or various hybrid approximations. The Bloch functions of the periodic systems are expanded as linear combinations of atom centered Gaussian functions. Powerful screening techniques are used to exploit real space locality. The code may be used to perform consistent studies of the physical, electronic and magnetic structure of molecules, polymers, surfaces and crystalline solids.

 

http://www.cse.scitech.ac.uk/cmg/CRYSTAL/

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DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.

 

• Predict binding modes of small molecule-protein complexes
• Search databases of ligands for compounds that inhibit enzyme activity
• Search databases of ligands for compounds that bind a particular protein
• Search databases of ligands for compounds that bind nucleic acid targets
• Examine possible binding orientations of protein-protein and protein-DNA complexes
• Help guide synthetic efforts by examining small molecules that are computationally derivatized

 

http://dock.compbio.ucsf.edu/

 

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DL_POLY is a general purpose molecular dynamics simulation package. It can be used to simulate a wide variety of molecular systems including:

 

 

http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/index.shtml

 

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Call it what you want - cutting edge, leading edge or bleeding edge - you're there, with problems of a size and complexity that nobody thought possible a few years ago.
Fortunately, there's a tool for those who live on the frontiers of scientific and engineering visualization. It's Ensight Gold, software for analyzing, visualizing and communicating high-end scientific and engineering datasets. EnSight Gold takes full advantage of parallel processing and rendering, provides support for an array of VR devices, and enables real-time collaboration.

EnSight Gold stakes out the territory where models contain millions and even billions of nodes. Which means you have some good company out on the frontier.

EnSight Gold's distributed architecture handles scientific and engineering analysis models containing up to billions of nodes while optimizing memory use. It builds upon the full functionality of CEI's EnSight, used by more than 1,500 scientists and engineers worldwide.

Features unique to EnSight Gold include:

• SMP parallel processing support for more than 2 processors.
• Supports multi-pipe display to drive VR planar and non-planar display environments such as a RAVE or multi-panel display wall.
• "Heads Up" Macro (HUM) for creating customized VR interfaces as well as interaction using VR input devices for head tracking and manipulation.
• Server-of-server (SoS) functionality for parallel processing of decomposed data on SMP or DMP architectures.
• Output to POV-Ray ray-tracing program for photorealistic images.
• Collaboration between remote users.
• Interfaces with EnLiten Gold for sharing of results in VR environments.
• Support for 3D input devices by Trackd or write your own using CEI's provided API.

 

http://www.ensight.com/ensight-gold.html

  

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Gaussian is the latest in the Gaussian series of electronic structure programs. Gaussian is used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.

Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures.

 

http://www.gaussian.com/

 

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LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a classical molecular dynamics code. LAMMPS models an ensemble of particles in a liquid, solid or gaseous state. It can be used to model atomic, polymeric, biological, metallic or granular systems.

 

http://lammps.sandia.gov/

 

 

 

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MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees.

 

http://mrbayes.csit.fsu.edu/

 

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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.

 

http://www.mpiblast.org/

 

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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 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.

 

http://www.ks.uiuc.edu/Research/namd/

 

 

 

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Quantum Pharmaceuticals applies quantum and statistical physic methods in solving numerous problems arising in drug hit identification, hit-to-lead optimization, and drug toxicity/pharmacokinetic profiling. We are proud to be one of the first companies aimed to perform preclinical studies by employing computational modeling on such a large scale.

The key feature of our technology is the ability to calculate intermolecular interactions with the accuracy compared with the accuracy of in-vitro experiments. Our technology employs original efficient algorithms for calculating electrostatic, Van der Waals energies, and entropy. Our scientists created fast implicit water for solvation energy calculation. Our scientific approach is rooted in the complexity analysis of quantum systems.

After processing numerous data Quantum Pharmaceuticals has discovered numeric relationships between IC50s of small molecules and its broad biological effects like ADME/TOX parameters, side effects, etc. It confirmed the premise that biological activity results from the capacity of small molecules to modulate the activity of the proteome.

 

http://q-pharm.com/quantum_science

 

  

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Glide offers the full spectrum of speed and accuracy from high-throughput virtual screening of millions of compounds to extremely accurate binding mode predictions, providing consistently high enrichment at every level.
The widespread use of combinatorial chemistry and high-throughput screening (HTS) in the pharmaceutical and biotechnology industries means that large numbers of compounds can now routinely be investigated for biological activity. However, screening large chemical libraries remains an expensive and time-consuming process, with significant rates of both false positives and false negatives.

High-speed computational methods can now enrich the fraction of suitable lead candidates in a chemical database, thereby creating the potential to greatly enhance productivity and dramatically reduce drug development costs. With an ever increasing number of drug discovery projects having access to high-resolution crystal structures of their targets, high-performance ligand-receptor docking is the clear computational strategy of choice to augment and accelerate structure-based drug design.

 

• Complete solution: Glide offers the full range of speed vs. accuracy options, from the HTVS (high-throughput virtual screening) mode for efficiently enriching million compound libraries, to the SP (standard precision) mode for reliably docking tens to hundreds of thousands of ligand with high accuracy, to the XP (extra precision) mode where further elimination of false positives is accomplished by more extensive sampling and advanced scoring, resulting in even higher enrichment.
• Virtual screening: Glide provides a rational workflow for virtual screening from HTVS to SP to XP, enriching the data at every level such that only an order of magnitude fewer compounds need to be studied at the next higher accuracy level.
• Accurate binding mode prediction: Glide reliably finds the correct binding modes for a large set of test cases. It outperforms other docking programs in achieving lower RMS deviations from native co-crystallized structures.
• Universal applicability: Glide exhibits excellent docking accuracy and high enrichment across a diverse range of receptor types.

 

http://www.schrodinger.com/ProductDescription.php?mID=6&sID=6&cID=0

 

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VASP is a complex package for performing ab-initio quantum-mechanical molecular dynamics (MD) simulations using pseudopotentials or the projector-augmented wave method and a plane wave basis set. The approach implemented in VASP is based on the (finite-temperature) local-density approximation with the free energy as variational quantity and an exact evaluation of the instantaneous electronic ground state at each MD time step. VASP uses efficient matrix diagonalisation schemes and an efficient Pulay/Broyden charge density mixing. These techniques avoid all problems possibly occurring in the original Car-Parrinello method, which is based on the simultaneous integration of electronic and ionic equations of motion. The interaction between ions and electrons is described by ultra-soft Vanderbilt pseudopotentials (US-PP) or by the projector-augmented wave (PAW) method. US-PP (and the PAW method) allow for a considerable reduction of the number of plane-waves per atom for transition metals and first row elements. Forces and the full stress tensor can be calculated with VASP and used to relax atoms into their instantaneous ground-state.

 

http://cms.mpi.univie.ac.at/vasp/

 

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VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.

 

http://www.ks.uiuc.edu/Research/vmd/

 

 

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