BioLiP2 an updated structure database for biologically
SUPPLEMENTARY INFORMATION zhanggroup org
We developed the BioLiP2 database https zhanggroup org BioLiP to extract biologically relevant protein ligand interactions from the PDB database BioLiP2 assesses the functional relevance of the ligands by geometric rules and experimental literature validations
Zang Group
I TASSER server new development for protein structure and
Org Lett 16 1546 1549 2014 Article Google Scholar Supplementary information Supplementary Information Supplementary Figs 1 23 and Tables 1 6 Source data
ZHANG Yang NUS Computing
Supplementary Information Introduction SSIPe is a method to calculate binding affinity changes Î Î G of protein protein interactions PPIs upon mutations at protein protein interface The method is a significant extension of BindProf BindProfX by integrating PPI interface structural profiles with sequence profiles and physics based
Supplementary Information Zhanggroup Org
Phys Rev Lett 133 236704 2024 Spiral Spin Liquid in a
Supplementary Figure 5 Detailed molecular models that highlight ASH2L IDRs and SPRY regions that undergo DPY30 induced changes in NMR spectra This figure is related to main Figure 4b Newly appeared peaks are highlight by sphere representation in the ASH2L DPY30 structural model SPRY green Linker IDRs blue Loop IDRs orange SDI pink
Topological semimetals with intrinsic chirality as spin
Zhang Group Zhang Group Family Office
SUPPLEMENTARY TEXTS Text S1 Contact selection based on effective number of homologous sequences N f and protein length According to the performance shown in Table S13 and S14 based on the training proteins Dataset S1 in SI the contact predictors are classified into four categories i NeBcon 1 ResPRE 2 and DeepPLM as very high ii
Dr Yang Zhang is a Professor in the Department of Computer Science the School of Computing National University of Singapore NUS He also serves as a Professor in the Department of Biochemistry at the Yong Loo Lin School of Medicine NUS and the Cancer Science Institute of Singapore
1 Supplemental information 2 3 A SPX domain vacuolar transporter links phosphate sensing and homeostasis in 4 Arabidopsis 5 6 Mingda Luan Fugeng Zhao Guangfang Sun Min Xu Aigen Fu Wenzhi Lan Sheng Luan 7 8 9 Correspondence 10 Sheng Luan sluan berkeley edu 11 12 Running Title 13 An autoinhibitory Pi sensor transporter 14 15 16
US align universal structure alignments of proteins nucleic
DeepFold is a program for ab initio protein structure prediction using deep learning restraints developed by Robin Pearce robpearc umich edu at the Zhang Lab The DeepFold online server can be found at https zhanggroup org DeepFold INSTALLATION AND IMPLEMENTATION OF THE DEEPFOLD SUITE
We probe electronic properties and study chemistry at molecular level We have opennings for PhD postdoc and research assisstant positions Additional fellowship for both PhD and postdoc positions from CAS is available for international applicants
GPU I TASSER a GPU accelerated I TASSER protein structure
In this article we report on the recent developments made to the I TASSER server which have dramatically improved the quality of the I TASSER modeling and the functionality of the server system
Services and tools developed in the Yang Zhang Lab
On a benchmark dataset of 71 protein structures GPU I TASSER achieves on average a 10 speedup with comparable structure prediction accuracy compared to the CPU version of the I TASSER The complete source code for GPU I TASSER can be downloaded and used without restriction from https zhanggroup org GPU I TASSER
SUPPLEMENTARY INFORMATION zhanggroup org
GPU I TASSER a GPU accelerated I TASSER protein Europe PMC
I TASSER Iterative Threading ASSEmbly Refinement is a hierarchical approach to protein structure prediction and structure based function annotation It first identifies structural templates from the PDB by multiple threading approach LOMETS with full length atomic models constructed by iterative template based fragment assembly simulations
Founded in 1995 by serial entrepreneur philanthropist and real estate investor Henry Zhang the Zhang Group is a single family office with investment globally dedicated to investing in revolutionary projects that push the boundaries of industry
在 71 种蛋白质结构的基准数据集上 与 I TASSER 的 CPU 版本相比 GPU I TASSER 平均实现了 10 倍的加速 结构预测精度相当 可用性和实现 GPU I TASSER 的完整源代码可以从 https zhanggroup org GPU I TASSER 不受限制地下载和使用
I TASSER server for protein structure and function prediction
GPU I TASSER GPU 加速的 I TASSER 蛋白质结构预测工具 Bioinformatics
Supplementary Text 1 Benchmark set using synthesized density maps To evaluate DEMO EM we collected a set of 357 redundantnon proteins from the PDB with the domain boundary
The frustrated honeycomb spin model can stabilize a subextensively degenerate spiral spin liquid with nontrivial topological excitations and defects but its material realization remains rare Here we report the experimental realization of this model in the structurally disorder free compound GdZnPO Using a single crystal sample we find that spin 7 2 rare earth mathrm Gd 3 ions
We developed the BioLiP2 database https zhanggroup org BioLiP to extract biologically relevant protein ligand interactions from the PDB database BioLiP2 assesses the functional
Supplementary Information Zhanggroup Org
GitHub robpearc DeepFold
Supplemental information
Supplementary Table 1 The average standard error of mean SEM and values for p TM score RMSD and alignment coverage in oligomeric structure alignments
Availability and implementation The complete source code for GPU I TASSER can be downloaded and used without restriction from https zhanggroup org GPU I TASSER Supplementary information Supplementary data are available at Bioinformatics online
Supplementary Information Supplementary Texts zhanggroup org
BioLiP2 an updated structure database for biologically