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Jianlin Cheng - Professor (Full) • Doctorate/PhD
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Jianlin Cheng

Professor (Full) • Doctorate/PhD

University of Missouri System • University of Missouri • Columbia, United States of America

Skills and expertise

Omics and technologies

  • Genome edition
  • cryo-EM
  • Protein interaction analysis

Programming languages

  • C++

Languages

  • English

Tools maintained

Qprob

Web
Desktop

Qprob

(1) 0 discussion(s)
A single-model quality assessment (QA) method. Different from other single-model QA methods, Qprob estimates the prediction error estimation of several different physicochemical, structural and…

Apollo

Desktop
Web

Apollo / Assessing Protein single or multiple models

(1) 0 discussion(s)
A web server to provide the community with access to all three model quality assessment approaches (i.e. single, clustering and hybrid). Apollo evaluates the absolute global and local qualities of a…

Hierarchical3DGenome

Desktop

Hierarchical3DGenome

(0) 0 discussion(s)
Constructs high-resolution 3D genome structures. Hierarchical3DGenome is an application that is able to reconstruct high-resolution models of chromosomes by applying a seven-steps process. The…

GenomeFlow

Desktop

GenomeFlow

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Constructs and investigates 3D genome models. GenomeFlow incorporates modeling with functional genomics data. It can serve for the recognition of chromosomal contacts by mapping raw Hi-C pair-end…

3DMax

Desktop

3DMax

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Reconstructs the 3D structure of chromosomes from Hi-C data. 3DMax combines the maximum likelihood inference approach with a gradient ascent method. It constructs optimized structures for…

DeepSF

Web

DeepSF

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Classifies proteins of variable-length into all known folds defined in SCOP 1.75 database. DeepSF is a 1D deep convolution neural network method that directly extracts hidden features from any…
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GMOL

Desktop

GMOL

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Facilitates visualization of genome structure. GMOL was created for Jmol. It adds and modifies several additional functions to make genome structure visualization possible and sufficient. This tool…

ClusterTAD

Desktop

ClusterTAD / clustering-based TAD detection method

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Detects Topologically Associated Domains (TADs) from Hi-C data. ClusterTAD is a clustering based method that employs standard clustering algorithms to extract topological domains from Hi-C contact…

HMMsato

Desktop

HMMsato

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Provides a method for improving profile-profile alignments. HMMsato binds torsion angles, relative solvent accessibility and evolutionary residue into Hidden Markov Mode (HMM)-based pairwise…

PSpro

Desktop

PSpro

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Allows users to forecast protein secondary structure (SS). PSpro is also efficient in predicting residue-residue contacts, contact map and solvent accessibility.

Betacon

Desktop

Betacon

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Predicts beta-sheet topology in proteins.

DNTor

Desktop

DNTor

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Calculates protein torsion angle prediction. DNTor is a deep learning machine that considers four methods: Deep Neural Network, Deep Recurrent Neural Network, Deep Restricted Boltzmann Machines and…

Chromosome3D

Web
Desktop

Chromosome3D

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Reconstructs chromosome three-dimensional models using distance restraints obtained from Hi-C interaction frequency (IF) data. Chromosome3D is robust with respect to the change of the granularity of…

DeepQA

Desktop

DeepQA

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A single-model quality assessment method based on deep belief network that utilizes a number of selected features describing the quality of a model from different perspectives, such as energy,…

LorDG

Desktop

LorDG / Lorentzian 3D Genome

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A restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data. LorDG method is robust to noise and performed well in…

UniCon3D

Desktop

UniCon3D

(0) 0 discussion(s)
A de novo protein structure prediction method that performs stepwise synthesis and assembly of foldon units via conditional sampling from a novel united-residue probabilistic model, which captures…

MTMG

Desktop

MTMG / Multi-Template Model Generation

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A stochastic point cloud sampling method to address the challenges in generating structural models from multiple templates. MTMG first superposes the backbones of template structures, and the Cα…

SMOQ

Desktop

SMOQ

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A tool for protein single model quality assessment. SMOQ can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines with protein sequence and…

ModelEvaluator

Desktop

ModelEvaluator

(0) 0 discussion(s)
A machine learning model evaluation method to predict the quantitative absolute quality score of a single model using structural features extracted from its 3D coordinates and predicted from its…

FUSION

Web

FUSION

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A fragment-free probabilistic graphical model for conformational sampling in continuous space. FUSION captures local relationships between protein sequence and structural features and allows for…

3Drefine

Web
Desktop

3Drefine

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An interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement…

MULTICOM

Web
Desktop

MULTICOM

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Combines multiple sources of information and complementary methods at all five stages of the protein structure prediction process including template identification, template combination, model…

Gen3D

Desktop

Gen3D

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A unique computational approach based on optimization procedures known as adaptation, simulated annealing, and genetic algorithm to construct 3D models of human chromosomes, using chromosomal contact…

DN-Fold

Web

DN-Fold

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A deep learning network method to predict if a given query-template protein pair belongs to the same structural fold. The input used stemmed from the protein sequence and structural features…

RF-Fold

Web

RF-Fold

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A random forest method to recognize protein folds. RF-Fold was systematically validated by varying the input features and the class distribution of training datasets on a standard fold recognition…

CONFOLD

Web
Desktop

CONFOLD

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Assists users in building three-dimensional (3D) protein models using predicted contacts and secondary structures. CONFOLD permits the correction of tertiary structures when predicted contacts are…
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RNAMiner

Web

RNAMiner

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A multi-level bioinformatics protocol and pipeline. RNAMiner includes five steps: Mapping RNA-Seq reads to a reference genome, calculating gene expression values, identifying differentially expressed…

DNCON

Web

DNCON

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Provides a method for protein residue–residue prediction. DNCON is a web application, based on two-level deep convolutional neural network method that is able to determine all contacts in a protein.…

QAcon

Web

QAcon

(0) 0 discussion(s)
Using protein structural and contact information with machine learning techniques. QAcon is a single-model quality assessment method utilizing structural features, physicochemical properties, and…

ConEVA

Web
Desktop

ConEVA / Protein Contact Evaluation

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Allows protein contact evaluation and comparison. ConEVA allows a user to choose from various contact types, distance thresholds, and sequence separation thresholds for defining contacts and enables…