Prof. Upinder S. Bhalla - Structural Bio Informatics
Structural Bioinformatics Resources @ CAPS:
High Performance Computing (Linux Clusters) Facilities:
1. Linome Cluster
Linome is the Linux Cluster located at National Center for Biological Sciences(NCBS) Bangalore,and is a common facility shared by Dr.R.Sowdhamini's Lab, NCBS and Dr.N.Srinivasan's Lab Molecular Biophysics Unit,IISc, Bangalore.
Linome Cluster Highlights
* 22 Processors - Composed of 11 nodes of dual Athlon XP 1900+ CPUs.
* System Memory - Each 2 CPU SMP node has 512 MB of memory.
* 100MBPS Network Interconnect - Each SMP node is connected using a 100MBPS switch running in full duplex mode.
* Parallel software tools - PVM, LAM/MPI and Condor batch system
Application Software:
* Sequence Analysis : Hmmer, Blast, SAM
* Alignment : MALIGN, Clustal-MPI
* Phylogenetic Analysis : Phylip, TREE-PUZZLE
* PVM Povray: A parallel ray tracing tool
* Gmandel: A parallel fractal generator which can use both PVM or MPI
* Molecular Dynamics : NMDA, Gromacs
2. Opterome Cluster:
Opterome Cluster Highlights:
* 15 node cluster with AMD Opteron Processors
* Network : Infiniband Connection * Parallel software tools : PVM, LAM/MPI and Condor batch system
Application Software:
* Sequence Analysis : Hmmer, Blast, SAM, MPI-BLAST, PROSAL
* Secondory Structure Prediction : PSI-PRED, HMM-TOP, * Alignment : MALIGN, ClustalW, Clustal-MPI
* Phylogenetic Analysis : Phylip, TREE-PUZZLE
* PVM Povray: A parallel ray tracing tool
* Gmandel: A parallel fractal generator which can use both PVM or MPI
* Molecular Dynamics : NMDA, Gromacs - 64 bit parallel computing
* Molecular Modelling, Docking & Energy Minimization : MODELLER, DOCK, GRAMM, ROSETTA, RAPPER, GAMESS, GRASP, AUTODOCK, AMBER
3. Quadrome Cluster - I:
Quadrome - I Cluster Highlights:
* 30 node cluster with Intel Quad Core processors
* Network : Infiniband Connection
* Parallel software tools : PVM, LAM/MPI and Condor batch system
Application Software:
* Sequence Analysis : Hmmer, Blast, SAM, MPI-BLAST, PROSAL
* Secondory Structure Prediction : PSI-PRED, HMM-TOP
* Alignment : MALIGN, ClustalW, Clustal-MPI
* Phylogenetic Analysis : Phylip, TREE-PUZZLE
* PVM Povray: A parallel ray tracing tool
* Gmandel: A parallel fractal generator which can use both PVM or MPI
* Molecular Dynamics : NMDA, Gromacs - 64 bit parallel computing
* Molecular Modelling, Docking & Energy Minimization : MODELLER, DOCK, GRAMM, ROSETTA, RAPPER, GAMESS, GRASP, AUTODOCK, AMBER
4. Quadrome Cluster - II:
Quadrome - II Cluster Highlights:
* 8 node cluster with Intel Quad Core processors
* Network : Infiniband Connection
* Parallel software tools : PVM, LAM/MPI and Condor batch system
Application Software:
* Sequence Analysis : Hmmer, Blast, SAM, MPI-BLAST, PROSAL
* Secondory Structure Prediction : PSI-PRED, HMM-TOP
* Alignment : MALIGN, ClustalW, Clustal-MPI
* Phylogenetic Analysis : Phylip, TREE-PUZZLE
* PVM Povray: A parallel ray tracing tool
* Gmandel: A parallel fractal generator which can use both PVM or MPI
* Molecular Dynamics : NMDA, Gromacs - 64 bit parallel computing
* Molecular Modelling, Docking & Energy Minimization : MODELLER, DOCK, GRAMM, ROSETTA, RAPPER, GAMESS, GRASP, AUTODOCK, AMBER
Databases Developed @ CAPS:
- MegaMotifbase [Structural Motifs Database]
- SMoS [ Structural Motifs of Superfamilies ]
- SUPFAM
- iMOTdb : Spatially Interacting Motifs in Proteins
- DDBASE [Protein domain database]
- DSDBASE [Protein disulphide database]
- GenDiS:Genomic Distribution of Protein Structural Superfamilies
- Protein superfamily alignment database(PASS2)
Web Servers Developed @ CAPS:
- IWS - Integrated Web Server for protein sequence and structure analysis
- PURE - Prediction of Unassigned REgions
- COILCHECK - Web Server for validation of coiled coils
- SMotif - Structural Motifs in Proteins
- FMALIGN
- iMOT: Interacting Motifs
- DIAL : Domain Identification Algorithm
- MODIP [MOdelling of DIsulphide bonds in Proteins]