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NMR processing:
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Side-chains:
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NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
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ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
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NMR model quality:
NOEs, other restraints:
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RPF scores
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Chemical shifts:
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Vasco
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RDCs:
DC
Anisofit
Pseudocontact shifts:
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Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
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STAN
Ramachandran Plot
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ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
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Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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Unread 03-15-2005, 08:09 AM
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Project description from Dr. Patel's website:
  • NMR Methods Development
    Our efforts have focused on enhancing isotope labeling methods to aid NMR resonance assignments, coupling constant methods to identify hydrogen bonding alignments, and residual dipolar coupling approaches to speed RNA resonance assignments and monitor junctional architecture and helical dynamics.

  • RNA Architecture and Dynamics
    Our laboratory has initiated a major program to structurally characterize higher order RNA architecture and dynamics using NMR and x-ray crystallography. Current efforts are focused on RNA triplet repeat disease sequences, internal loops, pseudoknots, and junctions.

  • Peptide-RNA Recognition: Viral and Phage Systems
    This project is focused on the structural characterization of the novel folds of bound arginine-rich peptides and the architecture of their RNA binding pockets in viral and phage systems. These studies are based on an approach where the components are minimalist modular domains that undergo adaptive structural transitions on complex formation.

  • Saccharide-RNA Recognition: Aminoglycoside Antibiotics
    Aminoglycoside antibiotics are polycationic saccharides that exhibit therapeutic potential against bacterial infections. Functionally, they interfere with translation and induce bacterial cell death through site-specific targeting of ribosomal 16S RNA. Our research has focused on aminoglycoside antibiotic-RNA complexes, involving tobramycin, neomycin B, apramycin, and streptomycin.

  • Adaptive Recognition in RNA and DNA Aptamers: Cofactors and Amino Acids
    Novel features of nucleic acid structure, recognition, and discrimination have been elucidated through the solution structural characterization of RNA and DNA aptamers that bind cofactors and amino acids with high affinity and specificity. The cofactors include ATP and FMN, while the amino acid studies have focused on argininamide.

  • Protein-RNA Recognition
    This new effort focuses on the crystallographic characterisation of protein-RNA complexes to elucidate the principles associated with molecular recognition. Several areas under current investigation include complexes that participate in RNA translation, transport, localization, and splicing.

  • Multi-stranded DNA Architectures: Triads, Tetrads, and Hexads
    This project is focused on the structure and recognition of multi-stranded DNA architectures adopted by guanine plus adenine rich sequences. Such guanine plus adenine rich sequences are frequently located within gene regulatory regions and recombination hot spot sites at the replication origin of single-stranded bacteriophages, and as tandem repeats in telomeric, centromeric, and triplet repeat disease sequences.

  • Antitumor Drug-DNA Complexes
    This program seeks to elucidate the structure of antitumor drugs bound to their sequence specific sites on DNA duplexes, triplexes, and quadruplexes. The emphasis here is to identify the principles of stacking, hydrogen bonding, and hydrophobic interactions that contribute to the specificity and affinity associated with molecular recognition.

  • Covalent Carcinogenic DNA Adducts
    Human DNA is continuously exposed to a variety of metabolically activated chemical intermediates that react covalently with nucleic acids to form adducts that locally perturb the architecture of duplex DNA. Our studies have focused on structural elucidation of adduct alignment as a function of chirality and sequence context.

  • Protein Structure and Recognition
    This program is a collaborative effort with colleagues at Sloan-Kettering to elucidate protein structures and their complexes. Current efforts are in the area of proteins involved in leukemia, DNA repair, and viral pathogenesis.
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