> Tag > Links tagged with 'monte carlo method'

Links tagged with 'monte carlo method'

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CE-MCTool Content

http://bioinformatics.albany.edu/~cemc/ [open in a new window]

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Protein > 3-D Structure Comparison
Sequence Comparison > Multiple Sequence Alignments

A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.

links directory index: 146
TitlePublication YearGoogle Scholar Citation Count
CE-MC: a multiple protein structure alignment server200481
A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization200165
NAR Web Server Issue 2004
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tagsalgorithms amino acid sequence amino acid sequence homology aspartic acid endopeptidases factual databases molecular sequence data monte carlo method protein kinases proteins secondary protein structure sequence alignment software design

ClusProTool Content

http://cluspro.bu.edu/login.php [open in a new window]

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Protein > Molecular Dynamics and Docking

ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.

links directory index: 511
TitlePublication YearGoogle Scholar Citation Count
Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19201033
PIPER: an FFT-based protein docking program with pairwise potentials2006100
ClusPro: an automated docking and discrimination method for the prediction of protein complexes2004247
ClusPro: a fully automated algorithm for protein-protein docking2004131
NAR Web Server Issue 2004
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tagsalgorithms antibodies antigens binding sites biological models chemical models cluster analysis computational biology discriminant analysis energy transfer enzyme inhibitors fourier analysis molecular dynamics simulation molecular models monte carlo method protein binding protein conformation protein interaction mapping protein multimerization proteins reproducibility of results sensitivity and specificity static electricity time factors

Combinatorial Extension of the Optimal PathDatabase Content

http://cl.sdsc.edu/ce.html [open in a new window]

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Protein > 3-D Structure Comparison

Calculates structural alignments between two protein chains; or between a single chain and the entire Protein Data Bank.

links directory index: 1542
TitlePublication YearGoogle Scholar Citation Count
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path19981542
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tagsalgorithms amino acid sequence amino acid sequence homology molecular sequence data monte carlo method protein conformation protein folding proteins sequence alignment

PepStrTool Content

http://www.imtech.res.in/raghava/pepstr/ [open in a new window]

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Other Molecules > Peptides
Protein > Sequence Features

The Pepstr server predicts the tertiary structure of small peptides with sequence length varying between 7 to 25 residues. The prediction strategy is based on the realization that β-turn is an important and consistent feature of small peptides in addition to regular structures. Thus, the methods uses both the regular secondary structure information predicted from PSIPRED and β-turns information predicted from BetaTurns.

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links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
PEPstr: a de novo method for tertiary structure prediction of small bioactive peptides200717
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tagsbeta-turns bioactive ligands monte carlo method peptides protein binding tertiary protein structure tertiary structure prediction

RosettaDesignTool Content

http://rosettadesign.med.unc.edu [open in a new window]

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Protein > 3-D Structure Prediction
Protein > Biochemical Features

RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.

links directory index: 1600
TitlePublication YearGoogle Scholar Citation Count
RosettaDesign server for protein design200649
Design of a novel globular protein fold with atomic-level accuracy2003716
A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins2003170
Accurate computer-based design of a new backbone conformation in the second turn of protein L200263
Computer-based redesign of a protein folding pathway2001158
Conversion of monomeric protein L to an obligate dimer by computational protein design200144
Native protein sequences are close to optimal for their structures2000400
NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence amino acid sequence homology bacterial proteins biomolecular nuclear magnetic resonance circular dichroism computational biology computer simulation crystallization dimerization dna-binding proteins guanidine kinetics magnetic resonance spectroscopy molecular models molecular sequence data monte carlo method mutagenesis mutation protein conformation protein databases protein denaturation protein engineering protein folding protein sequence analysis proteins secondary protein structure sequence alignment solubility temperature tertiary protein structure thermodynamics x-ray crystallography

TSEMATool Content

http://tsema.bioinfo.cnio.es/ [open in a new window]

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Protein > Networks & Interactions, Pathways and Enzymes
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

The Server for Efficient Mapping Assessment (TSEMA) predicts possible protein-protein interactions based on the comparision of phylogenetic trees derived from sequences of associated protein families.

links directory index: 325
TitlePublication YearGoogle Scholar Citation Count
TSEMA: interactive prediction of protein pairings between interacting families200616
Similarity of phylogenetic trees as indicator of protein-protein interaction2001309
NAR Web Server Issue 2006
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tagsbacterial genome chaperonin 60 computational biology escherichia coli proteins glutamate-trna ligase gtp-binding proteins molecular evolution monte carlo method phylogeny protein interaction mapping protein sequence analysis proteins proteome ribosomal proteins sequence alignment statistics as topic tertiary protein structure

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