Servers from Proteins@MSU
Fast Links to Servers
- Kinetics Servers
- Homology Modeling Servers
- Ultracentrifugation Servers
- Sequence Manipulation Servers
- Sequence Analysis Servers
- Sequence Alignment Servers
- Secondary Structure Servers
- Molecular Visualization Servers
- Structure Analysis Servers
- Structure Modification Servers
- Structure Generation Servers
- Hydrodynamic Servers
- Scattering Servers
- Spectroscopy Servers
- Density Map Servers
- Data Analysis Servers
- Mathematical Servers
- Map Projection Servers
Kinetics Servers
- receptor_ligand_kinetics
-
This server depicts the kinetics of receptor-ligand binding, i.e., of kinetic reactions of the
form R + L <=> C. The user may specify the starting concentrations of the receptor, ligand
and complex, as well as the forward/backward rate constants and the time scale for plotting.
- two_species_linear_kinetics
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This server depicts the kinetics of two interconverting species, i.e., of unimolecular reactions of
the form S <=> P. The user may specify the starting concentrations of the two kinetic species,
as well as the forward/backward rate constants and the time scale for plotting.
- three_species_linear_kinetics
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This server depicts the kinetics of three interconverting species, i.e., of unimolecular reactions
of the form U <=> I, I <=> N and U <=> N. The user may specify the starting concentrations of the
three kinetic species, as well as the six rate constants and the time scale for plotting.
Homology Modeling Servers
- construct_homolog_PDB
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This server produces a homology model of a protein from three inputs: (1) a FASTA file for
sequence of the homologous protein of unknown structure, (2) a PDB file for the parent structure;
and (3) a sequence alignment (in FASTA, MSF, CLUSTAL or PIR format) that includes sequences
similar to (ideally, identical to) both the homolog and parent PDB sequences. The resulting
homolog PDB file has all the corresponding mainchain atoms as well as the sidechain atoms of
exactly matching residues.
- PyMOL_highlight_conserved_residues
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This server reads a file containing one or more sequences (in FASTA, MSF, PIR or CLUSTAL format),
and generates a PyMOL macro file that highlights the absolutely conserved residues (i.e., those
that are identical in all sequences) in magenta and the conserved residues (those present in >50%
of the aligned sequences with identity of greater than the specified threshold) in purple.
- MOLMOL_highlight_conserved_residues
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This server reads a file containing one or more sequences (in FASTA, MSF, PIR or CLUSTAL format),
and generates a MOLMOL macro file that highlights the absolutely conserved residues (i.e., those
that are identical in all sequences) in magenta and the conserved residues (those present in >50%
of the aligned sequences with identity of greater than the specified threshold) in purple.
Ultracentrifugation Servers
- predict_sedimentation_equilibrium_plot
-
This server predicts the plot of normalized concentration of a single solute versus radius once sedimentation equilibrium
has been reached. The solute mass, temperature, rotation rate, cell geometry, solution density and solute partial specific
volume may all be specified. Useful for choosing a rotation rate for an expected molecular weight.
- view_Beckman_files
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This server reads one or more Beckman file and plots their optical signals.
- sedimentation_equilibrium_fit
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This server reads a Beckman file and fits the scan to the equilibrium distribution of one or more
independently sedimenting species.
- compute_mass_from_equilibrium_fit
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This server determines the buoyant and true mass from an exponential fit to
a sedimentation equilibrium ultracentrifugation run.
- compute_mass_from_Svedbergs
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This server estimates the true mass from the sedimentation coefficient s (in Svedbergs)
and other hydrodynamic data for a sedimentation velocity run. It estimates the mass
if the protein is spherical, and also for a specified range of axial ratios.
- convert_buoyant_to_true_mass
-
This server converts buoyant mass to true mass by dividing by the factor
[1.0 - (solution_density)*(solute_partial_specific_volume)].
Sequence Manipulation Servers
- format_sequence_file
-
This server formats a sequence or sequence-alignment file into any of several
file formats, including the FASTA, MSF, CLUSTAL, and PIR. Minor anomalies
in the original format are corrected (e.g., unexpected spaces or too many comment lines).
Other parameters include sequence capitalization and number of residues/line.
- translate_sequence_file
-
This server translates a DNA or RNA sequence into an amino-acid sequence using
one of several codon translation tables.
