J. Collins

发表

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists

Brad T. Sherman, Robert M. Stephens, Jean A. Roayaei, 2007, Genome Biology.

(Salen)Mn(III)-catalyzed epoxidation reaction as a multichannel process with different spin states. Electronic tuning of asymmetric catalysis: a theoretical study.

J. Collins, Y. Abashkin, S. Burt, 2001, Inorganic chemistry.

Theoretical study of the product specificity in the hydroxylation of camphor, norcamphor, 5,5-difluorocamphor, and pericyclocamphanone by cytochrome P-450cam.

J. Collins, G. Loew, 1988, The Journal of biological chemistry.

Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design.

R E Cachau, T. Bhat, J. Collins, 1994, Proceedings of the National Academy of Sciences of the United States of America.

A Comparison of Biomarker and Fingerprint-Based Classifiers of Disease

B. Luke, J. Collins, 2012 .

Design of sensitive fluorogenic substrates for human cathepsin D

J. Collins, S. Gulnik, L. Suvorov, 1997, FEBS letters.

Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from Plasmodium falciparum.

R E Cachau, P. Collins, T. Bhat, 1996, Proceedings of the National Academy of Sciences of the United States of America.

On photoabsorption of the neutral form of the green fluorescent protein chromophore.

I. Polyakov, J. Collins, B. Grigorenko, 2009, Biophysical chemistry.

The Role of Methylation in the Intrinsic Dynamics of B- and Z-DNA

N. A. Temiz, D. Donohue, B. Luke, 2012, PloS one.

Qualitative assessment of IC50 values of inhibitors of the neuronal nicotinic acetylcholine receptor using a single chromatographic experiment and multivariate cluster analysis.

J. Collins, S. Ravichandran, R. Moaddel, 2005, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

Calculated and experimental absolute stereochemistry of the styrene and .beta.-methylstyrene epoxides formed by cytochrome P 450cam

P. Ortiz de Montellano, J. Collins, D. L. Camper, 1992 .

Decoding nitric oxide release rates of amine-based diazeniumdiolates.

J. Collins, J. Ivanic, L. Keefer, 2013, The journal of physical chemistry. A.

Can structural features of kinase receptors provide clues on selectivity and inhibition? A molecular modeling study.

B. Luke, J. Collins, S. Ravichandran, 2015, Journal of molecular graphics & modelling.

The somatic autosomal mutation matrix in cancer genomes

N. A. Temiz, R. Stephens, M. Yi, 2015, Human Genetics.

Comparing biomarkers and proteomic fingerprints for classification studies

T. Veenstra, T. Ried, B. Luke, 2013 .

Homology modeling of a heme protein, lignin peroxidase, from the crystal structure of cytochrome c peroxidase.

J. Collins, G. Loew, P. Du, 1992, Protein engineering.

Modeling Structures and Spectra of Fluorescent Proteins in the Coordinate-Locking Cluster Approach: Application to the Photoswitchable Protein AsFP595

J. Collins, A. Nemukhin, I. Topol, 2012 .

Long homopurine•homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region

R. Stephens, M. Yi, R. Lempicki, 2006, Nucleic acids research.

Theoretical Studies of Cytochrome P-450

B. Luke, J. Collins, G. Loew, 1986 .

Theoretical studies of cytochrome P-450. Characterization of stable and transient active states, reaction mechanisms and substrate-enzyme interactions.

B. Luke, J. Collins, G. Loew, 1986, Enzyme.

Theoretical investigations of terminal alkenes as putative suicide substrates of cytochrome P-450

A. D. McLean, B. Luke, J. Collins, 1990 .

THEORETICAL AND EXPERIMENTAL ANALYSIS OF THE ABSOLUTE STEREOCHEMISTRY OF CIS-BETA -METHYLSTYRENE EPOXIDATION BY CYTOCHROME P450CAM

J. Collins, D. L. Camper, G. Loew, 1991 .

Proteomic Analysis Identifies Oxidative Stress Induction by Adaphostin

D. Newton, J. Collins, M. Hollingshead, 2007, Clinical Cancer Research.

Quantum mechanical study of putative intermediates in adduct formation by the suicide substrate ethylene with cytochrome P-450

B. Luke, J. Collins, G. Loew, 2009 .

Calculated electronic spectra of model ferric cytochrome P450 complexes

M. Zerner, J. Collins, G. Loew, 1986 .

An exhaustive DNA micro-satellite map of the human genome using high performance computing.

Bill Long, Bert Gold, Michael Dean, 2003, Genomics.

