Ram Samudrala
#36,027
Most Influential Person Now
American scientist and philosopher
Ram Samudrala's AcademicInfluence.com Rankings
Ram Samudralaphilosophy Degrees
Philosophy
#3962
World Rank
#6304
Historical Rank
#1207
USA Rank
Logic
#7902
World Rank
#9832
Historical Rank
#1249
USA Rank
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Philosophy
Ram Samudrala's Degrees
- PhD Biochemistry University of California, San Francisco
- Bachelors Biochemistry University of California, San Diego
Why Is Ram Samudrala Influential?
(Suggest an Edit or Addition)According to Wikipedia, Ram Samudrala is a professor of computational biology and bioinformatics at the University at Buffalo, United States. He researches protein folding, structure, function, interaction, design, and evolution.
Ram Samudrala's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- The Genomes of Oryza sativa: A History of Duplications (2005) (900)
- Data access for the 1,000 Plants (1KP) project (2014) (474)
- An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. (1998) (465)
- Pseudomonas aeruginosa uses a cyclic-di-GMP-regulated adhesin to reinforce the biofilm extracellular matrix (2010) (449)
- Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction (2000) (226)
- Accurate Prediction of Secreted Substrates and Identification of a Conserved Putative Secretion Signal for Type III Secretion Systems (2009) (201)
- Ab initio construction of protein tertiary structures using a hierarchical approach. (2000) (180)
- Genes for the cytoskeletal protein tubulin in the bacterial genus Prosthecobacter (2002) (175)
- A graph-theoretic algorithm for comparative modeling of protein structure. (1998) (165)
- Mouse transcriptome: Neutral evolution of ‘non-coding’ complementary DNAs (2004) (163)
- A novel knowledge-based approach to design inorganic-binding peptides (2007) (134)
- Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA. (2007) (123)
- Computational Prediction of Type III and IV Secreted Effectors in Gram-Negative Bacteria (2010) (111)
- Novel paradigms for drug discovery: computational multitarget screening. (2008) (108)
- Origin and evolution of new exons in rodents. (2005) (102)
- Ab initio protein structure prediction using a combined hierarchical approach (1999) (102)
- Incorporating background frequency improves entropy-based residue conservation measures (2006) (90)
- Structural Optimization and De Novo Design of Dengue Virus Entry Inhibitory Peptides (2010) (89)
- Caries induced cytokine network in the odontoblast layer of human teeth (2011) (89)
- Ab initio fold prediction of small helical proteins using distance geometry and knowledge-based scoring functions. (1999) (88)
- PROTINFO: new algorithms for enhanced protein structure predictions (2005) (83)
- Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design (2005) (83)
- A Combined Approach for Ab Initio Construction of Low Resolution Protein Tertiary Structures from Sequence (1998) (77)
- Probing the molecular mechanisms of quartz-binding peptides. (2010) (75)
- Improved prediction of HIV-1 protease-inhibitor binding energies by molecular dynamics simulations (2003) (73)
- Improved protein structure selection using decoy-dependent discriminatory functions (2004) (71)
- Functional annotation from predicted protein interaction networks (2005) (66)
- The mechanism of outer membrane penetration by the eubacterial flagellum and implications for spirochete evolution. (2007) (65)
- Simple Linear Model Provides Highly Accurate Genotypic Predictions of HIV-1 Drug Resistance (2003) (63)
- Identifying inhibitors of the SARS coronavirus proteinase (2003) (57)
- Preferential Promotion of Lycopersicon esculentum (Tomato) Growth by Plant Growth Promoting Bacteria Associated with Tomato (2014) (54)
- A comprehensive analysis of 40 blind protein structure predictions (2002) (53)
- Cementomimetics—constructing a cementum-like biomineralized microlayer via amelogenin-derived peptides (2012) (52)
- CANDO and the infinite drug discovery frontier. (2014) (51)
- PROTINFO: secondary and tertiary protein structure prediction (2003) (51)
- Prediction of HIV-1 Protease Inhibitor Resistance using a Protein–Inhibitor Flexible Docking Approach (2005) (49)