- cull_segment_of_sequence_file
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It's useful sometimes to extract a portion of a single sequence or full-length MSA. This server
reads in a sequence file (in FASTA, MSF, PIR or CLUSTAL format) containing one or more sequences
and creates a new sequence file for the sequence(s) between two residue limits.
- check_for_redundant_sequences
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This server calculates the sequence identity and longest segment of identical residues for every pair of
sequences found in a sequence file (which may be in FASTA, MSF, PIR or CLUSTAL format). The results are
sorted and presented in descending order of sequence identity. Useful for checking that a set of homologous
sequences does not contain redundant sequences.
- remove_redundant_sequences
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This server reads a file containing one or more sequences (in FASTA, MSF, PIR or CLUSTAL format),
and generates a revised sequence file in which no pair of sequences are closer than a specified amount.
- order_sequences_by_length
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This server reads a file containing one or more sequences (in FASTA, MSF, PIR or CLUSTAL format),
and ranks the sequences by their number of residues.
- filter_sequences_by_length
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This server reads a file containing one or more sequences (in FASTA, MSF, PIR or CLUSTAL format),
and generates a revised sequence file in which the length of every sequence falls between two specified limits.
- remove_deletions_from_sequence_file
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This server reads a file containing one or more sequences, and generates a revised sequence file in
which all deletions have been eliminated. Useful for getting the original sequences from a sequence alignment.
- resequence_PDB_file
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This server reads in a FASTA file and a PDB file, and assigns the
FASTA sequence to the PDB file. If the FASTA sequence has fewer
residues than the PDB structure, the original sequence is retained.
Sequence Analysis Servers
- sequence_molecular_weight
-
This server predicts the molecular weight for various types of
sequences (protein, nucleic acids, etc.) in various file formats.
- sequence_elemental_composition
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This server calculates the elemental composition for various types of
sequences (protein, nucleic acids, etc.) in various file formats.
- sequence_partial_specific_volume
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This server predicts the partial specific volume, molecular volume and molecular radius for various types
of sequences (protein, nucleic acids, etc.) in various file formats.
- sequence_translational_diffusion_constant
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This server predicts the diffusion constant for various types
of sequences (protein, nucleic acids, etc.) in various file formats.
- sequence_rotational_time_constants
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This server predicts the time constants for thermal rotational equilibration for various types
of sequences (protein, nucleic acids, etc.) in various file formats.
- find_motifs_in_sequence_file
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This server locates all instances of one or more motifs within a sequence file. Wild-card residues
may be denoted with an "X", e.g., the motif "PXXPXG". The sequence file may be in FASTA, MSF, PIR
or CLUSTAL format, and may contain multiple sequences.
- identify_cleavage_peptides
-
This server identifies all cleavage peptides within a specified range of molecular weights. The
cleavage site sequence is specified by 1-letter codes with a forward slash indicating the cleavage
site. For example, the cleavage site of Glu-C (which cuts after glutamate) would be denoted as
"E/". Similarly, the BamH1 restriction site would be represented by "G/GATCC".
- identify_peptides_within_Mw_range
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This server identifies all peptides within a specified range of molecular weights.
- identify_antigenic_peptides
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This server ranks peptides of a specified length by their charge or polarity, which
are correlated with antigenicity. More sophisticated servers for predicting antigenicity
are HLA_Bind and
SYFPEITHI.
- make_FASTA_from_PDB
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This server extracts the residue sequence of a protein in a PDB file,
using either its SEQRES or ATOM records.
- FASTA_sequence_composition
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This server determines the amino-acid compositions of a protein sequence,
and identifies unusually high or low contents of amino-acid types. It also
computes the nominal molecular weight and charge at neutral pH.
Sequence Alignment Servers
- align_two_sequences
-
This server finds the optimal alignment of two FASTA sequences (whether peptide or nucleic acid).
The gap opening and extension penalties can be specified. The residue scoring matrix defaults
to (+5/-5) for match/mismatch, but the BLOSUM62 matrix is preferable for aligning protein sequences.
The sequences may be aligned locally (Smith-Waterman algorithm) or globally (Needleman-Wunsch algorithm).
Good for checking sequencing results!
