Jeffrey K (Jeff) Weber  Jeffrey K (Jeff) Weber photo         

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Thomas J. Watson Research Center, Yorktown Heights, NY USA



Combining Docking Pose Rank and Structure with Deep Learning Improves Protein-Ligand Binding Mode Prediction over a Baseline Docking Approach
Joseph A. Morrone, Jeffrey K. Weber, Tien Huynh, Heng Luo, Wendy D. Cornell
Journal of Chemical Information and Modeling 60(9), 4170-4179, 2020

HIV-1 induced changes in HLA-C*03 : 04-presented peptide repertoires lead to reduced engagement of inhibitory natural killer cell receptors
Maja C. Ziegler, Annika Nelde, Jeffrey K. Weber, Christian M. Schreitmuller, Gloria Martrus, Tien Huynh, Madeleine J. Bunders, Sebastian Lunemann, Stefan Stevanovic, Ruhong Zhou, Marcus Altfeld
AIDS 34(12), 1713-1723, 2020
Abstract   natural killer cell, receptor, peptide, human leukocyte antigen, hla c, intracellular, cell, tandem mass spectrometry, cell biology, chemistry

In silico design and validation of high-affinity RNA aptamers targeting epithelial cellular adhesion molecule dimers
David R Bell, Jeffrey K Weber, Wang Yin, Tien Huynh, Wei Duan, Ruhong Zhou
Proceedings of the National Academy of Sciences of the United States of America 117(15), 8486-8493, 2020
Abstract   aptamer, systematic evolution of ligands by exponential enrichment, in silico, virtual screening, rational design, isothermal titration calorimetry, docking, nucleic acid, computational biology, chemistry


Rare Dissipative Transitions Punctuate the Initiation of Chemical Denaturation in Proteins
Jeffrey K. Weber, Seung-gu Kang, Ruhong Zhou
Biophysical Journal 114(4), 812-821, 2018
Abstract   dissipative system, protein folding, entropy production, denaturation, molecular dynamics, non equilibrium thermodynamics, protein structure, protein domain, chemical physics, chemistry

Molecular mechanism of Gd@C82(OH)22 increasing collagen expression: Implication for encaging tumor
Jing Liu, Seung gu Kang, Peng Wang, Yue Wang, Xiaonan Lv, Ying Liu, Fei Wang, Zonglin Gu, Zaixing Yang, Jeffrey K. Weber, Ning Tao, Zhihai Qin, Qing Miao, Chunying Chen, Ruhong Zhou, Yuliang Zhao
Biomaterials152, 24-36, 2018
Abstract   cancer cell, tumor necrosis factor alpha, metastasis, receptor, fibrosarcoma, fibroblast, cancer, cancer research, lung cancer, immunology, biology

T cell receptors for the HIV KK10 epitope from patients with differential immunologic control are functionally indistinguishable
Alok V. Joglekar, Zhe Liu, Jeffrey K. Weber, Yong Ouyang, John D. Jeppson, Won Jun Noh, Pedro A. Lamothe-Molina, Huabiao Chen, Seung-gu Kang, Michael T. Bethune, Ruhong Zhou, Bruce D. Walker, David Baltimore
Proceedings of the National Academy of Sciences of the United States of America 115(8), 1877-1882, 2018
Abstract   t cell, natural killer t cell, epitope, cd8, cytokine secretion, t cell receptor, cytotoxicity, in vitro, molecular biology, chemistry

Patient HLA class I genotype influences cancer response to checkpoint blockade immunotherapy
Diego Chowell, Luc G. T. Morris, Claud M. Grigg, Jeffrey K. Weber, Robert M. Samstein, Vladimir Makarov, Fengshen Kuo, Sviatoslav M. Kendall, David Requena, Nadeem Riaz, Benjamin Greenbaum, James Carroll, Edward Garon, David M. Hyman, Ahmet Zehir, David Solit, Michael Berger, Ruhong Zhou, Naiyer A. Rizvi, Timothy A. Chan
Science 359(6375), 582-587, 2018
Abstract   checkpoint blockade immunotherapy, immune checkpoint, human leukocyte antigen, t cell, antigen, cd8, loss of heterozygosity, cancer, immunology, medicine


Emerging -Sheet Rich Conformations in Supercompact Huntingtin Exon-1 Mutant Structures
Hongsuk Kang, Francisco X. Vazquez, Leili Zhang, Payel Das, Leticia Marisel Toledo-Sherman, Binquan Luan, Michael Levitt, Ruhong Zhou
Journal of the American Chemical Society 139(26), 8820-8827, 2017
Abstract   huntingtin protein, huntingtin, beta sheet, protein secondary structure, molecular dynamics, exon, mutant, hydrogen bond, biophysics, crystallography, chemistry

Phosphatidylserine-Induced Conformational Modulation of Immune Cell Exhaustion-Associated Receptor TIM3
Jeffrey K Weber, Ruhong Zhou
Scientific Reports 7(1), 13579-13579, 2017
Abstract   immune receptor, conformational change, receptor, binding site, protein structure, salt bridge, phosphorylation, small molecule, biophysics, chemistry