- Transcription of All amoC Copies Is Associated with Recovery of Nitrosomonas europaea from Ammonia Starvation (2007) (48)
- Accurate and automated classification of protein secondary structure with PsiCSI (2003) (48)
- Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils. (2012) (46)
- Viral entry inhibitors block dengue antibody-dependent enhancement in vitro. (2011) (45)
- Determinants of side chain conformational preferences in protein structures. (1998) (44)
- Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform. (2016) (42)
- Faculty Opinions recommendation of Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. (2002) (42)
- Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information (2008) (42)
- Structural and Functional Characterization of an Organic Hydroperoxide Resistance Protein from Mycoplasma gallisepticum (2008) (41)
- Constructing side chains on near-native main chains for ab initio protein structure prediction. (2000) (40)
- Molecular Design of Inorganic-Binding Polypeptides (2008) (39)
- Combating Ebola with Repurposed Therapeutics Using the CANDO Platform (2016) (37)
- FSSA: a novel method for identifying functional signatures from structural alignments (2005) (37)
- Bioverse: functional, structural and contextual annotation of proteins and proteomes (2003) (36)
- The evolution and functional repertoire of translation proteins following the origin of life (2010) (36)
- Disguising itself--insights into Plasmodium falciparum binding and immune evasion from the DBL crystal structure. (2006) (35)
- CANDOCK: Chemical atomic network based hierarchical flexible docking algorithm using generalized statistical potentials (2018) (35)
- IGF1R variants associated with isolated single suture craniosynostosis (2011) (33)
- A generalized knowledge‐based discriminatory function for biomolecular interactions (2009) (31)
- Solution study of engineered quartz binding peptides using replica exchange molecular dynamics. (2010) (30)
- Identification of amino acids in the Dr adhesin required for binding to decay‐accelerating factor (2002) (30)
- Protinfo PPC: A web server for atomic level prediction of protein complexes (2009) (28)
- Distance geometry generates native‐like folds for small helical proteins using the consensus distances of predicted protein structures (1998) (28)
- Identification of potential multitarget antimalarial drugs. (2005) (27)
- A Systematic Review of Computational Drug Discovery, Development, and Repurposing for Ebola Virus Disease Treatment (2017) (27)
- Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function (2020) (27)
- The Enzymatic and Metabolic Capabilities of Early Life (2012) (25)
- Crystal Structure and Mutational Analysis of the DaaE Adhesin of Escherichia coli* (2006) (25)
- Handling context‐sensitivity in protein structures using graph theory: Bona fide prediction (1997) (25)
- Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform. (2015) (25)
- Structural insights into the cellular retinaldehyde‐binding protein (CRALBP) (2005) (24)
- A knowledge-based scoring function based on residue triplets for protein structure prediction (2006) (24)
- Computational Multitarget Drug Discovery (2012) (23)
- Strategic Protein Target Analysis for Developing Drugs to Stop Dental Caries (2012) (22)
- BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes (2005) (21)
- Heptad-Repeat-2 Mutations Enhance the Stability of the Enfuvirtide-Resistant HIV-1 gp41 Hairpin Structure (2005) (21)
- Confronting the problem of interconnected structural changes in the comparative modeling of proteins (1995) (21)
- PIRSpred: a web server for reliable HIV-1 protein-inhibitor resistance/susceptibility prediction. (2005) (20)
- Antivirogram or Phenosense: A Comparison of their Reproducibility and an Analysis of their Correlation (2003) (19)
- Enhanced functional information from predicted protein networks. (2004) (19)
- Identification of potential HIV-1 targets of minocycline (2007) (18)
- A protein sequence meta-functional signature for calcium binding residue prediction (2010) (18)
- Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens (2013) (17)