- analyze_sequence_alignment
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This server reads a sequence alignment (in FASTA, MSF, PIR or CLUSTAL format) and prints it out in
an easy-to-read BLAST-like format. For each position in the alignment, the program prints the fraction
of sequences present, the consensus sequence and the degree of conservation, as assessed by three measures:
mean distance, HSSP distance and sequence entropy.
- MOLMOL_highlight_conserved_residues
-
This server reads a file containing one or more sequences (in FASTA, MSF, PIR or CLUSTAL format),
and generates a MOLMOL macro file that highlights the absolutely conserved residues (i.e., those
that are identical in all sequences) in magenta and the conserved residues (those present in >50%
of the aligned sequences with identity of greater than the specified threshold) in purple.
- rank_insertion_sites
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This server reads a sequence alignment (in FASTA, MSF, PIR or CLUSTAL format) and predicts good
sites for making insertions.
- sequence_profile
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This server reads a sequence alignment (in FASTA, MSF, PIR or CLUSTAL format) and generates
the corresponding sequence profile, i.e., the percentage amino-acid composition at every residue.
Secondary Structure Servers
- visualize_secondary_structure_predictions
-
This server reads in up to five secondary-structure predictions, converts them
to standard 3-state format and makes a colorbar graph of them.
- secondary_structure
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This server reads a PDB file and determines the secondary structure in three
ways: (1) from the HELIX and SHEET records in the PDB file; and (2) from a
DSSP file, if present; and (3) using the rules of DSSP. The results are
compared to any secondary structure predictions, if present.
- format_secondary_structure_prediction
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This server reads in sundry types of secondary-structure prediction files (e.g., PsiPRED, SAM, PROF, and SABLE)
and converts them to a standard 3-state format.
Molecular Visualization Servers
- generate_MOLMOL_macro
-
The program MOLMOL produces publication-quality pictures of molecules (including
ribbon diagrams, surfaces, etc.) and is one of the best molecular visualization packages.
This server extends MOLMOL by writing macros that can be interpreted by it, e.g.,
for coloring ribbons in rainbow colors from N- to C-terminus.
Structure Analysis Servers
- dihedral_angles
-
This server determines the backbone dihedral angles phi, psi and omega,
all the sidechain chi angles, the rotamer types and the secondary structure
of each residue. The results can be filtered to show the dihedral angles
of particular residues, e.g., all lysines, all residues with a trans chi1 rotamer, etc.
Structure Modification Servers
- backbone_CA_idealizer
-
This server idealizes a given PDB structure to have a specific bond geometry,
e.g., the Engh & Huber bond geometry, planar peptide bonds or exact sp2/sp3 geometry.
It minimizes the discrepancies between the given structure and one having the
specified bond geometry, using an energy function that penalizes incorrect
CA positions and CA-CA distances.
Structure Generation Servers
- generate_ideal_helix
-
This server is primarily for teaching purposes. It generates an ideal helix
(of arbitrary repeating backbone dihedral angles) and writes it to a PDB file.
- generate_spherical_shell_of_atoms
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This server generates a spherical shell of atoms as follows.
The atoms are placed on M layers spaced equally in cos(theta), where theta is the
altitude angle in a spherical coordinate system. Within each layer, N atoms are
spaced equally in the azimuthal angle phi. This server allows you to choose M
and N, and also whether to include atoms at the North and South poles. By
varying M and N, you can get cool polyhedra and maybe even a buckyball!
Hydrodynamic Servers
- compute_molecular_weight_from_translational_diffusion_constant
-
This server estimates the molecular weight from the translational
diffusion constant, the temperature and the solution viscosity.
The estimated molecular weight depends on the effective shape
of the protein, which is usually treated as an ellipsoid of
revolution. Such ellipsoidal shapes are described by the axial
ratio p = a/b, which is the ratio of the lengths of
the axial semiaxis a and an equatorial semiaxis b.
- compute_molecular_weight_from_larger_rotation_tau
-
This server estimates the molecular weight from the larger (i.e., longer, slower) of
two rotational time constants, as well as the temperature and the solution viscosity.
The estimated molecular weight depends on the effective shape
of the protein, which is usually treated as an ellipsoid of
revolution. Such ellipsoidal shapes are described by the axial
ratio p = a/b, which is the ratio of the lengths of
the axial semiaxis a and an equatorial semiaxis b.
- compute_molecular_weight_from_smaller_rotation_tau
-
This server estimates the molecular weight from the smaller (i.e., shorter, faster) of
two rotational time constants, as well as the temperature and the solution viscosity.