Spin density distribution in oxygen-liganded model heme proteins: Predictions of 17O hyperfine broadening of ESR spectra of metmyoglobin, cytochrome c peroxidase, catalase, and cytochrome P450

J. Collins, G. Loew, A. Waleh, 1987 .

Dynamic Flexibility of Protein−Inhibitor Complexes: A Study of the HIV-1 Protease/KNI-272 Complex

J. Collins, R. Kato, Xincai Luo, 1998 .

The full versus the virtual counterpoise correction for basis set superposition error in self-consistent field calculations

J. Collins, G. Gallup, 1986 .

Thioanisole Sulfoxidation by Cytochrome P450cam (CYP101): Experimental and Calculated Absolute Stereochemistries

J. Collins, G. Loew, J. Fruetel, 1994 .

Structure‐based subsite specificity mapping of human cathepsin D using statine‐based inhibitors

J. Collins, S. Gulnik, J. Erickson, 1997, Protein science : a publication of the Protein Society.

A molecular model of the enantioselective liquid chromatographic separation of (R,S)-ifosfamide and its N-dechloroethylated metabolites on a teicoplanin aglycon chiral stationary phase.

J. Collins, S. Ravichandran, Nagendra S. Singh, 2012, Journal of chromatography. A.

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools

Ming Yi, Duncan E. Donohue, Albino Bacolla, 2012, Nucleic Acids Res..

Theoretical investigation of the role of clay edges in prebiotic peptide bond formation

B. Luke, J. Collins, G. Loew, 1988, Origins of life and evolution of the biosphere.

Guanine Holes Are Prominent Targets for Mutation in Cancer and Inherited Disease

Ming Yi, Natalia Volfovsky, Jack R. Collins, 2013, PLoS genetics.

Energy surfaces in the cyclopropane radical ion and the photoelectron spectrum of cyclopropane

J. Collins, G. Gallup, 1982 .

Erratum to: The somatic autosomal mutation matrix in cancer genomes

R. Stephens, M. Yi, D. Cooper, 2015, Human Genetics.

The somatic autosomal mutation matrix in cancer genomes

R. Stephens, M. Yi, D. Cooper, 2015, Human Genetics.

Contributions to interatomic and intermolecular forces: II. Interaction energy of two He atoms

J. Collins, G. Gallup, 1983 .

Practical Valence-Bond Calculations

J. R. Collins, J. M. Norbeck, J. Collins, 1982 .

Structure and bonding of the remarkable donor acceptor complexes XBeO X NH NMe CO N C H C H H H CO O 3 3 2 2 2 2 4 2 2 2

J. Collins, G. Frenking, S. Dapprich, 1996 .

Searching for Non‐B DNA‐Forming Motifs Using nBMST (Non‐B DNA Motif Search Tool)

Kevin H. Bruce, R. Stephens, D. Donohue, 2012, Current protocols in human genetics.

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes

Ming Yi, Kevin H. Bruce, Albino Bacolla, 2010, Nucleic Acids Res..

Human topoisomerase I inhibition: docking camptothecin and derivatives into a structure-based active site model.

Y. Pommier, D. Jerina, B. Luke, 2002, Biochemistry.

Non-B DNA-forming Sequences and WRN Deficiency Independently Increase the Frequency of Base Substitution in Human Cells*

D. Cooper, J. Collins, A. Bacolla, 2011, The Journal of Biological Chemistry.

Interaction of noncompetitive inhibitors with the alpha3beta2 nicotinic acetylcholine receptor investigated by affinity chromatography and molecular docking.

J. Collins, S. Ravichandran, R. Moaddel, 2007, Journal of medicinal chemistry.

Interaction of noncompetitive inhibitors with an immobilized alpha3beta4 nicotinic acetylcholine receptor investigated by affinity chromatography, quantitative-structure activity relationship analysis, and molecular docking.

Jack R Collins, J. Collins, S. Ravichandran, 2004, Journal of medicinal chemistry.

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties.

Aleksandar Milosavljevic, Peter D Stenson, David N Cooper, 2008, Genome research.

Introducing the non-B DNA Motif Search Tool (nBMST)

R. Stephens, M. Yi, D. Donohue, 2011, Genome Biology.

Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from P. Falciparum

Jack R. Collins, Pavel Majer, Raul E. Cachau, 1996 .

Structural conservation of interferon gamma among vertebrates.