- The Genomes of Oryza sativa (2005) (17)
- Identifying Protein Features Responsible for Improved Drug Repurposing Accuracies Using the CANDO Platform: Implications for Drug Design (2018) (17)
- Comprehensive computational analysis of Hmd enzymes and paralogs in methanogenic Archaea (2009) (16)
- Virtual screening of HIV-1 protease inhibitors against human cytomegalovirus protease using docking and molecular dynamics (2005) (16)
- Exploration of interaction scoring criteria in the CANDO platform (2019) (15)
- HIV-1 genotypic drug-resistance interpretation algorithms need to include hypersusceptibility-associated mutations. (2004) (15)
- Prediction and integration of regulatory and protein-protein interactions. (2009) (15)
- Fingerprinting CANDO: Increased Accuracy with Structure- and Ligand-Based Shotgun Drug Repurposing (2019) (15)
- Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications (2019) (14)
- De Novo Protein Structure Prediction (2007) (14)
- Shotgun drug repurposing biotechnology to tackle epidemics and pandemics (2020) (14)
- Improving the accuracy of template-based predictions by mixing and matching between initial models (2008) (14)
- Accelerated protein structure comparison using TM-score-GPU (2012) (14)
- fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data (2014) (14)
- A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex. (2021) (13)
- Comment on "Evidence for Positive Epistasis in HIV-1" (2006) (13)
- Evaluating the performance of drug-repurposing technologies (2020) (13)
- Fingerprinting CANDO: Increased Accuracy with Structure and Ligand Based Shotgun Drug Repurposing (2019) (13)
- Diversity of protein structures and difficulties in fold recognition: the curious case of protein G (2009) (12)
- Scoring functions for ab initio protein structure prediction. (2000) (12)
- Distal Effect of Amino Acid Substitutions in CYP2C9 Polymorphic Variants Causes Differences in Interatomic Interactions against (S)-Warfarin (2013) (12)
- An enhanced Java graph applet interface for visualizing interactomes (2005) (11)
- Genomic organization and sequence variation of the human integrin subunit α8 gene (ITGA8) (2004) (11)
- Scoring functions for de novo protein structure prediction revisited. (2008) (11)
- Evolutionary Transients in the Rice Transcriptome (2010) (11)
- Improved accuracy of HIV-1 genotypic susceptibility interpretation using a consensus approach. (2004) (11)
- GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition (2011) (10)
- An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data (2006) (10)
- cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data (2020) (10)
- The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection. (2006) (10)
- A novel method for predicting and using distance constraints of high accuracy for refining protein structure prediction (2009) (9)
- INTEGRATOR: interactive graphical search of large protein interactomes over the Web (2006) (9)
- Computational Systems Biology (2009) (8)
- Faculty Opinions recommendation of RNA structure: advances and assessment of 3D structure prediction. (2018) (8)
- Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform (2020) (8)
- Composite Sequence–Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development (2015) (7)
- A fluorescence-based, gain-of-signal, live cell system to evaluate SARS-CoV-2 main protease inhibition (2021) (7)
- Inferring molecular interactions pathways from eQTL data. (2009) (6)
- Automated functional classification of experimental and predicted protein structures (2006) (6)
- LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates (2011) (6)
- Genomic organization and sequence variation of the human integrin subunit alpha8 gene (ITGA8). (2004) (6)
- The Bioverse API and web application. (2009) (6)
- Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches. (1999) (6)
- cando.py: Open source software for analyzing large scale drug-protein-disease data (2019) (5)
- Structure Prediction of Partial-Length Protein Sequences (2013) (5)
- Weak Agreement between Antivirogram and PhenoSense Assays in Predicting Reduced Susceptibility to Antiretroviral Drugs (2004) (5)