The estimated molecular weight depends on the effective shape
of the protein, which is usually treated as an ellipsoid of
revolution. Such ellipsoidal shapes are described by the axial
ratio p = a/b, which is the ratio of the lengths of
the axial semiaxis a and an equatorial semiaxis b.
- plot_Perrin_translational_friction_factor
-
This server produces a plot of the Perrin translational friction factor F
versus the axial ratio p = a/b of an ellipsoid of revolution, where a is the
length of the semiaxis of rotation, and b is the length of an equatorial semiaxis.
Thus, p >1 for prolate (cigar-shaped) ellipsoids, and p <1 for oblate
(disc-shaped) ellipsoids; for spheres, p=1.
- plot_Perrin_rotational_friction_factors
-
This server produces a plot of the two Perrin rotational friction factors Fa and Fb
versus the axial ratio p = a/b of an ellipsoid of revolution, where a is the
length of the semiaxis of rotation, and b is the length of an equatorial semiaxis.
Thus, p >1 for prolate (cigar-shaped) ellipsoids, and p <1 for oblate
(disc-shaped) ellipsoids; for spheres, p=1.
- plot_intrinsic_viscosity_shape_factor
-
This server produces a plot of the intrinsic viscosity shape factor ν (also known as the Simha factor)
versus the axial ratio p = a/b of an ellipsoid of revolution, where a is the
length of the semiaxis of rotation, and b is the length of an equatorial semiaxis.
Thus, p >1 for prolate (cigar-shaped) ellipsoids, and p <1 for oblate
(disc-shaped) ellipsoids; for spheres, p=1.
Scattering Servers
- neutron_scattering_intensity
-
This server generates the predicted neutron scattering plot (intensity vs. Q) from a PDB file and
a specified isotopic substitution.
- compare_neutron_scattering_intensities
-
This server generates the predicted neutron scattering plot (intensity vs. Q) from a PDB file
for a specified isotopic substitution (shown in red) and for the unsubstituted structure (shown in blue).
Good for showing the effects of different isotopic substitutions on scattering.
- neutron_scattering_intensity_2conformations
-
This server generates the predicted neutron scattering plot (intensity vs. Q) for two PDB files and
a specified isotopic substitution. It also computes the RMSD between the two plots and the CA RMSD as well.
Very good for assessing the sensitivity of neutron scattering to small changes in protein conformation.
Spectroscopy Servers
- carbonyl_13C_chemical_shift_spectrum
-
This server generates a generic carbonyl 13C chemical shift spectrum from a FASTA file, the fractional
incorporation and secondary structure percentages.
Density Map Servers
- density_map_from_PDB
-
This server generates an electron density map (in binary MRC format) for a given
chain (or all chains) in a PDB file. The atoms of the PDB file are smoothed
into Gaussians of a specified radius. The resulting map may be viewed using
any electron density viewer, e.g., Chimera.
Optionally, the sidechains can be deleted to help visualize the chain trace.
Data Analysis Servers
- convert_Xfig_file
-
This server converts an Xfig file into one of several graphics languages.
- plot_xydata
-
This server provides a publication-quality plot of up to 15 data sets in different colors.
Titles, subtitles, axis labels, etc. can all be specified. Linear and logarithmic scales
are available for both axes, as are various settings for tick marks.
- linear_fit
-
This server carries out and plots linear regression on two columns of data in a file.
Titles, subtitles, axis labels, etc. can all be specified. Linear and logarithmic scales
are available for both axes, as are various settings for tick marks.
Mathematical Servers
- solve_mathematical_equation
-
This server finds all solutions (including complex and infinite solutions) for
several types of polynomial and trigonometic equations.
Map Projection Servers
- map_graticule
-
This server produces a map graticule (regularly spaced parallels of latitude
and meridians of longitude)
and projects it into 2D using famous and/or cool-looking map projections.
- Tissot_indicatrices
-
This server generates the Tissot indicatrices at regularly spaced latitudes and longitudes,
then projects them into 2D using various map projections.
- map_projection
-
This server reads vectors from a data file (specified by 3D Cartesian coordinates, latitude/longitude
pairs or altitude/azimuth pairs) and projects them into 2D using famous and/or cool-looking map projections.
