Software
BLAST® (Basic Local Alignment Search Tool) is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. The BLAST programs have been designed for speed, with a minimal sacrifice of sensitivity to distant sequence relationships.
CAChe - computer-aided chemistry modeling package for experimental chemists
Clustal W - a common purpose multiple sequence alignment program for DNA or proteins.
Chimera - UCSF Chimera is a highly extensible, interactive molecular graphics program.
FASTA3 - Sequence similarity and homology searching against nucleotide and protein database using Fasta3. Please note that this service will be phased out shortly. Use the new version above.
Proteomes and Genomes FASTA - This tool uses the Fasta programs to provide sequence similarity and homology searching against complete proteome or genome databases.
Fold classification based on Structure-Structure alignment of Proteins - The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB). The classification and alignments are automatically maintained and continuously updated using the Dali search engine.
Gaussian - 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. (also GaussView)
GOLD - GOLD is a program for calculating the docking modes of small molecules into protein binding sites. (Also includes SILVER for Post-processing of Docking Results.)
Gromacs - "The Worlds Fastest Molecular Dynamics." Howto create inputs for gromacs simulations - PowerPoint , PDF
InterProScan - allows you to query your protein sequence against InterPro.
MaxSprout - MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace.
MOE - ChemComp MOE is a comprehensive software system addressing the needs of today's research disciplines including Bioinformatics, Cheminformatics, Protein Modeling, Structure-Based Design, High Throughput Discovery and Molecular Modeling and Simulations.
NAMD - Scalable Molecular Dynamics, NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Protein Explorer - software for looking at macromolecular structure and its relation to function (this software is the newest version of RASMOL).
Swiss Pdb-Viewer - Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time.
Structural Classifications of Proteins (SCOP) - Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. T
VMD - Visual Molecular Dynamics (VMD) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
WU Blast - Washington University BLAST Archives
WU Blast2 - Washington University Basic Local Alignment Search Tool Version 2.0
https://materialsproject.org/
http://psi-k.net/
CAChe - computer-aided chemistry modeling package for experimental chemists
Clustal W - a common purpose multiple sequence alignment program for DNA or proteins.
Chimera - UCSF Chimera is a highly extensible, interactive molecular graphics program.
FASTA3 - Sequence similarity and homology searching against nucleotide and protein database using Fasta3. Please note that this service will be phased out shortly. Use the new version above.
Proteomes and Genomes FASTA - This tool uses the Fasta programs to provide sequence similarity and homology searching against complete proteome or genome databases.
Fold classification based on Structure-Structure alignment of Proteins - The FSSP database is based on exhaustive all-against-all 3D structure comparison of protein structures currently in the Protein Data Bank (PDB). The classification and alignments are automatically maintained and continuously updated using the Dali search engine.
Gaussian - 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. (also GaussView)
GOLD - GOLD is a program for calculating the docking modes of small molecules into protein binding sites. (Also includes SILVER for Post-processing of Docking Results.)
Gromacs - "The Worlds Fastest Molecular Dynamics." Howto create inputs for gromacs simulations - PowerPoint , PDF
InterProScan - allows you to query your protein sequence against InterPro.
MaxSprout - MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace.
MOE - ChemComp MOE is a comprehensive software system addressing the needs of today's research disciplines including Bioinformatics, Cheminformatics, Protein Modeling, Structure-Based Design, High Throughput Discovery and Molecular Modeling and Simulations.
NAMD - Scalable Molecular Dynamics, NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
Protein Explorer - software for looking at macromolecular structure and its relation to function (this software is the newest version of RASMOL).
Swiss Pdb-Viewer - Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time.
Structural Classifications of Proteins (SCOP) - Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. T
VMD - Visual Molecular Dynamics (VMD) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
WU Blast - Washington University BLAST Archives
WU Blast2 - Washington University Basic Local Alignment Search Tool Version 2.0
https://materialsproject.org/
http://psi-k.net/