Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids (Q34188922)

31 July 2017

title

Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids (English)

1 reference

31 July 2017

Bohdan Schneider

1 reference

31 July 2017

Wei Ge

1 reference

31 July 2017

Wilma K Olson

series ordinal

1 reference

31 July 2017

language of work or name

English

0 references

publication date

22 October 2004

1 reference

31 July 2017

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

31 July 2017

page(s)

1166-1190

1 reference

SHELXL: high-resolution refinement

31 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

The CCP4 suite: programs for protein crystallography

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Stereochemistry of polypeptide chain configurations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Crystal structures of nucleosome core particles in complex with minor groove DNA-binding ligands

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Protein and drug interactions in the minor groove of DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

A standard reference frame for the description of nucleic acid base-pair geometry.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Locating monovalent cations in the grooves of B-DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Sequence recognition of DNA by lexitropsins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Water and ion binding around r(UpA)12 and d(TpA)12 oligomers--comparison with RNA and DNA (CpG)12 duplexes.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

A-form conformational motifs in ligand-bound DNA structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Sequence-specific DNA recognition by polyamides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

DNA minor groove recognition of a non-self-complementary AT-rich sequence by a tris-benzimidazole ligand

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Structure of the side-by-side binding of distamycin to d(GTATATAC)2

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Hydration of the phosphate group in double-helical DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

An analysis of the relationship between hydration and protein-DNA interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

A structural basis for recognition of A.T and T.A base pairs in the minor groove of B-DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

A role for CH...O interactions in protein-DNA recognition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Recognition of the four Watson-Crick base pairs in the DNA minor groove by synthetic ligands

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Structural basis for G.C recognition in the DNA minor groove

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Crystal structure of the nucleosome core particle at 2.8 Å resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Targeting the minor groove of DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Crystal structures of the side-by-side binding of distamycin to AT-containing DNA octamers d(ICITACIC) and d(ICATATIC)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Development and validation of a genetic algorithm for flexible docking

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

C-H...O hydrogen bonding in biology

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Designer DNA-binding drugs: the crystal structure of a meta-hydroxy analogue of Hoechst 33258 bound to d(CGCGAATTCGCG)2

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Effects of the A.T/T.A degeneracy of pyrrole--imidazole polyamide recognition in the minor groove of DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Recognition of DNA by designed ligands at subnanomolar concentrations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Hydration of the DNA bases is local

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

GroupBuild: a fragment-based method for de novo drug design

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

A systematic method for studying the spatial distribution of water molecules around nucleic acid bases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Crystal structure of C-T-C-T-C-G-A-G-A-G. Implications for the structure of the Holliday junction

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Binding of two distamycin A molecules in the minor groove of an alternating B–DNA duplex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Flexible ligand docking using a genetic algorithm.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Variability in DNA minor groove width recognised by ligand binding: the crystal structure of a bis-benzimidazole compound bound to the DNA duplex d(CGCGAATTCGCG)2

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

A geometric approach to macromolecule-ligand interactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Crystal structure of a naturally occurring dinucleoside phosphate: Uridylyl 3′,5′-adenosine phosphate model for RNA chain folding

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Double helix at atomic resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

The molecular origin of DNA-drug specificity in netropsin and distamycin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Structural characterization of a 2:1 distamycin A.d(CGCAAATTGGC) complex by two-dimensional NMR.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

The structure of DAPI bound to DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Molecular structure of the netropsin-d(CGCGATATCGCG) complex: DNA conformation in an alternating AT segment

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

The computer program LUDI: a new method for the de novo design of enzyme inhibitors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Structural consequences of a carcinogenic alkylation lesion on DNA: effect of O6-ethylguanine on the molecular structure of the d(CGC[e6G]AATTCGCG)-netropsin complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Anisotropic flexibility of DNA and the nucleosomal structure

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Ligands recognizing the minor groove of DNA: development and applications

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

On the pairing rules for recognition in the minor groove of DNA by pyrrole-imidazole polyamides

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

SPROUT: a program for structure generation.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1305121

Crystalline A-dna: the X-ray analysis of the fragment d(G-G-T-A-T-A-C-C)

28 October 2018

1 reference

12 December 2020

Structure of a B-DNA dodecamer. III. Geometry of hydration

1 reference

12 December 2020

On the prediction of binding properties of drug molecules by comparative molecular field analysis

1 reference

12 December 2020

Do C-H...O hydrogen bonds contribute to the stability of nucleic acid base pairs?

1 reference

12 December 2020

Ordered water structure around a B-DNA dodecamer. A quantitative study

1 reference

12 December 2020

The thermodynamics of polyamide-DNA recognition: hairpin polyamide binding in the minor groove of duplex DNA

1 reference

12 December 2020

B-DNA twisting correlates with base-pair morphology.

1 reference

12 December 2020

THE CRYSTAL AND MOLECULAR STRUCTURE OF D(+)-BARIUM URIDINE-5'-PHOSPHATE

1 reference

12 December 2020

X-ray structures of the B-DNA dodecamer d(CGCGTTAACGCG) with an inverted central tetranucleotide and its netropsin complex

1 reference

12 December 2020

DNA conformation is determined by economics in the hydration of phosphate groups

1 reference

12 December 2020

Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation

1 reference

12 December 2020

10.1529/BIOPHYSJ.104.043612

Identifiers

DOI

1 reference

31 July 2017

1 reference

31 July 2017

1 reference