- Computational representation of biological systems. (2009) (5)
- A Deep-Learning Proteomic-Scale Approach for Drug Design (2021) (5)
- Identifying Protein Features and Pathways Responsible for Toxicity Using Machine Learning and Tox21: Implications for Predictive Toxicology (2021) (4)
- Protein structure prediction based on optimal hydrophobic core formation (2012) (4)
- Modeling genome structure and function (2002) (4)
- Shotgun drug repurposing biotechnology to tackle epidemics and pandemics (2020) (4)
- Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease (2022) (3)
- Correction: Distal Effect of Amino Acid Substitutions in CYP2C9 Polymorphic Variants Causes Differences in Interatomic Interactions against (S)-Warfarin (2013) (3)
- Antiviral Approaches against Influenza Virus (2023) (3)
- A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2–RNA complex (2020) (3)
- Foundations for a Realism-based Drug Repurposing Ontology (2019) (3)
- Disease risk of missense mutations using structural inference from predicted function. (2010) (3)
- Title Caries Induced Cytokine Network in the Odontoblast Layer of Human Teeth Permalink (2011) (2)
- Multiscale Analysis and Validation of Effective Drug Combinations Targeting Driver KRAS Mutations in Non-Small Cell Lung Cancer (2022) (2)
- Accurate Prediction of Inhibitor Binding to HIV-1 Protease Using CANDOCK (2022) (2)
- Optimal COVID-19 therapeutic candidate discovery using the CANDO platform (2022) (2)
- The Promise and Challenge of Digital Biology (2013) (2)
- Faculty Opinions recommendation of Protein-DNA interactions: amino acid conservation and the effects of mutations on binding specificity. (2006) (1)
- Identification of potential multitarget antimalarial drugs [letter] (2005) (1)
- Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. (2019) (1)
- Multi scale modeling of relationships between protein classes and drug behavior across all diseases using the CANDO platform (2015) (1)
- Faculty Opinions recommendation of Structure-based development of new RAS-effector inhibitors from a combination of active and inactive RAS-binding compounds. (2019) (1)
- Effective holistic characterization of small molecule effects using heterogeneous biological networks (2022) (1)
- 9 CHAPTER Prediction and Annotation of Plant Protein Interaction Networks (0)
- Identifying protein subsets and features responsible for improved drug repurposing accuracies using the CANDO platform (2018) (0)
- Multiscale modelling of relationships between protein classes and drug behavior using the CANDO platform (2015) (0)
- Theoretical model of the cellular retinaldehyde binding protein in its closed conformation (2005) (0)
- Computational shotgun drug repurposing for myriad diseases (2015) (0)
- Faculty Opinions recommendation of Machine learning models identify molecules active against the Ebola virus in vitro. (2017) (0)
- Faculty Opinions recommendation of Concurrent evolution of anti-aging gene duplications and cellular phenotypes in long-lived turtles. (2021) (0)
- Association of C>U RNA Editing with Human Disease Variants (2020) (0)
- Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens (2013) (0)
- Faculty Opinions recommendation of GPCR_LigandClassify.py; a rigorous machine learning classifier for GPCR targeting compounds. (2021) (0)
- Faculty Opinions recommendation of A novel computational approach for drug repurposing using systems biology. (2018) (0)
- Faculty Opinions recommendation of Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction. (2019) (0)
- Faculty Opinions recommendation of Cognate ligand domain mapping for enzymes. (2007) (0)
- Gepi - Genetically engineered polypeptides for inorganics: Peptide-based molecular tool set (2006) (0)
- Faculty Opinions recommendation of Creation and implications of a phenome-genome network. (2015) (0)
- Faculty Opinions recommendation of High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. (2007) (0)
- Gepi - Genetically engineered polypeptides for inorganics (2006) (0)
- 352 Computational methods for predicting drug combinations for targeting KRAS mutations relevant to non-small cell lung cancer (2022) (0)
