Nanoscale Molecular Dynamics is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model. It is noted for its parallel efficiency and is often used to simulate large systems. It has been developed by the collaboration of the Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of Illinois at Urbana–Champaign.
Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models. The term structural has the same meaning as in structural biology, and structural bioinformatics can be seen as a part of computational structural biology. The main objective of structural bioinformatics is the creation of new methods of analysing and manipulating biological macromolecular data in order to solve problems in biology and generate new knowledge.
Ghemical is a computational chemistry software package written in C++ and released under the GNU General Public License. The program has graphical user interface based on GTK+2 and supports quantum mechanical and molecular mechanic models, with geometry optimization, molecular dynamics, and a large set of visualization tools. Ghemical relies on external code to provide the quantum-mechanical calculations — MOPAC provides the semi-empirical MNDO, MINDO, AM1, and PM3 methods, and MPQC methods based on Hartree–Fock calculations.
Internal Coordinate Mechanics (ICM) is a software program and algorithm to predict low-energy conformations of molecules by sampling the space of internal coordinates defining molecular geometry. In ICM each molecule is constructed as a tree from an entry atom where each next atom is built iteratively from the preceding three atoms via three internal variables. The rings kept rigid or imposed via additional restraints. ICM is used for modelling peptides and interactions with substrates and coenzymes.
BALL is a C++ class framework and set of algorithms and data structures for molecular modelling and computational structural bioinformatics, a Python interface to this library, and a graphical user interface to BALL, the molecule viewer BALLView.
Tinker, previously stylized as TINKER, is a suite of computer software applications for molecular dynamics simulation. The codes provide a complete and general set of tools for molecular mechanics and molecular dynamics, with some special features for biomolecules. The core of the software is a modular set of callable routines which allow manipulating coordinates and evaluating potential energy and derivatives via straightforward means.
Molecular biophysics is a rapidly evolving interdisciplinary area of research that combines concepts in physics, chemistry, engineering, mathematics and biology. It seeks to understand biomolecular systems and explain biological function in terms of molecular structure, structural organization, and dynamic behaviour at various levels of complexity. This discipline covers topics such as the measurement of molecular forces, molecular associations, allosteric interactions, Brownian motion, and cable theory. Additional areas of study can be found on Outline of Biophysics. The discipline has required development of specialized equipment and procedures capable of imaging and manipulating minute living structures, as well as novel experimental approaches.
Chemical Computing Group is a software company specializing in research software for computational chemistry, bioinformatics, cheminformatics, docking, pharmacophore searching and molecular simulation. The company's main customer base consists of pharmaceutical and biotechnology companies, as well as academic research groups. It is a private company that was founded in 1994; it is based in Montreal, Quebec, Canada. Its main product, Molecular Operating Environment (MOE), is written in a self-contained programming system, the Scientific Vector Language (SVL).
The Center for Simulation of Advanced Rockets (CSAR) is an interdisciplinary research group at the University of Illinois at Urbana-Champaign, and is part of the United States Department of Energy's Advanced Simulation and Computing Program. CSAR's goal is to accurately predict the performance, reliability, and safety of solid propellant rockets.
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential (GEEP). The Gaussian and Augmented Plane Waves method (GAPW) as an extension of the GPW method allows for all-electron calculations. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture.
Tachyon is a parallel/multiprocessor ray tracing software. It is a parallel ray tracing library for use on distributed memory parallel computers, shared memory computers, and clusters of workstations. Tachyon implements rendering features such as ambient occlusion lighting, depth-of-field focal blur, shadows, reflections, and others. It was originally developed for the Intel iPSC/860 by John Stone for his M.S. thesis at University of Missouri-Rolla. Tachyon subsequently became a more functional and complete ray tracing engine, and it is now incorporated into a number of other open source software packages such as VMD, and SageMath. Tachyon is released under a permissive license.
DelPhi is a scientific application which calculates electrostatic potentials in and around macromolecules and the corresponding electrostatic energies. It incorporates the effects of ionic strength mediated screening by evaluating the Poisson-Boltzmann equation at a finite number of points within a three-dimensional grid box. DelPhi is commonly used in protein science to visualize variations in electrostatics along a protein or other macromolecular surface and to calculate the electrostatic components of various energies.
Zaida Ann "Zan" Luthey-Schulten is the William and Janet Lycan Professor of Chemistry at the University of Illinois at Urbana-Champaign. She was promoted to professor in 2004. She is also involved with the NASA Astrobiology Institute.
Klaus Schulten was a German-American computational biophysicist and the Swanlund Professor of Physics at the University of Illinois at Urbana-Champaign. Schulten used supercomputing techniques to apply theoretical physics to the fields of biomedicine and bioengineering and dynamically model living systems. His mathematical, theoretical, and technological innovations led to key discoveries about the motion of biological cells, sensory processes in vision, animal navigation, light energy harvesting in photosynthesis, and learning in neural networks.
Nancy Makri is the Edward William and Jane Marr Gutgsell Endowed Professor of Chemistry and Physics at the University of Illinois at Urbana–Champaign, where she is the principal investigator of the Makri Research Group for the theoretical understanding of condensed phase quantum dynamics. She studies theoretical quantum dynamics of polyatomic systems, and has developed methods for long-time numerical path integral simulations of quantum dissipative systems.
Molecular Operating Environment (MOE) is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. MOE scientific applications are used by biologists, medicinal chemists and computational chemists in pharmaceutical, biotechnology and academic research. MOE runs on Windows, Linux, Unix, and macOS. Main application areas in MOE include structure-based design, fragment-based design, ligand-based design, pharmacophore discovery, medicinal chemistry applications, biologics applications, structural biology and bioinformatics, protein and antibody modeling, molecular modeling and simulations, virtual screening, cheminformatics & QSAR. The Scientific Vector Language (SVL) is the built-in command, scripting and application development language of MOE.
PLUMED is an open-source library implementing enhanced-sampling algorithms, various free-energy methods, and analysis tools for molecular dynamics simulations. It is designed to be used together with ACEMD, AMBER, DL_POLY, GROMACS, LAMMPS, NAMD, OpenMM, ABIN, CP2K, i-PI, PINY-MD, and Quantum ESPRESSO, but it can also be used to together with analysis and visualization tools VMD, HTMD, and OpenPathSampling.