Directional mechanical stability of Bacteriophage 29 motors 3WJ-pRNA: Extraordinary robustness along portal axis
Zhonghe Xu, Yang Sun, Jeffrey K. Weber, Yi Cao, Wei Wang, Daniel Jasinski, Peixuan Guo, Ruhong Zhou, Jingyuan Li
Science Advances 3(5), 1-8, 2017
Abstract   molecular motor, prohead, force spectroscopy, dna condensation, helix, coaxial, molecular dynamics, rigidity, biophysics, nanotechnology

Graphene-Induced Pore Formation on Cell Membranes
Guangxin Duan, Yuanzhao Zhang, Binquan Luan, Jeffrey K. Weber, Royce W. Zhou, Zaixing Yang, Lin Zhao, Jiaying Xu, Judong Luo, Ruhong Zhou
Scientific Reports 7(1), 2017
Abstract   membrane, bilayer, graphene, nanomaterials, viability assay, molecular dynamics, cytotoxicity, biophysics, cell, chemistry

PEGylated graphene oxide elicits strong immunological responses despite surface passivation
Nana Luo, Jeffrey K. Weber, Shuang Wang, Binquan Luan, Hua Yue, Xiaobo Xi, Jing Du, Zaixing Yang, Wei Wei, Ruhong Zhou, Guanghui Ma
Nature Communications 8(1), 14537-14537, 2017
Abstract   cytokine secretion, nanomaterials, signal transduction, integrin, cytokine, cell membrane, immune system, membrane, biophysics, nanotechnology, chemistry


Particle Size-Dependent Antibacterial Activity and Murine Cell Cytotoxicity Induced by Graphene Oxide Nanomaterials
Lin Zhao, Guangxin Duan, Zaixing Yang, Jeffrey K. Weber, Xu Liu, Shunyi Lu, Xuanyu Meng, JiaYing Xu
Journal of Nanomaterials2016
Abstract   antibacterial activity, graphene, cytotoxicity, nanomaterials, nanoparticle, particle size, biophysics, cytotoxic t cell, quantum dot, chemistry, nanotechnology

Sequential protein unfolding through a carbon nanotube pore
Xu, Zhonghe and Zhang, Shuang and Weber, Jeffrey K and Luan, Binquan and Zhou, Ruhong and Li, Jingyuan
Nanoscale, Royal Society of Chemistry, 2016

Single-Walled Carbon Nanotubes Inhibit the Cytochrome P450 Enzyme, CYP3A4
Ramy El-Sayed, Kunal Bhattacharya, Zhonglin Gu, Zaixing Yang, Jeffrey K. Weber, Hu Li, Klaus Leifer, Yichen Zhao, Muhammet S. Toprak, Ruhong Zhou, Bengt Fadeel
Scientific Reports 6(1), 21316-21316, 2016
Abstract   cytochrome p 450 cyp3a, enzyme assay, bovine serum albumin, cytochrome p 450 cyp3a inhibitors, polyethylene glycol, metabolite, enzyme, cyp3a4, biophysics, chemistry, biochemistry

Folding and Stabilization of Native-Sequence-Reversed Proteins
Yuanzhao Zhang, Jeffrey K Weber, Ruhong Zhou
Scientific Reports 6(1), 25138-25138, 2016
Abstract   protein design, protein structure, protein structure prediction, protein folding, amino acid, molecular dynamics, computational biology, chemistry, native protein, protein size

Tunable, Strain-Controlled Nanoporous MoS2 Filter for Water Desalination
Weifeng Li, Yanmei Yang, Jeffrey K. Weber, Gang Zhang, Ruhong Zhou
ACS Nano 10(2), 1829-1835, 2016
Abstract   desalination, nanoporous, nanosheet, nanopore, seawater, graphene, nanotechnology, materials science, fresh water, water desalination


A novel form of -strand assembly observed in A(33-42) adsorbed onto graphene
Xiaofeng Wang, Jeffrey K. Weber, Lei Liu, Mingdong Dong, Ruhong Zhou, Jingyuan Li
Nanoscale 7(37), 15341-15348, 2015
Abstract   hydrophobic effect, antiparallel, peptide, hydrogen bond, molecule, molecular dynamics, graphene, biophysics, adsorption, combinatorial chemistry, chemistry

Surface curvature relation to protein adsorption for carbon-based nanomaterials
Gu, Zonglin and Yang, Zaixing and Chong, Yu and Ge, Cuicui and Weber, Jeffrey K and Bell, David R and Zhou, Ruhong
Scientific reports5, 10886, Nature Publishing Group, 2015

A Peptide-Coated Gold Nanocluster Exhibits Unique Behavior in Protein Activity Inhibition
Deyi An, Jiguo Su, Jeffrey K. Weber, Xueyun Gao, Ruhong Zhou, Jingyuan Li
Journal of the American Chemical Society 137(26), 8412-8418, 2015
Abstract   peptide, protein structure, nanoclusters, active site, static electricity, nanoparticle, surface modification, coating, biophysics, chemistry, nanotechnology

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