- The Rapid Development of Early Protein Biosynthesis (2010) (0)
- Faculty Opinions recommendation of New Knowledge-Based Scoring Function with Inclusion of Backbone Conformational Entropies from Protein Structures. (2018) (0)
- Contents page 1 (2020) (0)
- The impact of nucleosome structure on CRISPR/Cas9 fidelity (2023) (0)
- CHAPTER 13 Computational Multitarget Drug Discovery (2012) (0)
- Improvements in Shotgun Drug Repurposing Accuracy: Combining OpenBabel with Bioinformatic Docking Data in the CANDO Platform (2018) (0)
- Rice protein models from the Nutritious Rice for the World Project (2016) (0)
- Faculty Opinions recommendation of New statistical potential for quality assessment of protein models and a survey of energy functions. (2010) (0)
- Faculty Opinions recommendation of A deep learning approach to antibiotic discovery. (2020) (0)
- Faculty Opinions recommendation of Drug discovery using chemical systems biology: weak inhibition of multiple kinases may contribute to the anti-cancer effect of nelfinavir. (2011) (0)
- Mycobacterium Cytidylate Kinase Appears to Be an Undruggable Target (2016) (0)
- Faculty Opinions recommendation of Drug repurposing: progress, challenges and recommendations. (2019) (0)
- Faculty Opinions recommendation of Discarding functional residues from the substitution table improves predictions of active sites within three-dimensional structures. (2008) (0)
- Faculty Opinions recommendation of Machine learning identifies candidates for drug repurposing in Alzheimer's disease. (2021) (0)
- Think Outside of the Box—Think Genomic (2003) (0)
- Knowledge-based design of inorganic-binding peptides (2008) (0)
- Prediction and Annotation of Plant Protein Interaction Networks (2009) (0)
- Exploration of interaction scoring criteria in the CANDO platform (2019) (0)
- Evolution of the Protein Repertoire (2012) (0)
- Peptide-Functionalized NanoInterfaces (2008) (0)
- Faculty Opinions recommendation of Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. (2010) (0)
- CASP 3 ab initio protein structure prediction results using a simple distance geometry-based method (2002) (0)
- Bioinformatic characterization of plant networks (2008) (0)
- Interactomics: Computational analysis of novel drug opportunities (2015) (0)
- Title: On the Protein Structure Prediction with Maximal Hydrophobic Core Formation (2012) (0)
- Faculty Opinions recommendation of Prediction of water and metal binding sites and their affinities by using the Fold-X force field. (2005) (0)
- Faculty Opinions recommendation of A Novel Drug Repositioning Approach based on Collaborative Metric Learning. (2019) (0)
- Faculty Opinions recommendation of Interrogating protein interaction networks through structural biology. (2002) (0)
- Faculty Opinions recommendation of Deep learning methods for protein torsion angle prediction. (2020) (0)
- Faculty Opinions recommendation of Assessing the limits of genomic data integration for predicting protein networks. (2005) (0)
- Title of Article: Scoring Functions for Ab Initio Protein Structure Prediction Suggested Running Head: Scoring Functions for Ab Initio Methods (2007) (0)
- Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. Corrigendum (2019) (0)
- TECHNICAL COMMENT ABSTRACTS (2006) (0)
- Plenary Presentation: Bioinformatic characterization of plant networks (2010) (0)
- The Bioverse : An object-oriented genomic database and webserver written in Python (2002) (0)
- Faculty Opinions recommendation of Drug-Drug Interaction Predicting by Neural Network Using Integrated Similarity. (2020) (0)
- Linking Genome and Exposome: Computational Analysis of Human Variation in Chemical-Target Interactions (2020) (0)
- Faculty Opinions recommendation of The 2F5 epitope is helical in the HIV-1 entry inhibitor T-20. (2005) (0)
- Accurate informatic modeling of tooth enamel pellicle interactions by training substitution matrices with Mat4Pep (2018) (0)
- A synthetic molecule stalls pre-mRNA splicing by enhancing cancer-relevant U2AF2–RNA complexes (2019) (0)
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What Schools Are Affiliated With Ram Samudrala?
Ram Samudrala is affiliated with the following schools:
