Modeling and Simulation

• AMBER
  Assisted Model Building with Energy Refinement - a molecular dynamics and energy minimization program
• AutoDock3.0
  A suite of automated docking tools designed to predict how small molecules, such as substrate or drug candidates, bind to a receptor of known 3D structure
• CHARMM
  Chemistry at HARvard Molecular Mechanics - a molecular dynamics and energy minimization program
• Disulfide by Design
  An application for the rational design of disulfide bonds in proteins and for exporting mutant PDB files containing the modeled disulfides for visualization in other molecular modeling software, for Windows
• FTDOCK
  A program for carrying out rigid-body docking between biomolecules
• GROMOS
  A general-purpose molecular dynamics computer simulation package for the study of biomolecular systems
• GROMACS
  Complete modelling package for proteins, membrane systems and more, including fast molecular dynamics, normal mode analysis, essential dynamics analysis and many trajectory analysis utilities
• ICM
  MolSoft ICM programs and modules for applications including for structure analysis, modeling, docking, homology modeling and virtual ligand screening

• JACKAL
  Suite of tools for model building, structure prediction and refinement, reconstruction, and minimization; for SGI, Linux, and Sun Solaris
• LOOPP
  Linear Optimization of Protein Potentials. Cornell Theory Center program for potential optimization and alignments of sequences and structures
• MAMMOTH
  MAtching Molecular Models Obtained from THeory - a program for automated pairwise and multiple structural alignments; for SGI, Linux, and Sun Solaris
• MidasPlus
  A program for displaying, manipulating and analysing macromolecules
• MODELLER
  A program for automated protein homology modeling
• MOIL
  Cornell Theory Center package for molecular dynamics simulation of biological molecules
• NAMD
  A parallel object-oriented molecular dynamics simulation program
• WAM - Web Antibody Modelling
  A server for automated structure modeling from antibody Fv sequences
• 123D
  A program which threads a sequence through a set of structures using substitution matrix, secondary structure prediction and contact capacity potential