J. Collins, H. Young, R. Savan, 2009, Cytokine & growth factor reviews.

Modeling absorption of the kindling fluorescent protein with the neutral form of the chromophore

J. Collins, A. Nemukhin, A. Savitsky, 2012 .

The Use of Urine Proteomic and Metabonomic Patterns for the Diagnosis of Interstitial Cystitis and Bacterial Cystitis

T. Veenstra, H. Issaq, B. Luke, 2004, Disease markers.

Rational design and synthesis of conformationally constrained inhibitors of human cathepsin D

J. Collins, S. Gulnik, J. Erickson, 2002 .

Examining the significance of fingerprint-based classifiers

Jack R. Collins, Brian T. Luke, B. Luke, 2008, BMC Bioinformatics.

Reply to “does the boys and bernardi function counterpoise method actually overcorrect the basis set superposition error?”

J. Collins, G. Gallup, 1986 .

AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes

Jack R. Collins, Brian T. Luke, Hue Vuong, 2015, Bioinform..

Comparison of computational models for simulating heme proteins: A study of cytochrome C peroxidase

J. Collins, G. Loew, 1992 .

Estimating orientation factors in the FRET theory of fluorescent proteins: the TagRFP-KFP pair and beyond.

J. Collins, A. Nemukhin, M. Khrenova, 2015, Biophysical journal.

A generalized method for the superposition of resonance structures

J. Collins, G. Gallup, 1991 .

Are there neutral helium compounds which are stable in their ground state?: A theoretical investigation of HeBCH and HeBeO

J. Collins, G. Frenking, W. Koch, 1986 .

Modeling spectral tuning in monomeric teal fluorescent protein mTFP1.

Jack Collins, J. Collins, A. Nemukhin, 2010, Biophysical chemistry.

Multiphoton Photochemistry of Red Fluorescent Proteins in Solution and Live Cells

M. Drobizhev, T. Hughes, A. Rebane, 2014, The journal of physical chemistry. B.

Helium chemistry: theoretical predictions and experimental challenge

D. Cremer, J. Collins, G. Frenking, 1987 .

Flap opening in HIV-1 protease simulated by ‘activated’ molecular dynamics

Jack R. Collins, John W. Erickson, Stanley K. Burt, 1995, Nature Structural Biology.

Mechanism of the chemical step for the guanosine triphosphate (GTP) hydrolysis catalyzed by elongation factor Tu.

J. Collins, B. Grigorenko, A. Nemukhin, 2008, Biochimica et biophysica acta.

Activated dynamics of flap opening in HIV-1 protease.

J. Collins, J. Erickson, S. Burt, 1995, Advances in experimental medicine and biology.

Steric and electronic criteria for teratogenicity of short chain aliphatic acids

J. Collins, D. L. Camper, G. Loew, 1990 .

Density Functional Modeling of Ligand-Metal Interactions and Enzymatic Activities in Metalloenzymes

J. Collins, Y. Abashkin, N. Russo, 1996 .

Conformation dependence of pKa's of the chromophores from the purple asFP595 and yellow zFP538 fluorescent proteins.

J. Collins, B. Grigorenko, A. Nemukhin, 2008, Theochem.

Fixation of nitrogen and carbon monoxide by beryllium oxide: theoretical investigation of the structures and stabilities of NNBeO, OCBeO, and COBeO

J. Collins, G. Frenking, W. Koch, 1988 .

AVIA 3.0: interactive portal for genomic variant and sample level analysis

Sarangan Ravichandran, Anney Che, Brian T Luke, 2020, Bioinform..

Molecular dynamics simulations of the resting and hydrogen peroxide-bound states of cytochrome c peroxidase.

J. Collins, G. Loew, P. Du, 1992, Biochemistry.

Theoretical studies on the hydrolysis of mono-phosphate and tri-phosphate in gas phase and aqueous solution.

J. Collins, I. Topol, S. Burt, 2003, Journal of the American Chemical Society.

Valproic acid metabolism by cytochrome P450 : a theoretical study of stereoelectronic modulators of product distribution

Jack R. Collins, Gilda H. Loew, J. Collins, 1991 .

Theoretical investigation of the role of clay edges in prebiotic peptide bond formation

B. Luke, J. Collins, G. Loew, 1988, Origins of life and evolution of the biosphere.

Effect of fluorination of camphor on its binding orientation in p450cam

J. Collins, G. Loew, 1990 .

Introducing the non-B DNA Motif Search Tool (nBMST)

Kevin H. Bruce, R. Stephens, M. Yi, 2011, Genome Biology.

Quantum Chemistry in Studies of Fluorescent and Photosensing Proteins

J. Collins, A. Nemukhin, M. Khrenova, 2013 .